diff --git a/CHANGELOG b/CHANGELOG
index 0048d485917d880f7cddd5332e3eeeb0a55b7d87..bcfe0e157fa1a99532d33e26cf714e9951345177 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,6 +5,13 @@
Changelog
================================================================================
+Release 3.1.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: reintroduces backwards compatibility in BuildRawModel.
+ See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details
+
+
Release 3.1.0
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index bc2a47113508185ead6ce033b2bae1e6339a2272..1dd665c0179a07cbe951f8f2ef888dee4c59f5af 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,7 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 3)
set(PROMOD3_VERSION_MINOR 1)
-set(PROMOD3_VERSION_PATCH 0)
+set(PROMOD3_VERSION_PATCH 1)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
@@ -101,7 +101,7 @@ if(NOT DISABLE_DOCUMENTATION)
# this URL should always point to the latest version of OST
set(OST_DOC_URL "https://www.openstructure.org/docs")
endif()
-find_package(OPENSTRUCTURE 2.0.0 REQUIRED
+find_package(OPENSTRUCTURE 2.1.0 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
if(CMAKE_COMPILER_IS_GNUCXX)
diff --git a/container/Dockerfile b/container/Dockerfile
index a1a3449287c8fad24879279595c40b398b8e9d73..669aacc73d445849b09c286219cfafb188aca244 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -1,9 +1,9 @@
-ARG OPENSTRUCTURE_VERSION="2.0.0-bionic"
-FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_VERSION}
+ARG OPENSTRUCTURE_IMAGE_TAG="2.1.0-bionic"
+FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
-ARG PROMOD_VERSION="3.1.0"
+ARG PROMOD_VERSION="3.1.1"
ARG SRC_FOLDER="/usr/local/src"
diff --git a/container/Singularity b/container/Singularity
index f5665c8d6d89976cae2f70a8c95c6eafdc52596d..2b9f8f1fee08920e12d46138000dc05af4585b86 100644
--- a/container/Singularity
+++ b/container/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/promod3:3.1.0-OST2.0.0-bionic
+From: registry.scicore.unibas.ch/schwede/promod3:3.1.1-OST2.1.0-bionic
%post
##############################################################################
# POST
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 8f97db296b46d1a2ca12e70f367b0552bdb81200..08c65e05183e857dd016281843395d512b1bc7f9 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -286,7 +286,7 @@ rst_epilog = """
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
-.. |ost_version| replace:: 2.0.0
+.. |ost_version| replace:: 2.1.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
diff --git a/doc/container/index.rst b/doc/container/index.rst
index 00732135f52658da7c45670d682a39dc8cc77654..b67bc86ab7cfebdda5b37ec57894070b3044eb3d 100644
--- a/doc/container/index.rst
+++ b/doc/container/index.rst
@@ -13,6 +13,7 @@
.. See the License for the specific language governing permissions and
.. limitations under the License.
+.. _container:
|project| and Containers
========================
diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
index 30d7e8538d76e3ed66aeb3a97859262a7d105ce4..cd006fdb96d1e5f14a1bb50653a5ac8f436ac109 100644
--- a/doc/container/singularity.rst
+++ b/doc/container/singularity.rst
@@ -20,7 +20,8 @@ Singularity
We do not provide a "standalone" Singularity image, but rather bootstrap from a
Docker image.
-Build the image with:
+Change to the directory containing the Singularity file
+(<PROMOD3_CHECKOUT>/container) and build the image with:
.. code-block:: bash
@@ -56,6 +57,43 @@ To list all available |project| modelling actions:
singularity run --app PM promod.img help
+So you can either run an action with:
+
+.. code-block:: bash
+
+ singularity run --app PM promod.img build-model [options]
+
+or an arbitrary Python script using OpenStructure / |project| with:
+
+.. code-block:: bash
+
+ singularity run --app PM promod.img my_script.py [options]
+
+The Notebook app provides a jupyter notebook playground with OST, |project|, and
+nglview available. You can fire it up with:
+
+.. code-block:: bash
+
+ singularity run --app Notebook promod.img
+
+connect to the notebook, start a new OST kernel and test it with the following
+code snippet:
+
+.. code-block:: python
+
+ from ost import io
+ from promod3 import loop
+ import nglview
+
+ # generate backbone with dihedrals of a helix and store it
+ sequence = "HELLYEAH"
+ bb_list = loop.BackboneList(sequence)
+ io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+ # display stored file
+ view = nglview.show_file("test.pdb")
+ view
+
The Compound Library
--------------------
diff --git a/doc/gettingstarted.rst b/doc/gettingstarted.rst
index 46292a7a8a9d64cc1380dfea331837ddd8c82f21..e1fe6f904db45d0ff25f14db156710998af781d4 100644
--- a/doc/gettingstarted.rst
+++ b/doc/gettingstarted.rst
@@ -19,7 +19,7 @@ Getting Started
Get and Run |project|
--------------------------------------------------------------------------------
-First steps to get |project| up and running:
+Either utilize :ref:`containers <container>` or start from source code:
#. Fetch the source code from https://git.scicore.unibas.ch/schwede/ProMod3.git.
Or directly pull it with git:
diff --git a/doc/html/_sources/actions/index.txt b/doc/html/_sources/actions/index.rst.txt
similarity index 100%
rename from doc/html/_sources/actions/index.txt
rename to doc/html/_sources/actions/index.rst.txt
diff --git a/doc/html/_sources/actions/index_dev.txt b/doc/html/_sources/actions/index_dev.rst.txt
similarity index 100%
rename from doc/html/_sources/actions/index_dev.txt
rename to doc/html/_sources/actions/index_dev.rst.txt
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.rst.txt
similarity index 99%
rename from doc/html/_sources/buildsystem.txt
rename to doc/html/_sources/buildsystem.rst.txt
index e2540e8a97f08381498d204f85c8b66e19e6e0f0..5960348cf6d2e6cb2598440d7ffa10784a63ef2e 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.rst.txt
@@ -40,7 +40,7 @@ The currently preferred versions are:
* |python|_ 3.6.0
* |boost|_ 1.68.0
* |eigen3|_ 3.3.1
-* |sphinx|_ 1.3.1
+* |sphinx|_ 1.4.9
--------------------------------------------------------------------------------
Using |cmake|
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.rst.txt
similarity index 93%
rename from doc/html/_sources/changelog.txt
rename to doc/html/_sources/changelog.rst.txt
index 1fb6710efc8d360311e9eeab1e1043e3437ee240..bcfe0e157fa1a99532d33e26cf714e9951345177 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.rst.txt
@@ -5,6 +5,20 @@
Changelog
================================================================================
+Release 3.1.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: reintroduces backwards compatibility in BuildRawModel.
+ See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details
+
+
+Release 3.1.0
+--------------------------------------------------------------------------------
+
+* Introduce alignment processing steps in BuildRawModel
+* Several minor bug fixes, improvements, and speed-ups.
+
+
Release 3.0.0
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/cmake/index.txt b/doc/html/_sources/cmake/index.rst.txt
similarity index 100%
rename from doc/html/_sources/cmake/index.txt
rename to doc/html/_sources/cmake/index.rst.txt
diff --git a/doc/html/_sources/container/docker.txt b/doc/html/_sources/container/docker.rst.txt
similarity index 100%
rename from doc/html/_sources/container/docker.txt
rename to doc/html/_sources/container/docker.rst.txt
diff --git a/doc/html/_sources/container/index.txt b/doc/html/_sources/container/index.rst.txt
similarity index 98%
rename from doc/html/_sources/container/index.txt
rename to doc/html/_sources/container/index.rst.txt
index 00732135f52658da7c45670d682a39dc8cc77654..b67bc86ab7cfebdda5b37ec57894070b3044eb3d 100644
--- a/doc/html/_sources/container/index.txt
+++ b/doc/html/_sources/container/index.rst.txt
@@ -13,6 +13,7 @@
.. See the License for the specific language governing permissions and
.. limitations under the License.
+.. _container:
|project| and Containers
========================
diff --git a/doc/html/_sources/container/singularity.txt b/doc/html/_sources/container/singularity.rst.txt
similarity index 73%
rename from doc/html/_sources/container/singularity.txt
rename to doc/html/_sources/container/singularity.rst.txt
index 30d7e8538d76e3ed66aeb3a97859262a7d105ce4..cd006fdb96d1e5f14a1bb50653a5ac8f436ac109 100644
--- a/doc/html/_sources/container/singularity.txt
+++ b/doc/html/_sources/container/singularity.rst.txt
@@ -20,7 +20,8 @@ Singularity
We do not provide a "standalone" Singularity image, but rather bootstrap from a
Docker image.
-Build the image with:
+Change to the directory containing the Singularity file
+(<PROMOD3_CHECKOUT>/container) and build the image with:
.. code-block:: bash
@@ -56,6 +57,43 @@ To list all available |project| modelling actions:
singularity run --app PM promod.img help
+So you can either run an action with:
+
+.. code-block:: bash
+
+ singularity run --app PM promod.img build-model [options]
+
+or an arbitrary Python script using OpenStructure / |project| with:
+
+.. code-block:: bash
+
+ singularity run --app PM promod.img my_script.py [options]
+
+The Notebook app provides a jupyter notebook playground with OST, |project|, and
+nglview available. You can fire it up with:
+
+.. code-block:: bash
+
+ singularity run --app Notebook promod.img
+
+connect to the notebook, start a new OST kernel and test it with the following
+code snippet:
+
+.. code-block:: python
+
+ from ost import io
+ from promod3 import loop
+ import nglview
+
+ # generate backbone with dihedrals of a helix and store it
+ sequence = "HELLYEAH"
+ bb_list = loop.BackboneList(sequence)
+ io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+ # display stored file
+ view = nglview.show_file("test.pdb")
+ view
+
The Compound Library
--------------------
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.rst.txt
similarity index 100%
rename from doc/html/_sources/contributing.txt
rename to doc/html/_sources/contributing.rst.txt
diff --git a/doc/html/_sources/core/geometry.txt b/doc/html/_sources/core/geometry.rst.txt
similarity index 100%
rename from doc/html/_sources/core/geometry.txt
rename to doc/html/_sources/core/geometry.rst.txt
diff --git a/doc/html/_sources/core/graph_minimizer.txt b/doc/html/_sources/core/graph_minimizer.rst.txt
similarity index 100%
rename from doc/html/_sources/core/graph_minimizer.txt
rename to doc/html/_sources/core/graph_minimizer.rst.txt
diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.rst.txt
similarity index 100%
rename from doc/html/_sources/core/helper.txt
rename to doc/html/_sources/core/helper.rst.txt
diff --git a/doc/html/_sources/core/index.txt b/doc/html/_sources/core/index.rst.txt
similarity index 100%
rename from doc/html/_sources/core/index.txt
rename to doc/html/_sources/core/index.rst.txt
diff --git a/doc/html/_sources/core/pm3argparse.txt b/doc/html/_sources/core/pm3argparse.rst.txt
similarity index 100%
rename from doc/html/_sources/core/pm3argparse.txt
rename to doc/html/_sources/core/pm3argparse.rst.txt
diff --git a/doc/html/_sources/core/runtime_profiling.txt b/doc/html/_sources/core/runtime_profiling.rst.txt
similarity index 100%
rename from doc/html/_sources/core/runtime_profiling.txt
rename to doc/html/_sources/core/runtime_profiling.rst.txt
diff --git a/doc/html/_sources/core/setcompoundschemlib.txt b/doc/html/_sources/core/setcompoundschemlib.rst.txt
similarity index 100%
rename from doc/html/_sources/core/setcompoundschemlib.txt
rename to doc/html/_sources/core/setcompoundschemlib.rst.txt
diff --git a/doc/html/_sources/dev_setup.txt b/doc/html/_sources/dev_setup.rst.txt
similarity index 100%
rename from doc/html/_sources/dev_setup.txt
rename to doc/html/_sources/dev_setup.rst.txt
diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.rst.txt
similarity index 100%
rename from doc/html/_sources/developers.txt
rename to doc/html/_sources/developers.rst.txt
diff --git a/doc/html/_sources/gettingstarted.txt b/doc/html/_sources/gettingstarted.rst.txt
similarity index 97%
rename from doc/html/_sources/gettingstarted.txt
rename to doc/html/_sources/gettingstarted.rst.txt
index 46292a7a8a9d64cc1380dfea331837ddd8c82f21..e1fe6f904db45d0ff25f14db156710998af781d4 100644
--- a/doc/html/_sources/gettingstarted.txt
+++ b/doc/html/_sources/gettingstarted.rst.txt
@@ -19,7 +19,7 @@ Getting Started
Get and Run |project|
--------------------------------------------------------------------------------
-First steps to get |project| up and running:
+Either utilize :ref:`containers <container>` or start from source code:
#. Fetch the source code from https://git.scicore.unibas.ch/schwede/ProMod3.git.
Or directly pull it with git:
diff --git a/doc/html/_sources/index.txt b/doc/html/_sources/index.rst.txt
similarity index 100%
rename from doc/html/_sources/index.txt
rename to doc/html/_sources/index.rst.txt
diff --git a/doc/html/_sources/license.txt b/doc/html/_sources/license.rst.txt
similarity index 100%
rename from doc/html/_sources/license.txt
rename to doc/html/_sources/license.rst.txt
diff --git a/doc/html/_sources/loop/all_atom.txt b/doc/html/_sources/loop/all_atom.rst.txt
similarity index 100%
rename from doc/html/_sources/loop/all_atom.txt
rename to doc/html/_sources/loop/all_atom.rst.txt
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.rst.txt
similarity index 100%
rename from doc/html/_sources/loop/backbone.txt
rename to doc/html/_sources/loop/backbone.rst.txt
diff --git a/doc/html/_sources/loop/index.txt b/doc/html/_sources/loop/index.rst.txt
similarity index 100%
rename from doc/html/_sources/loop/index.txt
rename to doc/html/_sources/loop/index.rst.txt
diff --git a/doc/html/_sources/loop/load_loop_objects.txt b/doc/html/_sources/loop/load_loop_objects.rst.txt
similarity index 100%
rename from doc/html/_sources/loop/load_loop_objects.txt
rename to doc/html/_sources/loop/load_loop_objects.rst.txt
diff --git a/doc/html/_sources/loop/mm_system_creation.txt b/doc/html/_sources/loop/mm_system_creation.rst.txt
similarity index 100%
rename from doc/html/_sources/loop/mm_system_creation.txt
rename to doc/html/_sources/loop/mm_system_creation.rst.txt
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.rst.txt
similarity index 100%
rename from doc/html/_sources/loop/structure_db.txt
rename to doc/html/_sources/loop/structure_db.rst.txt
diff --git a/doc/html/_sources/loop/torsion_sampler.txt b/doc/html/_sources/loop/torsion_sampler.rst.txt
similarity index 100%
rename from doc/html/_sources/loop/torsion_sampler.txt
rename to doc/html/_sources/loop/torsion_sampler.rst.txt
diff --git a/doc/html/_sources/modelling/algorithms.txt b/doc/html/_sources/modelling/algorithms.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/algorithms.txt
rename to doc/html/_sources/modelling/algorithms.rst.txt
diff --git a/doc/html/_sources/modelling/gap_handling.txt b/doc/html/_sources/modelling/gap_handling.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/gap_handling.txt
rename to doc/html/_sources/modelling/gap_handling.rst.txt
diff --git a/doc/html/_sources/modelling/index.txt b/doc/html/_sources/modelling/index.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/index.txt
rename to doc/html/_sources/modelling/index.rst.txt
diff --git a/doc/html/_sources/modelling/loop_candidates.txt b/doc/html/_sources/modelling/loop_candidates.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/loop_candidates.txt
rename to doc/html/_sources/modelling/loop_candidates.rst.txt
diff --git a/doc/html/_sources/modelling/loop_closing.txt b/doc/html/_sources/modelling/loop_closing.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/loop_closing.txt
rename to doc/html/_sources/modelling/loop_closing.rst.txt
diff --git a/doc/html/_sources/modelling/model_checking.txt b/doc/html/_sources/modelling/model_checking.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/model_checking.txt
rename to doc/html/_sources/modelling/model_checking.rst.txt
diff --git a/doc/html/_sources/modelling/monte_carlo.txt b/doc/html/_sources/modelling/monte_carlo.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/monte_carlo.txt
rename to doc/html/_sources/modelling/monte_carlo.rst.txt
diff --git a/doc/html/_sources/modelling/pipeline.txt b/doc/html/_sources/modelling/pipeline.rst.txt
similarity index 81%
rename from doc/html/_sources/modelling/pipeline.txt
rename to doc/html/_sources/modelling/pipeline.rst.txt
index 3e90542c05f05af6398f4dd9bc514be793c4dcaf..3dd2f3128c8f90265f201114ca546b48f59b36a0 100644
--- a/doc/html/_sources/modelling/pipeline.txt
+++ b/doc/html/_sources/modelling/pipeline.rst.txt
@@ -176,77 +176,9 @@ Build Raw Modelling Handle
:return: A deep copy of the current handle
:rtype: :class:`ModellingHandle`
+
-
-.. function:: BuildRawModel(aln, include_ligands=False, chain_names=\
- "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz",\
- spdbv_style=False)
-
- Builds a raw (pseudo) model from the alignment. Can either take a single
- alignment handle or an alignment handle list. Every list item is treated as a
- single chain in the final raw model.
-
- Each alignment handle must contain exactly two sequences and the second
- sequence is considered the template sequence, which must have a
- :class:`~ost.mol.EntityView` attached.
-
- This is a basic protein core modelling algorithm that copies backbone
- coordinates based on the sequence alignment. For matching residues, the
- side chain coordinates are also copied. Gaps are ignored. Hydrogen an
- deuterium atoms are not copied into the model.
-
- The function tries to reuse as much as possible from the template. Modified
- residues are treated as follows:
-
- - Selenium methionine residues are converted to methionine
-
- - Side chains which contain all atoms of the parent amino acid, e.g.
- phosphoserine are copied as a whole with the modifications stripped off.
-
- Residues with missing backbone atoms and D-peptides are generally skipped and
- treated as gaps. Missing Cbeta atoms in backbone are ok and reconstructed.
- If all residues are skipped (e.g. Calpha traces), we report an error and
- return an empty model.
-
- Residue numbers are set such that missing residue in gaps are honoured and
- subsequent loop modelling can insert new residues without having to renumber.
- **The numbering of residues starts for every chain with the value 1**.
-
- The returned :class:`ModellingHandle` stores the obtained raw model as well
- as information about insertions and deletions in the gaps list.
-
- :param aln: Single alignment handle for raw model with single chain or
- list of alignment handles for raw model with multiple chains.
- :type aln: :class:`~ost.seq.AlignmentHandle` / :class:`~ost.seq.AlignmentList`
-
- :param include_ligands: True, if we wish to include ligands in the model. This
- searches for ligands in all OST handles of the views
- attached to the alignments. Ligands are identified
- with the `ligand` property in the handle (set by OST
- based on HET records) or by the chain name '_' (as set
- in SMTL). All ligands are added to a new chain named
- '_'.
- :type include_ligands: :class:`bool`
-
- :param chain_names: Chains are named by a single chanacter taken from this.
- :type chain_names: :class:`str`
-
- :param spdbv_style: True, if we need a model in the old SPDBV style.
- :type spdbv_style: :class:`bool`
-
- :return: Raw (pseudo) model from the alignment.
- :rtype: :class:`ModellingHandle`
-
- :raises: A :exc:`RuntimeError` when:
-
- - the alignments do not have two sequences
- - the second sequence does not have an attached structure
- - the residues of the template structure do not match with the
- alignment sequence (note that you can set an "offset" (see
- :meth:`~ost.seq.AlignmentHandle.SetSequenceOffset`) for the
- template sequence (but not for the target))
- - the target sequence has a non-zero offset (cannot be honored as
- the resulting model will always start its residue numbering at 1)
+.. autofunction:: BuildRawModel
The Default Pipeline
--------------------------------------------------------------------------------
@@ -443,3 +375,11 @@ Modelling Steps
:members:
.. autofunction:: AddModellingIssue
+
+
+Alignment Fiddling
+--------------------------------------------------------------------------------
+
+.. autofunction:: DeleteGapCols
+
+.. autofunction:: PullTerminalDeletions
diff --git a/doc/html/_sources/modelling/sidechain_reconstruction.txt b/doc/html/_sources/modelling/sidechain_reconstruction.rst.txt
similarity index 100%
rename from doc/html/_sources/modelling/sidechain_reconstruction.txt
rename to doc/html/_sources/modelling/sidechain_reconstruction.rst.txt
diff --git a/doc/html/_sources/portableIO.txt b/doc/html/_sources/portableIO.rst.txt
similarity index 100%
rename from doc/html/_sources/portableIO.txt
rename to doc/html/_sources/portableIO.rst.txt
diff --git a/doc/html/_sources/references.txt b/doc/html/_sources/references.rst.txt
similarity index 100%
rename from doc/html/_sources/references.txt
rename to doc/html/_sources/references.rst.txt
diff --git a/doc/html/_sources/scoring/all_atom_scorers.txt b/doc/html/_sources/scoring/all_atom_scorers.rst.txt
similarity index 100%
rename from doc/html/_sources/scoring/all_atom_scorers.txt
rename to doc/html/_sources/scoring/all_atom_scorers.rst.txt
diff --git a/doc/html/_sources/scoring/backbone_score_env.txt b/doc/html/_sources/scoring/backbone_score_env.rst.txt
similarity index 100%
rename from doc/html/_sources/scoring/backbone_score_env.txt
rename to doc/html/_sources/scoring/backbone_score_env.rst.txt
diff --git a/doc/html/_sources/scoring/backbone_scorers.txt b/doc/html/_sources/scoring/backbone_scorers.rst.txt
similarity index 100%
rename from doc/html/_sources/scoring/backbone_scorers.txt
rename to doc/html/_sources/scoring/backbone_scorers.rst.txt
diff --git a/doc/html/_sources/scoring/index.txt b/doc/html/_sources/scoring/index.rst.txt
similarity index 100%
rename from doc/html/_sources/scoring/index.txt
rename to doc/html/_sources/scoring/index.rst.txt
diff --git a/doc/html/_sources/scoring/other_scoring_functions.txt b/doc/html/_sources/scoring/other_scoring_functions.rst.txt
similarity index 100%
rename from doc/html/_sources/scoring/other_scoring_functions.txt
rename to doc/html/_sources/scoring/other_scoring_functions.rst.txt
diff --git a/doc/html/_sources/sidechain/disulfid.txt b/doc/html/_sources/sidechain/disulfid.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/disulfid.txt
rename to doc/html/_sources/sidechain/disulfid.rst.txt
diff --git a/doc/html/_sources/sidechain/frame.txt b/doc/html/_sources/sidechain/frame.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/frame.txt
rename to doc/html/_sources/sidechain/frame.rst.txt
diff --git a/doc/html/_sources/sidechain/graph.txt b/doc/html/_sources/sidechain/graph.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/graph.txt
rename to doc/html/_sources/sidechain/graph.rst.txt
diff --git a/doc/html/_sources/sidechain/index.txt b/doc/html/_sources/sidechain/index.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/index.txt
rename to doc/html/_sources/sidechain/index.rst.txt
diff --git a/doc/html/_sources/sidechain/loading.txt b/doc/html/_sources/sidechain/loading.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/loading.txt
rename to doc/html/_sources/sidechain/loading.rst.txt
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/rotamer.txt
rename to doc/html/_sources/sidechain/rotamer.rst.txt
diff --git a/doc/html/_sources/sidechain/rotamer_constructor.txt b/doc/html/_sources/sidechain/rotamer_constructor.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/rotamer_constructor.txt
rename to doc/html/_sources/sidechain/rotamer_constructor.rst.txt
diff --git a/doc/html/_sources/sidechain/rotamer_lib.txt b/doc/html/_sources/sidechain/rotamer_lib.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/rotamer_lib.txt
rename to doc/html/_sources/sidechain/rotamer_lib.rst.txt
diff --git a/doc/html/_sources/sidechain/subrotamer_optimizer.txt b/doc/html/_sources/sidechain/subrotamer_optimizer.rst.txt
similarity index 100%
rename from doc/html/_sources/sidechain/subrotamer_optimizer.txt
rename to doc/html/_sources/sidechain/subrotamer_optimizer.rst.txt
diff --git a/doc/html/_sources/user_contributions.txt b/doc/html/_sources/user_contributions.rst.txt
similarity index 100%
rename from doc/html/_sources/user_contributions.txt
rename to doc/html/_sources/user_contributions.rst.txt
diff --git a/doc/html/_sources/users.txt b/doc/html/_sources/users.rst.txt
similarity index 100%
rename from doc/html/_sources/users.txt
rename to doc/html/_sources/users.rst.txt
diff --git a/doc/html/_static/ajax-loader.gif b/doc/html/_static/ajax-loader.gif
deleted file mode 100644
index 61faf8cab23993bd3e1560bff0668bd628642330..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/ajax-loader.gif and /dev/null differ
diff --git a/doc/html/_static/basic.css b/doc/html/_static/basic.css
index 0b79414a16adfcf062bf14fc3c040bc335eb79ad..c41d718e429affb53084be2e5d2a2fe26aea164b 100644
--- a/doc/html/_static/basic.css
+++ b/doc/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -81,10 +81,26 @@ div.sphinxsidebar input {
font-size: 1em;
}
+div.sphinxsidebar #searchbox form.search {
+ overflow: hidden;
+}
+
div.sphinxsidebar #searchbox input[type="text"] {
- width: 170px;
+ float: left;
+ width: 80%;
+ padding: 0.25em;
+ box-sizing: border-box;
}
+div.sphinxsidebar #searchbox input[type="submit"] {
+ float: left;
+ width: 20%;
+ border-left: none;
+ padding: 0.25em;
+ box-sizing: border-box;
+}
+
+
img {
border: 0;
max-width: 100%;
@@ -122,6 +138,8 @@ ul.keywordmatches li.goodmatch a {
table.contentstable {
width: 90%;
+ margin-left: auto;
+ margin-right: auto;
}
table.contentstable p.biglink {
@@ -149,9 +167,14 @@ table.indextable td {
vertical-align: top;
}
-table.indextable dl, table.indextable dd {
+table.indextable ul {
margin-top: 0;
margin-bottom: 0;
+ list-style-type: none;
+}
+
+table.indextable > tbody > tr > td > ul {
+ padding-left: 0em;
}
table.indextable tr.pcap {
@@ -183,8 +206,20 @@ div.genindex-jumpbox {
padding: 0.4em;
}
+/* -- domain module index --------------------------------------------------- */
+
+table.modindextable td {
+ padding: 2px;
+ border-collapse: collapse;
+}
+
/* -- general body styles --------------------------------------------------- */
+div.body {
+ min-width: 450px;
+ max-width: 800px;
+}
+
div.body p, div.body dd, div.body li, div.body blockquote {
-moz-hyphens: auto;
-ms-hyphens: auto;
@@ -196,6 +231,16 @@ a.headerlink {
visibility: hidden;
}
+a.brackets:before,
+span.brackets > a:before{
+ content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+ content: "]";
+}
+
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
@@ -217,10 +262,6 @@ div.body td {
text-align: left;
}
-.field-list ul {
- padding-left: 1em;
-}
-
.first {
margin-top: 0 !important;
}
@@ -248,6 +289,12 @@ img.align-center, .figure.align-center, object.align-center {
margin-right: auto;
}
+img.align-default, .figure.align-default {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
.align-left {
text-align: left;
}
@@ -256,6 +303,10 @@ img.align-center, .figure.align-center, object.align-center {
text-align: center;
}
+.align-default {
+ text-align: center;
+}
+
.align-right {
text-align: right;
}
@@ -322,6 +373,16 @@ table.docutils {
border-collapse: collapse;
}
+table.align-center {
+ margin-left: auto;
+ margin-right: auto;
+}
+
+table.align-default {
+ margin-left: auto;
+ margin-right: auto;
+}
+
table caption span.caption-number {
font-style: italic;
}
@@ -337,10 +398,6 @@ table.docutils td, table.docutils th {
border-bottom: 1px solid #aaa;
}
-table.field-list td, table.field-list th {
- border: 0 !important;
-}
-
table.footnote td, table.footnote th {
border: 0 !important;
}
@@ -359,6 +416,16 @@ table.citation td {
border-bottom: none;
}
+th > p:first-child,
+td > p:first-child {
+ margin-top: 0px;
+}
+
+th > p:last-child,
+td > p:last-child {
+ margin-bottom: 0px;
+}
+
/* -- figures --------------------------------------------------------------- */
div.figure {
@@ -377,6 +444,34 @@ div.figure p.caption span.caption-number {
div.figure p.caption span.caption-text {
}
+/* -- field list styles ----------------------------------------------------- */
+
+table.field-list td, table.field-list th {
+ border: 0 !important;
+}
+
+.field-list ul {
+ margin: 0;
+ padding-left: 1em;
+}
+
+.field-list p {
+ margin: 0;
+}
+
+.field-name {
+ -moz-hyphens: manual;
+ -ms-hyphens: manual;
+ -webkit-hyphens: manual;
+ hyphens: manual;
+}
+
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+ vertical-align: top;
+}
+
/* -- other body styles ----------------------------------------------------- */
@@ -400,11 +495,57 @@ ol.upperroman {
list-style: upper-roman;
}
+li > p:first-child {
+ margin-top: 0px;
+}
+
+li > p:last-child {
+ margin-bottom: 0px;
+}
+
+dl.footnote > dt,
+dl.citation > dt {
+ float: left;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+ margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+ content: "";
+ clear: both;
+}
+
+dl.field-list {
+ display: flex;
+ flex-wrap: wrap;
+}
+
+dl.field-list > dt {
+ flex-basis: 20%;
+ font-weight: bold;
+ word-break: break-word;
+}
+
+dl.field-list > dt:after {
+ content: ":";
+}
+
+dl.field-list > dd {
+ flex-basis: 70%;
+ padding-left: 1em;
+ margin-left: 0em;
+ margin-bottom: 0em;
+}
+
dl {
margin-bottom: 15px;
}
-dd p {
+dd > p:first-child {
margin-top: 0px;
}
@@ -418,24 +559,19 @@ dd {
margin-left: 30px;
}
-dt:target, .highlighted {
+dt:target, span.highlighted {
background-color: #fbe54e;
}
+rect.highlighted {
+ fill: #fbe54e;
+}
+
dl.glossary dt {
font-weight: bold;
font-size: 1.1em;
}
-.field-list ul {
- margin: 0;
- padding-left: 1em;
-}
-
-.field-list p {
- margin: 0;
-}
-
.optional {
font-size: 1.3em;
}
@@ -482,6 +618,12 @@ dl.glossary dt {
font-style: oblique;
}
+.classifier:before {
+ font-style: normal;
+ margin: 0.5em;
+ content: ":";
+}
+
abbr, acronym {
border-bottom: dotted 1px;
cursor: help;
@@ -592,6 +734,16 @@ span.eqno {
float: right;
}
+span.eqno a.headerlink {
+ position: relative;
+ left: 0px;
+ z-index: 1;
+}
+
+div.math:hover a.headerlink {
+ visibility: visible;
+}
+
/* -- printout stylesheet --------------------------------------------------- */
@media print {
diff --git a/doc/html/_static/comment-bright.png b/doc/html/_static/comment-bright.png
deleted file mode 100644
index 551517b8c83b76f734ff791f847829a760ad1903..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/comment-bright.png and /dev/null differ
diff --git a/doc/html/_static/comment-close.png b/doc/html/_static/comment-close.png
deleted file mode 100644
index 09b54be46da3f0d4a5061da289dc91d8a2cdbc9c..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/comment-close.png and /dev/null differ
diff --git a/doc/html/_static/comment.png b/doc/html/_static/comment.png
deleted file mode 100644
index 92feb52b8824c6b0f59b658b1196c61de9162a95..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/comment.png and /dev/null differ
diff --git a/doc/html/_static/doctools.js b/doc/html/_static/doctools.js
index 816349563588e87ca99c7cf2d6e54268e52e761d..b33f87fcb249ea9b0e0a07fa9c5f2595ea925709 100644
--- a/doc/html/_static/doctools.js
+++ b/doc/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -45,7 +45,7 @@ jQuery.urlencode = encodeURIComponent;
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
- if (typeof s == 'undefined')
+ if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
@@ -66,29 +66,54 @@ jQuery.getQueryParameters = function(s) {
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
- function highlight(node) {
- if (node.nodeType == 3) {
+ function highlight(node, addItems) {
+ if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
- if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
- var span = document.createElement("span");
- span.className = className;
+ if (pos >= 0 &&
+ !jQuery(node.parentNode).hasClass(className) &&
+ !jQuery(node.parentNode).hasClass("nohighlight")) {
+ var span;
+ var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+ if (isInSVG) {
+ span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+ } else {
+ span = document.createElement("span");
+ span.className = className;
+ }
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
+ if (isInSVG) {
+ var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+ var bbox = node.parentElement.getBBox();
+ rect.x.baseVal.value = bbox.x;
+ rect.y.baseVal.value = bbox.y;
+ rect.width.baseVal.value = bbox.width;
+ rect.height.baseVal.value = bbox.height;
+ rect.setAttribute('class', className);
+ addItems.push({
+ "parent": node.parentNode,
+ "target": rect});
+ }
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
- highlight(this);
+ highlight(this, addItems);
});
}
}
- return this.each(function() {
- highlight(this);
+ var addItems = [];
+ var result = this.each(function() {
+ highlight(this, addItems);
});
+ for (var i = 0; i < addItems.length; ++i) {
+ jQuery(addItems[i].parent).before(addItems[i].target);
+ }
+ return result;
};
/*
@@ -124,28 +149,30 @@ var Documentation = {
this.fixFirefoxAnchorBug();
this.highlightSearchWords();
this.initIndexTable();
-
+ if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+ this.initOnKeyListeners();
+ }
},
/**
* i18n support
*/
TRANSLATIONS : {},
- PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+ PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
LOCALE : 'unknown',
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
gettext : function(string) {
var translated = Documentation.TRANSLATIONS[string];
- if (typeof translated == 'undefined')
+ if (typeof translated === 'undefined')
return string;
- return (typeof translated == 'string') ? translated : translated[0];
+ return (typeof translated === 'string') ? translated : translated[0];
},
ngettext : function(singular, plural, n) {
var translated = Documentation.TRANSLATIONS[singular];
- if (typeof translated == 'undefined')
+ if (typeof translated === 'undefined')
return (n == 1) ? singular : plural;
return translated[Documentation.PLURALEXPR(n)];
},
@@ -180,7 +207,7 @@ var Documentation = {
* see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
*/
fixFirefoxAnchorBug : function() {
- if (document.location.hash)
+ if (document.location.hash && $.browser.mozilla)
window.setTimeout(function() {
document.location.href += '';
}, 10);
@@ -216,7 +243,7 @@ var Documentation = {
var src = $(this).attr('src');
var idnum = $(this).attr('id').substr(7);
$('tr.cg-' + idnum).toggle();
- if (src.substr(-9) == 'minus.png')
+ if (src.substr(-9) === 'minus.png')
$(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
else
$(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
@@ -248,7 +275,7 @@ var Documentation = {
var path = document.location.pathname;
var parts = path.split(/\//);
$.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
- if (this == '..')
+ if (this === '..')
parts.pop();
});
var url = parts.join('/');
@@ -284,4 +311,4 @@ _ = Documentation.gettext;
$(document).ready(function() {
Documentation.init();
-});
\ No newline at end of file
+});
diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js
new file mode 100644
index 0000000000000000000000000000000000000000..64a0640507439eaf96ea9479493c555be9e9adce
--- /dev/null
+++ b/doc/html/_static/documentation_options.js
@@ -0,0 +1,10 @@
+var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+ VERSION: '3.1.1',
+ LANGUAGE: 'None',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true,
+ SOURCELINK_SUFFIX: '.txt',
+ NAVIGATION_WITH_KEYS: false
+};
\ No newline at end of file
diff --git a/doc/html/_static/down-pressed.png b/doc/html/_static/down-pressed.png
deleted file mode 100644
index 7c30d004b71b32bb2fc06b3bd4dc8278baab0946..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/down-pressed.png and /dev/null differ
diff --git a/doc/html/_static/down.png b/doc/html/_static/down.png
deleted file mode 100644
index f48098a43b0c36342db9e1a9a7372e79b2484a59..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/down.png and /dev/null differ
diff --git a/doc/html/_static/file.png b/doc/html/_static/file.png
index 254c60bfbe2715ae2edca48ebccfd074deb8031d..a858a410e4faa62ce324d814e4b816fff83a6fb3 100644
Binary files a/doc/html/_static/file.png and b/doc/html/_static/file.png differ
diff --git a/doc/html/_static/jquery-1.11.1.js b/doc/html/_static/jquery-3.2.1.js
similarity index 52%
rename from doc/html/_static/jquery-1.11.1.js
rename to doc/html/_static/jquery-3.2.1.js
index d4b67f7e6c1a94df167f31657769717a71581066..d2d8ca4790e52b0537f3cbb7dcd766099b789583 100644
--- a/doc/html/_static/jquery-1.11.1.js
+++ b/doc/html/_static/jquery-3.2.1.js
@@ -1,27 +1,29 @@
/*!
- * jQuery JavaScript Library v1.11.1
- * http://jquery.com/
+ * jQuery JavaScript Library v3.2.1
+ * https://jquery.com/
*
* Includes Sizzle.js
- * http://sizzlejs.com/
+ * https://sizzlejs.com/
*
- * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors
+ * Copyright JS Foundation and other contributors
* Released under the MIT license
- * http://jquery.org/license
+ * https://jquery.org/license
*
- * Date: 2014-05-01T17:42Z
+ * Date: 2017-03-20T18:59Z
*/
+( function( global, factory ) {
-(function( global, factory ) {
+ "use strict";
if ( typeof module === "object" && typeof module.exports === "object" ) {
- // For CommonJS and CommonJS-like environments where a proper window is present,
- // execute the factory and get jQuery
- // For environments that do not inherently posses a window with a document
- // (such as Node.js), expose a jQuery-making factory as module.exports
- // This accentuates the need for the creation of a real window
+
+ // For CommonJS and CommonJS-like environments where a proper `window`
+ // is present, execute the factory and get jQuery.
+ // For environments that do not have a `window` with a `document`
+ // (such as Node.js), expose a factory as module.exports.
+ // This accentuates the need for the creation of a real `window`.
// e.g. var jQuery = require("jquery")(window);
- // See ticket #14549 for more info
+ // See ticket #14549 for more info.
module.exports = global.document ?
factory( global, true ) :
function( w ) {
@@ -35,23 +37,27 @@
}
// Pass this if window is not defined yet
-}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
+} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
-// Can't do this because several apps including ASP.NET trace
-// the stack via arguments.caller.callee and Firefox dies if
-// you try to trace through "use strict" call chains. (#13335)
-// Support: Firefox 18+
-//
+// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
+// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
+// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
+// enough that all such attempts are guarded in a try block.
+"use strict";
+
+var arr = [];
-var deletedIds = [];
+var document = window.document;
-var slice = deletedIds.slice;
+var getProto = Object.getPrototypeOf;
-var concat = deletedIds.concat;
+var slice = arr.slice;
-var push = deletedIds.push;
+var concat = arr.concat;
-var indexOf = deletedIds.indexOf;
+var push = arr.push;
+
+var indexOf = arr.indexOf;
var class2type = {};
@@ -59,27 +65,46 @@ var toString = class2type.toString;
var hasOwn = class2type.hasOwnProperty;
+var fnToString = hasOwn.toString;
+
+var ObjectFunctionString = fnToString.call( Object );
+
var support = {};
+ function DOMEval( code, doc ) {
+ doc = doc || document;
+
+ var script = doc.createElement( "script" );
+
+ script.text = code;
+ doc.head.appendChild( script ).parentNode.removeChild( script );
+ }
+/* global Symbol */
+// Defining this global in .eslintrc.json would create a danger of using the global
+// unguarded in another place, it seems safer to define global only for this module
+
+
+
var
- version = "1.11.1",
+ version = "3.2.1",
// Define a local copy of jQuery
jQuery = function( selector, context ) {
+
// The jQuery object is actually just the init constructor 'enhanced'
// Need init if jQuery is called (just allow error to be thrown if not included)
return new jQuery.fn.init( selector, context );
},
- // Support: Android<4.1, IE<9
+ // Support: Android <=4.0 only
// Make sure we trim BOM and NBSP
rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
// Matches dashed string for camelizing
rmsPrefix = /^-ms-/,
- rdashAlpha = /-([\da-z])/gi,
+ rdashAlpha = /-([a-z])/g,
// Used by jQuery.camelCase as callback to replace()
fcamelCase = function( all, letter ) {
@@ -87,14 +112,12 @@ var
};
jQuery.fn = jQuery.prototype = {
+
// The current version of jQuery being used
jquery: version,
constructor: jQuery,
- // Start with an empty selector
- selector: "",
-
// The default length of a jQuery object is 0
length: 0,
@@ -105,13 +128,14 @@ jQuery.fn = jQuery.prototype = {
// Get the Nth element in the matched element set OR
// Get the whole matched element set as a clean array
get: function( num ) {
- return num != null ?
- // Return just the one element from the set
- ( num < 0 ? this[ num + this.length ] : this[ num ] ) :
+ // Return all the elements in a clean array
+ if ( num == null ) {
+ return slice.call( this );
+ }
- // Return all the elements in a clean array
- slice.call( this );
+ // Return just the one element from the set
+ return num < 0 ? this[ num + this.length ] : this[ num ];
},
// Take an array of elements and push it onto the stack
@@ -123,23 +147,20 @@ jQuery.fn = jQuery.prototype = {
// Add the old object onto the stack (as a reference)
ret.prevObject = this;
- ret.context = this.context;
// Return the newly-formed element set
return ret;
},
// Execute a callback for every element in the matched set.
- // (You can seed the arguments with an array of args, but this is
- // only used internally.)
- each: function( callback, args ) {
- return jQuery.each( this, callback, args );
+ each: function( callback ) {
+ return jQuery.each( this, callback );
},
map: function( callback ) {
- return this.pushStack( jQuery.map(this, function( elem, i ) {
+ return this.pushStack( jQuery.map( this, function( elem, i ) {
return callback.call( elem, i, elem );
- }));
+ } ) );
},
slice: function() {
@@ -157,23 +178,23 @@ jQuery.fn = jQuery.prototype = {
eq: function( i ) {
var len = this.length,
j = +i + ( i < 0 ? len : 0 );
- return this.pushStack( j >= 0 && j < len ? [ this[j] ] : [] );
+ return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] );
},
end: function() {
- return this.prevObject || this.constructor(null);
+ return this.prevObject || this.constructor();
},
// For internal use only.
// Behaves like an Array's method, not like a jQuery method.
push: push,
- sort: deletedIds.sort,
- splice: deletedIds.splice
+ sort: arr.sort,
+ splice: arr.splice
};
jQuery.extend = jQuery.fn.extend = function() {
- var src, copyIsArray, copy, name, options, clone,
- target = arguments[0] || {},
+ var options, name, src, copy, copyIsArray, clone,
+ target = arguments[ 0 ] || {},
i = 1,
length = arguments.length,
deep = false;
@@ -182,25 +203,27 @@ jQuery.extend = jQuery.fn.extend = function() {
if ( typeof target === "boolean" ) {
deep = target;
- // skip the boolean and the target
+ // Skip the boolean and the target
target = arguments[ i ] || {};
i++;
}
// Handle case when target is a string or something (possible in deep copy)
- if ( typeof target !== "object" && !jQuery.isFunction(target) ) {
+ if ( typeof target !== "object" && !jQuery.isFunction( target ) ) {
target = {};
}
- // extend jQuery itself if only one argument is passed
+ // Extend jQuery itself if only one argument is passed
if ( i === length ) {
target = this;
i--;
}
for ( ; i < length; i++ ) {
+
// Only deal with non-null/undefined values
- if ( (options = arguments[ i ]) != null ) {
+ if ( ( options = arguments[ i ] ) != null ) {
+
// Extend the base object
for ( name in options ) {
src = target[ name ];
@@ -212,13 +235,15 @@ jQuery.extend = jQuery.fn.extend = function() {
}
// Recurse if we're merging plain objects or arrays
- if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) {
+ if ( deep && copy && ( jQuery.isPlainObject( copy ) ||
+ ( copyIsArray = Array.isArray( copy ) ) ) ) {
+
if ( copyIsArray ) {
copyIsArray = false;
- clone = src && jQuery.isArray(src) ? src : [];
+ clone = src && Array.isArray( src ) ? src : [];
} else {
- clone = src && jQuery.isPlainObject(src) ? src : {};
+ clone = src && jQuery.isPlainObject( src ) ? src : {};
}
// Never move original objects, clone them
@@ -236,7 +261,8 @@ jQuery.extend = jQuery.fn.extend = function() {
return target;
};
-jQuery.extend({
+jQuery.extend( {
+
// Unique for each copy of jQuery on the page
expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
@@ -249,150 +275,98 @@ jQuery.extend({
noop: function() {},
- // See test/unit/core.js for details concerning isFunction.
- // Since version 1.3, DOM methods and functions like alert
- // aren't supported. They return false on IE (#2968).
isFunction: function( obj ) {
- return jQuery.type(obj) === "function";
- },
-
- isArray: Array.isArray || function( obj ) {
- return jQuery.type(obj) === "array";
+ return jQuery.type( obj ) === "function";
},
isWindow: function( obj ) {
- /* jshint eqeqeq: false */
- return obj != null && obj == obj.window;
+ return obj != null && obj === obj.window;
},
isNumeric: function( obj ) {
- // parseFloat NaNs numeric-cast false positives (null|true|false|"")
- // ...but misinterprets leading-number strings, particularly hex literals ("0x...")
- // subtraction forces infinities to NaN
- return !jQuery.isArray( obj ) && obj - parseFloat( obj ) >= 0;
- },
- isEmptyObject: function( obj ) {
- var name;
- for ( name in obj ) {
- return false;
- }
- return true;
+ // As of jQuery 3.0, isNumeric is limited to
+ // strings and numbers (primitives or objects)
+ // that can be coerced to finite numbers (gh-2662)
+ var type = jQuery.type( obj );
+ return ( type === "number" || type === "string" ) &&
+
+ // parseFloat NaNs numeric-cast false positives ("")
+ // ...but misinterprets leading-number strings, particularly hex literals ("0x...")
+ // subtraction forces infinities to NaN
+ !isNaN( obj - parseFloat( obj ) );
},
isPlainObject: function( obj ) {
- var key;
+ var proto, Ctor;
- // Must be an Object.
- // Because of IE, we also have to check the presence of the constructor property.
- // Make sure that DOM nodes and window objects don't pass through, as well
- if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) {
+ // Detect obvious negatives
+ // Use toString instead of jQuery.type to catch host objects
+ if ( !obj || toString.call( obj ) !== "[object Object]" ) {
return false;
}
- try {
- // Not own constructor property must be Object
- if ( obj.constructor &&
- !hasOwn.call(obj, "constructor") &&
- !hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
- return false;
- }
- } catch ( e ) {
- // IE8,9 Will throw exceptions on certain host objects #9897
- return false;
- }
+ proto = getProto( obj );
- // Support: IE<9
- // Handle iteration over inherited properties before own properties.
- if ( support.ownLast ) {
- for ( key in obj ) {
- return hasOwn.call( obj, key );
- }
+ // Objects with no prototype (e.g., `Object.create( null )`) are plain
+ if ( !proto ) {
+ return true;
}
- // Own properties are enumerated firstly, so to speed up,
- // if last one is own, then all properties are own.
- for ( key in obj ) {}
+ // Objects with prototype are plain iff they were constructed by a global Object function
+ Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor;
+ return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString;
+ },
+
+ isEmptyObject: function( obj ) {
+
+ /* eslint-disable no-unused-vars */
+ // See https://github.com/eslint/eslint/issues/6125
+ var name;
- return key === undefined || hasOwn.call( obj, key );
+ for ( name in obj ) {
+ return false;
+ }
+ return true;
},
type: function( obj ) {
if ( obj == null ) {
return obj + "";
}
+
+ // Support: Android <=2.3 only (functionish RegExp)
return typeof obj === "object" || typeof obj === "function" ?
- class2type[ toString.call(obj) ] || "object" :
+ class2type[ toString.call( obj ) ] || "object" :
typeof obj;
},
// Evaluates a script in a global context
- // Workarounds based on findings by Jim Driscoll
- // http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
- globalEval: function( data ) {
- if ( data && jQuery.trim( data ) ) {
- // We use execScript on Internet Explorer
- // We use an anonymous function so that context is window
- // rather than jQuery in Firefox
- ( window.execScript || function( data ) {
- window[ "eval" ].call( window, data );
- } )( data );
- }
+ globalEval: function( code ) {
+ DOMEval( code );
},
// Convert dashed to camelCase; used by the css and data modules
+ // Support: IE <=9 - 11, Edge 12 - 13
// Microsoft forgot to hump their vendor prefix (#9572)
camelCase: function( string ) {
return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
},
- nodeName: function( elem, name ) {
- return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
- },
-
- // args is for internal usage only
- each: function( obj, callback, args ) {
- var value,
- i = 0,
- length = obj.length,
- isArray = isArraylike( obj );
-
- if ( args ) {
- if ( isArray ) {
- for ( ; i < length; i++ ) {
- value = callback.apply( obj[ i ], args );
-
- if ( value === false ) {
- break;
- }
- }
- } else {
- for ( i in obj ) {
- value = callback.apply( obj[ i ], args );
+ each: function( obj, callback ) {
+ var length, i = 0;
- if ( value === false ) {
- break;
- }
+ if ( isArrayLike( obj ) ) {
+ length = obj.length;
+ for ( ; i < length; i++ ) {
+ if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
+ break;
}
}
-
- // A special, fast, case for the most common use of each
} else {
- if ( isArray ) {
- for ( ; i < length; i++ ) {
- value = callback.call( obj[ i ], i, obj[ i ] );
-
- if ( value === false ) {
- break;
- }
- }
- } else {
- for ( i in obj ) {
- value = callback.call( obj[ i ], i, obj[ i ] );
-
- if ( value === false ) {
- break;
- }
+ for ( i in obj ) {
+ if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
+ break;
}
}
}
@@ -400,7 +374,7 @@ jQuery.extend({
return obj;
},
- // Support: Android<4.1, IE<9
+ // Support: Android <=4.0 only
trim: function( text ) {
return text == null ?
"" :
@@ -412,7 +386,7 @@ jQuery.extend({
var ret = results || [];
if ( arr != null ) {
- if ( isArraylike( Object(arr) ) ) {
+ if ( isArrayLike( Object( arr ) ) ) {
jQuery.merge( ret,
typeof arr === "string" ?
[ arr ] : arr
@@ -426,42 +400,18 @@ jQuery.extend({
},
inArray: function( elem, arr, i ) {
- var len;
-
- if ( arr ) {
- if ( indexOf ) {
- return indexOf.call( arr, elem, i );
- }
-
- len = arr.length;
- i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0;
-
- for ( ; i < len; i++ ) {
- // Skip accessing in sparse arrays
- if ( i in arr && arr[ i ] === elem ) {
- return i;
- }
- }
- }
-
- return -1;
+ return arr == null ? -1 : indexOf.call( arr, elem, i );
},
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
merge: function( first, second ) {
var len = +second.length,
j = 0,
i = first.length;
- while ( j < len ) {
- first[ i++ ] = second[ j++ ];
- }
-
- // Support: IE<9
- // Workaround casting of .length to NaN on otherwise arraylike objects (e.g., NodeLists)
- if ( len !== len ) {
- while ( second[j] !== undefined ) {
- first[ i++ ] = second[ j++ ];
- }
+ for ( ; j < len; j++ ) {
+ first[ i++ ] = second[ j ];
}
first.length = i;
@@ -490,14 +440,13 @@ jQuery.extend({
// arg is for internal usage only
map: function( elems, callback, arg ) {
- var value,
+ var length, value,
i = 0,
- length = elems.length,
- isArray = isArraylike( elems ),
ret = [];
// Go through the array, translating each of the items to their new values
- if ( isArray ) {
+ if ( isArrayLike( elems ) ) {
+ length = elems.length;
for ( ; i < length; i++ ) {
value = callback( elems[ i ], i, arg );
@@ -527,7 +476,7 @@ jQuery.extend({
// Bind a function to a context, optionally partially applying any
// arguments.
proxy: function( fn, context ) {
- var args, proxy, tmp;
+ var tmp, args, proxy;
if ( typeof context === "string" ) {
tmp = fn[ context ];
@@ -553,45 +502,49 @@ jQuery.extend({
return proxy;
},
- now: function() {
- return +( new Date() );
- },
+ now: Date.now,
// jQuery.support is not used in Core but other projects attach their
// properties to it so it needs to exist.
support: support
-});
+} );
+
+if ( typeof Symbol === "function" ) {
+ jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ];
+}
// Populate the class2type map
-jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) {
+jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ),
+function( i, name ) {
class2type[ "[object " + name + "]" ] = name.toLowerCase();
-});
+} );
+
+function isArrayLike( obj ) {
-function isArraylike( obj ) {
- var length = obj.length,
+ // Support: real iOS 8.2 only (not reproducible in simulator)
+ // `in` check used to prevent JIT error (gh-2145)
+ // hasOwn isn't used here due to false negatives
+ // regarding Nodelist length in IE
+ var length = !!obj && "length" in obj && obj.length,
type = jQuery.type( obj );
if ( type === "function" || jQuery.isWindow( obj ) ) {
return false;
}
- if ( obj.nodeType === 1 && length ) {
- return true;
- }
-
return type === "array" || length === 0 ||
typeof length === "number" && length > 0 && ( length - 1 ) in obj;
}
var Sizzle =
/*!
- * Sizzle CSS Selector Engine v1.10.19
- * http://sizzlejs.com/
+ * Sizzle CSS Selector Engine v2.3.3
+ * https://sizzlejs.com/
*
- * Copyright 2013 jQuery Foundation, Inc. and other contributors
+ * Copyright jQuery Foundation and other contributors
* Released under the MIT license
* http://jquery.org/license
*
- * Date: 2014-04-18
+ * Date: 2016-08-08
*/
(function( window ) {
@@ -618,7 +571,7 @@ var i,
contains,
// Instance-specific data
- expando = "sizzle" + -(new Date()),
+ expando = "sizzle" + 1 * new Date(),
preferredDoc = window.document,
dirruns = 0,
done = 0,
@@ -632,10 +585,6 @@ var i,
return 0;
},
- // General-purpose constants
- strundefined = typeof undefined,
- MAX_NEGATIVE = 1 << 31,
-
// Instance methods
hasOwn = ({}).hasOwnProperty,
arr = [],
@@ -643,12 +592,13 @@ var i,
push_native = arr.push,
push = arr.push,
slice = arr.slice,
- // Use a stripped-down indexOf if we can't use a native one
- indexOf = arr.indexOf || function( elem ) {
+ // Use a stripped-down indexOf as it's faster than native
+ // https://jsperf.com/thor-indexof-vs-for/5
+ indexOf = function( list, elem ) {
var i = 0,
- len = this.length;
+ len = list.length;
for ( ; i < len; i++ ) {
- if ( this[i] === elem ) {
+ if ( list[i] === elem ) {
return i;
}
}
@@ -659,25 +609,21 @@ var i,
// Regular expressions
- // Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace
+ // http://www.w3.org/TR/css3-selectors/#whitespace
whitespace = "[\\x20\\t\\r\\n\\f]",
- // http://www.w3.org/TR/css3-syntax/#characters
- characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+",
- // Loosely modeled on CSS identifier characters
- // An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors
- // Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
- identifier = characterEncoding.replace( "w", "w#" ),
+ // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
+ identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+",
// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
- attributes = "\\[" + whitespace + "*(" + characterEncoding + ")(?:" + whitespace +
+ attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace +
// Operator (capture 2)
"*([*^$|!~]?=)" + whitespace +
// "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
"*\\]",
- pseudos = ":(" + characterEncoding + ")(?:\\((" +
+ pseudos = ":(" + identifier + ")(?:\\((" +
// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
// 1. quoted (capture 3; capture 4 or capture 5)
"('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
@@ -688,6 +634,7 @@ var i,
")\\)|)",
// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
+ rwhitespace = new RegExp( whitespace + "+", "g" ),
rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
@@ -699,9 +646,9 @@ var i,
ridentifier = new RegExp( "^" + identifier + "$" ),
matchExpr = {
- "ID": new RegExp( "^#(" + characterEncoding + ")" ),
- "CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ),
- "TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ),
+ "ID": new RegExp( "^#(" + identifier + ")" ),
+ "CLASS": new RegExp( "^\\.(" + identifier + ")" ),
+ "TAG": new RegExp( "^(" + identifier + "|[*])" ),
"ATTR": new RegExp( "^" + attributes ),
"PSEUDO": new RegExp( "^" + pseudos ),
"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
@@ -723,9 +670,9 @@ var i,
rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
rsibling = /[+~]/,
- rescape = /'|\\/g,
- // CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
+ // CSS escapes
+ // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
funescape = function( _, escaped, escapedWhitespace ) {
var high = "0x" + escaped - 0x10000;
@@ -739,7 +686,41 @@ var i,
String.fromCharCode( high + 0x10000 ) :
// Supplemental Plane codepoint (surrogate pair)
String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
- };
+ },
+
+ // CSS string/identifier serialization
+ // https://drafts.csswg.org/cssom/#common-serializing-idioms
+ rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,
+ fcssescape = function( ch, asCodePoint ) {
+ if ( asCodePoint ) {
+
+ // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER
+ if ( ch === "\0" ) {
+ return "\uFFFD";
+ }
+
+ // Control characters and (dependent upon position) numbers get escaped as code points
+ return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " ";
+ }
+
+ // Other potentially-special ASCII characters get backslash-escaped
+ return "\\" + ch;
+ },
+
+ // Used for iframes
+ // See setDocument()
+ // Removing the function wrapper causes a "Permission Denied"
+ // error in IE
+ unloadHandler = function() {
+ setDocument();
+ },
+
+ disabledAncestor = addCombinator(
+ function( elem ) {
+ return elem.disabled === true && ("form" in elem || "label" in elem);
+ },
+ { dir: "parentNode", next: "legend" }
+ );
// Optimize for push.apply( _, NodeList )
try {
@@ -771,104 +752,128 @@ try {
}
function Sizzle( selector, context, results, seed ) {
- var match, elem, m, nodeType,
- // QSA vars
- i, groups, old, nid, newContext, newSelector;
+ var m, i, elem, nid, match, groups, newSelector,
+ newContext = context && context.ownerDocument,
- if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
- setDocument( context );
- }
+ // nodeType defaults to 9, since context defaults to document
+ nodeType = context ? context.nodeType : 9;
- context = context || document;
results = results || [];
- if ( !selector || typeof selector !== "string" ) {
+ // Return early from calls with invalid selector or context
+ if ( typeof selector !== "string" || !selector ||
+ nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
+
return results;
}
- if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) {
- return [];
- }
+ // Try to shortcut find operations (as opposed to filters) in HTML documents
+ if ( !seed ) {
- if ( documentIsHTML && !seed ) {
-
- // Shortcuts
- if ( (match = rquickExpr.exec( selector )) ) {
- // Speed-up: Sizzle("#ID")
- if ( (m = match[1]) ) {
- if ( nodeType === 9 ) {
- elem = context.getElementById( m );
- // Check parentNode to catch when Blackberry 4.6 returns
- // nodes that are no longer in the document (jQuery #6963)
- if ( elem && elem.parentNode ) {
- // Handle the case where IE, Opera, and Webkit return items
- // by name instead of ID
- if ( elem.id === m ) {
- results.push( elem );
+ if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
+ setDocument( context );
+ }
+ context = context || document;
+
+ if ( documentIsHTML ) {
+
+ // If the selector is sufficiently simple, try using a "get*By*" DOM method
+ // (excepting DocumentFragment context, where the methods don't exist)
+ if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {
+
+ // ID selector
+ if ( (m = match[1]) ) {
+
+ // Document context
+ if ( nodeType === 9 ) {
+ if ( (elem = context.getElementById( m )) ) {
+
+ // Support: IE, Opera, Webkit
+ // TODO: identify versions
+ // getElementById can match elements by name instead of ID
+ if ( elem.id === m ) {
+ results.push( elem );
+ return results;
+ }
+ } else {
return results;
}
+
+ // Element context
} else {
- return results;
- }
- } else {
- // Context is not a document
- if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) &&
- contains( context, elem ) && elem.id === m ) {
- results.push( elem );
- return results;
+
+ // Support: IE, Opera, Webkit
+ // TODO: identify versions
+ // getElementById can match elements by name instead of ID
+ if ( newContext && (elem = newContext.getElementById( m )) &&
+ contains( context, elem ) &&
+ elem.id === m ) {
+
+ results.push( elem );
+ return results;
+ }
}
- }
- // Speed-up: Sizzle("TAG")
- } else if ( match[2] ) {
- push.apply( results, context.getElementsByTagName( selector ) );
- return results;
+ // Type selector
+ } else if ( match[2] ) {
+ push.apply( results, context.getElementsByTagName( selector ) );
+ return results;
- // Speed-up: Sizzle(".CLASS")
- } else if ( (m = match[3]) && support.getElementsByClassName && context.getElementsByClassName ) {
- push.apply( results, context.getElementsByClassName( m ) );
- return results;
+ // Class selector
+ } else if ( (m = match[3]) && support.getElementsByClassName &&
+ context.getElementsByClassName ) {
+
+ push.apply( results, context.getElementsByClassName( m ) );
+ return results;
+ }
}
- }
- // QSA path
- if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
- nid = old = expando;
- newContext = context;
- newSelector = nodeType === 9 && selector;
+ // Take advantage of querySelectorAll
+ if ( support.qsa &&
+ !compilerCache[ selector + " " ] &&
+ (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
- // qSA works strangely on Element-rooted queries
- // We can work around this by specifying an extra ID on the root
- // and working up from there (Thanks to Andrew Dupont for the technique)
- // IE 8 doesn't work on object elements
- if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
- groups = tokenize( selector );
+ if ( nodeType !== 1 ) {
+ newContext = context;
+ newSelector = selector;
- if ( (old = context.getAttribute("id")) ) {
- nid = old.replace( rescape, "\\$&" );
- } else {
- context.setAttribute( "id", nid );
- }
- nid = "[id='" + nid + "'] ";
+ // qSA looks outside Element context, which is not what we want
+ // Thanks to Andrew Dupont for this workaround technique
+ // Support: IE <=8
+ // Exclude object elements
+ } else if ( context.nodeName.toLowerCase() !== "object" ) {
- i = groups.length;
- while ( i-- ) {
- groups[i] = nid + toSelector( groups[i] );
+ // Capture the context ID, setting it first if necessary
+ if ( (nid = context.getAttribute( "id" )) ) {
+ nid = nid.replace( rcssescape, fcssescape );
+ } else {
+ context.setAttribute( "id", (nid = expando) );
+ }
+
+ // Prefix every selector in the list
+ groups = tokenize( selector );
+ i = groups.length;
+ while ( i-- ) {
+ groups[i] = "#" + nid + " " + toSelector( groups[i] );
+ }
+ newSelector = groups.join( "," );
+
+ // Expand context for sibling selectors
+ newContext = rsibling.test( selector ) && testContext( context.parentNode ) ||
+ context;
}
- newContext = rsibling.test( selector ) && testContext( context.parentNode ) || context;
- newSelector = groups.join(",");
- }
- if ( newSelector ) {
- try {
- push.apply( results,
- newContext.querySelectorAll( newSelector )
- );
- return results;
- } catch(qsaError) {
- } finally {
- if ( !old ) {
- context.removeAttribute("id");
+ if ( newSelector ) {
+ try {
+ push.apply( results,
+ newContext.querySelectorAll( newSelector )
+ );
+ return results;
+ } catch ( qsaError ) {
+ } finally {
+ if ( nid === expando ) {
+ context.removeAttribute( "id" );
+ }
}
}
}
@@ -881,7 +886,7 @@ function Sizzle( selector, context, results, seed ) {
/**
* Create key-value caches of limited size
- * @returns {Function(string, Object)} Returns the Object data after storing it on itself with
+ * @returns {function(string, object)} Returns the Object data after storing it on itself with
* property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
* deleting the oldest entry
*/
@@ -910,22 +915,22 @@ function markFunction( fn ) {
/**
* Support testing using an element
- * @param {Function} fn Passed the created div and expects a boolean result
+ * @param {Function} fn Passed the created element and returns a boolean result
*/
function assert( fn ) {
- var div = document.createElement("div");
+ var el = document.createElement("fieldset");
try {
- return !!fn( div );
+ return !!fn( el );
} catch (e) {
return false;
} finally {
// Remove from its parent by default
- if ( div.parentNode ) {
- div.parentNode.removeChild( div );
+ if ( el.parentNode ) {
+ el.parentNode.removeChild( el );
}
// release memory in IE
- div = null;
+ el = null;
}
}
@@ -936,7 +941,7 @@ function assert( fn ) {
*/
function addHandle( attrs, handler ) {
var arr = attrs.split("|"),
- i = attrs.length;
+ i = arr.length;
while ( i-- ) {
Expr.attrHandle[ arr[i] ] = handler;
@@ -952,8 +957,7 @@ function addHandle( attrs, handler ) {
function siblingCheck( a, b ) {
var cur = b && a,
diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
- ( ~b.sourceIndex || MAX_NEGATIVE ) -
- ( ~a.sourceIndex || MAX_NEGATIVE );
+ a.sourceIndex - b.sourceIndex;
// Use IE sourceIndex if available on both nodes
if ( diff ) {
@@ -994,6 +998,62 @@ function createButtonPseudo( type ) {
};
}
+/**
+ * Returns a function to use in pseudos for :enabled/:disabled
+ * @param {Boolean} disabled true for :disabled; false for :enabled
+ */
+function createDisabledPseudo( disabled ) {
+
+ // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable
+ return function( elem ) {
+
+ // Only certain elements can match :enabled or :disabled
+ // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled
+ // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled
+ if ( "form" in elem ) {
+
+ // Check for inherited disabledness on relevant non-disabled elements:
+ // * listed form-associated elements in a disabled fieldset
+ // https://html.spec.whatwg.org/multipage/forms.html#category-listed
+ // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled
+ // * option elements in a disabled optgroup
+ // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled
+ // All such elements have a "form" property.
+ if ( elem.parentNode && elem.disabled === false ) {
+
+ // Option elements defer to a parent optgroup if present
+ if ( "label" in elem ) {
+ if ( "label" in elem.parentNode ) {
+ return elem.parentNode.disabled === disabled;
+ } else {
+ return elem.disabled === disabled;
+ }
+ }
+
+ // Support: IE 6 - 11
+ // Use the isDisabled shortcut property to check for disabled fieldset ancestors
+ return elem.isDisabled === disabled ||
+
+ // Where there is no isDisabled, check manually
+ /* jshint -W018 */
+ elem.isDisabled !== !disabled &&
+ disabledAncestor( elem ) === disabled;
+ }
+
+ return elem.disabled === disabled;
+
+ // Try to winnow out elements that can't be disabled before trusting the disabled property.
+ // Some victims get caught in our net (label, legend, menu, track), but it shouldn't
+ // even exist on them, let alone have a boolean value.
+ } else if ( "label" in elem ) {
+ return elem.disabled === disabled;
+ }
+
+ // Remaining elements are neither :enabled nor :disabled
+ return false;
+ };
+}
+
/**
* Returns a function to use in pseudos for positionals
* @param {Function} fn
@@ -1022,7 +1082,7 @@ function createPositionalPseudo( fn ) {
* @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
*/
function testContext( context ) {
- return context && typeof context.getElementsByTagName !== strundefined && context;
+ return context && typeof context.getElementsByTagName !== "undefined" && context;
}
// Expose support vars for convenience
@@ -1046,36 +1106,31 @@ isXML = Sizzle.isXML = function( elem ) {
* @returns {Object} Returns the current document
*/
setDocument = Sizzle.setDocument = function( node ) {
- var hasCompare,
- doc = node ? node.ownerDocument || node : preferredDoc,
- parent = doc.defaultView;
+ var hasCompare, subWindow,
+ doc = node ? node.ownerDocument || node : preferredDoc;
- // If no document and documentElement is available, return
+ // Return early if doc is invalid or already selected
if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
return document;
}
- // Set our document
+ // Update global variables
document = doc;
- docElem = doc.documentElement;
-
- // Support tests
- documentIsHTML = !isXML( doc );
-
- // Support: IE>8
- // If iframe document is assigned to "document" variable and if iframe has been reloaded,
- // IE will throw "permission denied" error when accessing "document" variable, see jQuery #13936
- // IE6-8 do not support the defaultView property so parent will be undefined
- if ( parent && parent !== parent.top ) {
- // IE11 does not have attachEvent, so all must suffer
- if ( parent.addEventListener ) {
- parent.addEventListener( "unload", function() {
- setDocument();
- }, false );
- } else if ( parent.attachEvent ) {
- parent.attachEvent( "onunload", function() {
- setDocument();
- });
+ docElem = document.documentElement;
+ documentIsHTML = !isXML( document );
+
+ // Support: IE 9-11, Edge
+ // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936)
+ if ( preferredDoc !== document &&
+ (subWindow = document.defaultView) && subWindow.top !== subWindow ) {
+
+ // Support: IE 11, Edge
+ if ( subWindow.addEventListener ) {
+ subWindow.addEventListener( "unload", unloadHandler, false );
+
+ // Support: IE 9 - 10 only
+ } else if ( subWindow.attachEvent ) {
+ subWindow.attachEvent( "onunload", unloadHandler );
}
}
@@ -1083,83 +1138,106 @@ setDocument = Sizzle.setDocument = function( node ) {
---------------------------------------------------------------------- */
// Support: IE<8
- // Verify that getAttribute really returns attributes and not properties (excepting IE8 booleans)
- support.attributes = assert(function( div ) {
- div.className = "i";
- return !div.getAttribute("className");
+ // Verify that getAttribute really returns attributes and not properties
+ // (excepting IE8 booleans)
+ support.attributes = assert(function( el ) {
+ el.className = "i";
+ return !el.getAttribute("className");
});
/* getElement(s)By*
---------------------------------------------------------------------- */
// Check if getElementsByTagName("*") returns only elements
- support.getElementsByTagName = assert(function( div ) {
- div.appendChild( doc.createComment("") );
- return !div.getElementsByTagName("*").length;
+ support.getElementsByTagName = assert(function( el ) {
+ el.appendChild( document.createComment("") );
+ return !el.getElementsByTagName("*").length;
});
- // Check if getElementsByClassName can be trusted
- support.getElementsByClassName = rnative.test( doc.getElementsByClassName ) && assert(function( div ) {
- div.innerHTML = "<div class='a'></div><div class='a i'></div>";
-
- // Support: Safari<4
- // Catch class over-caching
- div.firstChild.className = "i";
- // Support: Opera<10
- // Catch gEBCN failure to find non-leading classes
- return div.getElementsByClassName("i").length === 2;
- });
+ // Support: IE<9
+ support.getElementsByClassName = rnative.test( document.getElementsByClassName );
// Support: IE<10
// Check if getElementById returns elements by name
- // The broken getElementById methods don't pick up programatically-set names,
+ // The broken getElementById methods don't pick up programmatically-set names,
// so use a roundabout getElementsByName test
- support.getById = assert(function( div ) {
- docElem.appendChild( div ).id = expando;
- return !doc.getElementsByName || !doc.getElementsByName( expando ).length;
+ support.getById = assert(function( el ) {
+ docElem.appendChild( el ).id = expando;
+ return !document.getElementsByName || !document.getElementsByName( expando ).length;
});
- // ID find and filter
+ // ID filter and find
if ( support.getById ) {
- Expr.find["ID"] = function( id, context ) {
- if ( typeof context.getElementById !== strundefined && documentIsHTML ) {
- var m = context.getElementById( id );
- // Check parentNode to catch when Blackberry 4.6 returns
- // nodes that are no longer in the document #6963
- return m && m.parentNode ? [ m ] : [];
- }
- };
Expr.filter["ID"] = function( id ) {
var attrId = id.replace( runescape, funescape );
return function( elem ) {
return elem.getAttribute("id") === attrId;
};
};
+ Expr.find["ID"] = function( id, context ) {
+ if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+ var elem = context.getElementById( id );
+ return elem ? [ elem ] : [];
+ }
+ };
} else {
- // Support: IE6/7
- // getElementById is not reliable as a find shortcut
- delete Expr.find["ID"];
-
Expr.filter["ID"] = function( id ) {
var attrId = id.replace( runescape, funescape );
return function( elem ) {
- var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id");
+ var node = typeof elem.getAttributeNode !== "undefined" &&
+ elem.getAttributeNode("id");
return node && node.value === attrId;
};
};
+
+ // Support: IE 6 - 7 only
+ // getElementById is not reliable as a find shortcut
+ Expr.find["ID"] = function( id, context ) {
+ if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+ var node, i, elems,
+ elem = context.getElementById( id );
+
+ if ( elem ) {
+
+ // Verify the id attribute
+ node = elem.getAttributeNode("id");
+ if ( node && node.value === id ) {
+ return [ elem ];
+ }
+
+ // Fall back on getElementsByName
+ elems = context.getElementsByName( id );
+ i = 0;
+ while ( (elem = elems[i++]) ) {
+ node = elem.getAttributeNode("id");
+ if ( node && node.value === id ) {
+ return [ elem ];
+ }
+ }
+ }
+
+ return [];
+ }
+ };
}
// Tag
Expr.find["TAG"] = support.getElementsByTagName ?
function( tag, context ) {
- if ( typeof context.getElementsByTagName !== strundefined ) {
+ if ( typeof context.getElementsByTagName !== "undefined" ) {
return context.getElementsByTagName( tag );
+
+ // DocumentFragment nodes don't have gEBTN
+ } else if ( support.qsa ) {
+ return context.querySelectorAll( tag );
}
} :
+
function( tag, context ) {
var elem,
tmp = [],
i = 0,
+ // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
results = context.getElementsByTagName( tag );
// Filter out possible comments
@@ -1177,7 +1255,7 @@ setDocument = Sizzle.setDocument = function( node ) {
// Class
Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
- if ( typeof context.getElementsByClassName !== strundefined && documentIsHTML ) {
+ if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) {
return context.getElementsByClassName( className );
}
};
@@ -1194,63 +1272,87 @@ setDocument = Sizzle.setDocument = function( node ) {
// We allow this because of a bug in IE8/9 that throws an error
// whenever `document.activeElement` is accessed on an iframe
// So, we allow :focus to pass through QSA all the time to avoid the IE error
- // See http://bugs.jquery.com/ticket/13378
+ // See https://bugs.jquery.com/ticket/13378
rbuggyQSA = [];
- if ( (support.qsa = rnative.test( doc.querySelectorAll )) ) {
+ if ( (support.qsa = rnative.test( document.querySelectorAll )) ) {
// Build QSA regex
// Regex strategy adopted from Diego Perini
- assert(function( div ) {
+ assert(function( el ) {
// Select is set to empty string on purpose
// This is to test IE's treatment of not explicitly
// setting a boolean content attribute,
// since its presence should be enough
- // http://bugs.jquery.com/ticket/12359
- div.innerHTML = "<select msallowclip=''><option selected=''></option></select>";
+ // https://bugs.jquery.com/ticket/12359
+ docElem.appendChild( el ).innerHTML = "<a id='" + expando + "'></a>" +
+ "<select id='" + expando + "-\r\\' msallowcapture=''>" +
+ "<option selected=''></option></select>";
// Support: IE8, Opera 11-12.16
// Nothing should be selected when empty strings follow ^= or $= or *=
// The test attribute must be unknown in Opera but "safe" for WinRT
- // http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
- if ( div.querySelectorAll("[msallowclip^='']").length ) {
+ // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
+ if ( el.querySelectorAll("[msallowcapture^='']").length ) {
rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
}
// Support: IE8
// Boolean attributes and "value" are not treated correctly
- if ( !div.querySelectorAll("[selected]").length ) {
+ if ( !el.querySelectorAll("[selected]").length ) {
rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
}
+ // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+
+ if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
+ rbuggyQSA.push("~=");
+ }
+
// Webkit/Opera - :checked should return selected option elements
// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
// IE8 throws error here and will not see later tests
- if ( !div.querySelectorAll(":checked").length ) {
+ if ( !el.querySelectorAll(":checked").length ) {
rbuggyQSA.push(":checked");
}
+
+ // Support: Safari 8+, iOS 8+
+ // https://bugs.webkit.org/show_bug.cgi?id=136851
+ // In-page `selector#id sibling-combinator selector` fails
+ if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) {
+ rbuggyQSA.push(".#.+[+~]");
+ }
});
- assert(function( div ) {
+ assert(function( el ) {
+ el.innerHTML = "<a href='' disabled='disabled'></a>" +
+ "<select disabled='disabled'><option/></select>";
+
// Support: Windows 8 Native Apps
// The type and name attributes are restricted during .innerHTML assignment
- var input = doc.createElement("input");
+ var input = document.createElement("input");
input.setAttribute( "type", "hidden" );
- div.appendChild( input ).setAttribute( "name", "D" );
+ el.appendChild( input ).setAttribute( "name", "D" );
// Support: IE8
// Enforce case-sensitivity of name attribute
- if ( div.querySelectorAll("[name=d]").length ) {
+ if ( el.querySelectorAll("[name=d]").length ) {
rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
}
// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
// IE8 throws error here and will not see later tests
- if ( !div.querySelectorAll(":enabled").length ) {
+ if ( el.querySelectorAll(":enabled").length !== 2 ) {
+ rbuggyQSA.push( ":enabled", ":disabled" );
+ }
+
+ // Support: IE9-11+
+ // IE's :disabled selector does not pick up the children of disabled fieldsets
+ docElem.appendChild( el ).disabled = true;
+ if ( el.querySelectorAll(":disabled").length !== 2 ) {
rbuggyQSA.push( ":enabled", ":disabled" );
}
// Opera 10-11 does not throw on post-comma invalid pseudos
- div.querySelectorAll("*,:x");
+ el.querySelectorAll("*,:x");
rbuggyQSA.push(",.*:");
});
}
@@ -1261,14 +1363,14 @@ setDocument = Sizzle.setDocument = function( node ) {
docElem.oMatchesSelector ||
docElem.msMatchesSelector) )) ) {
- assert(function( div ) {
+ assert(function( el ) {
// Check to see if it's possible to do matchesSelector
// on a disconnected node (IE 9)
- support.disconnectedMatch = matches.call( div, "div" );
+ support.disconnectedMatch = matches.call( el, "*" );
// This should fail with an exception
// Gecko does not error, returns false instead
- matches.call( div, "[s!='']:x" );
+ matches.call( el, "[s!='']:x" );
rbuggyMatches.push( "!=", pseudos );
});
}
@@ -1281,7 +1383,7 @@ setDocument = Sizzle.setDocument = function( node ) {
hasCompare = rnative.test( docElem.compareDocumentPosition );
// Element contains another
- // Purposefully does not implement inclusive descendent
+ // Purposefully self-exclusive
// As in, an element does not contain itself
contains = hasCompare || rnative.test( docElem.contains ) ?
function( a, b ) {
@@ -1335,16 +1437,16 @@ setDocument = Sizzle.setDocument = function( node ) {
(!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
// Choose the first element that is related to our preferred document
- if ( a === doc || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
+ if ( a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
return -1;
}
- if ( b === doc || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
+ if ( b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
return 1;
}
// Maintain original order
return sortInput ?
- ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) :
+ ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
0;
}
@@ -1366,12 +1468,12 @@ setDocument = Sizzle.setDocument = function( node ) {
// Parentless nodes are either documents or disconnected
if ( !aup || !bup ) {
- return a === doc ? -1 :
- b === doc ? 1 :
+ return a === document ? -1 :
+ b === document ? 1 :
aup ? -1 :
bup ? 1 :
sortInput ?
- ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) :
+ ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
0;
// If the nodes are siblings, we can do a quick check
@@ -1404,7 +1506,7 @@ setDocument = Sizzle.setDocument = function( node ) {
0;
};
- return doc;
+ return document;
};
Sizzle.matches = function( expr, elements ) {
@@ -1421,6 +1523,7 @@ Sizzle.matchesSelector = function( elem, expr ) {
expr = expr.replace( rattributeQuotes, "='$1']" );
if ( support.matchesSelector && documentIsHTML &&
+ !compilerCache[ expr + " " ] &&
( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) {
@@ -1434,7 +1537,7 @@ Sizzle.matchesSelector = function( elem, expr ) {
elem.document && elem.document.nodeType !== 11 ) {
return ret;
}
- } catch(e) {}
+ } catch (e) {}
}
return Sizzle( expr, document, null, [ elem ] ).length > 0;
@@ -1469,6 +1572,10 @@ Sizzle.attr = function( elem, name ) {
null;
};
+Sizzle.escape = function( sel ) {
+ return (sel + "").replace( rcssescape, fcssescape );
+};
+
Sizzle.error = function( msg ) {
throw new Error( "Syntax error, unrecognized expression: " + msg );
};
@@ -1653,7 +1760,7 @@ Expr = Sizzle.selectors = {
return pattern ||
(pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
classCache( className, function( elem ) {
- return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== strundefined && elem.getAttribute("class") || "" );
+ return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" );
});
},
@@ -1675,7 +1782,7 @@ Expr = Sizzle.selectors = {
operator === "^=" ? check && result.indexOf( check ) === 0 :
operator === "*=" ? check && result.indexOf( check ) > -1 :
operator === "$=" ? check && result.slice( -check.length ) === check :
- operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 :
+ operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 :
operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
false;
};
@@ -1694,11 +1801,12 @@ Expr = Sizzle.selectors = {
} :
function( elem, context, xml ) {
- var cache, outerCache, node, diff, nodeIndex, start,
+ var cache, uniqueCache, outerCache, node, nodeIndex, start,
dir = simple !== forward ? "nextSibling" : "previousSibling",
parent = elem.parentNode,
name = ofType && elem.nodeName.toLowerCase(),
- useCache = !xml && !ofType;
+ useCache = !xml && !ofType,
+ diff = false;
if ( parent ) {
@@ -1707,7 +1815,10 @@ Expr = Sizzle.selectors = {
while ( dir ) {
node = elem;
while ( (node = node[ dir ]) ) {
- if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) {
+ if ( ofType ?
+ node.nodeName.toLowerCase() === name :
+ node.nodeType === 1 ) {
+
return false;
}
}
@@ -1721,11 +1832,21 @@ Expr = Sizzle.selectors = {
// non-xml :nth-child(...) stores cache data on `parent`
if ( forward && useCache ) {
+
// Seek `elem` from a previously-cached index
- outerCache = parent[ expando ] || (parent[ expando ] = {});
- cache = outerCache[ type ] || [];
- nodeIndex = cache[0] === dirruns && cache[1];
- diff = cache[0] === dirruns && cache[2];
+
+ // ...in a gzip-friendly way
+ node = parent;
+ outerCache = node[ expando ] || (node[ expando ] = {});
+
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ node.uniqueID ] ||
+ (outerCache[ node.uniqueID ] = {});
+
+ cache = uniqueCache[ type ] || [];
+ nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
+ diff = nodeIndex && cache[ 2 ];
node = nodeIndex && parent.childNodes[ nodeIndex ];
while ( (node = ++nodeIndex && node && node[ dir ] ||
@@ -1735,29 +1856,55 @@ Expr = Sizzle.selectors = {
// When found, cache indexes on `parent` and break
if ( node.nodeType === 1 && ++diff && node === elem ) {
- outerCache[ type ] = [ dirruns, nodeIndex, diff ];
+ uniqueCache[ type ] = [ dirruns, nodeIndex, diff ];
break;
}
}
- // Use previously-cached element index if available
- } else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) {
- diff = cache[1];
-
- // xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...)
} else {
- // Use the same loop as above to seek `elem` from the start
- while ( (node = ++nodeIndex && node && node[ dir ] ||
- (diff = nodeIndex = 0) || start.pop()) ) {
+ // Use previously-cached element index if available
+ if ( useCache ) {
+ // ...in a gzip-friendly way
+ node = elem;
+ outerCache = node[ expando ] || (node[ expando ] = {});
- if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) {
- // Cache the index of each encountered element
- if ( useCache ) {
- (node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ];
- }
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ node.uniqueID ] ||
+ (outerCache[ node.uniqueID ] = {});
+
+ cache = uniqueCache[ type ] || [];
+ nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
+ diff = nodeIndex;
+ }
- if ( node === elem ) {
- break;
+ // xml :nth-child(...)
+ // or :nth-last-child(...) or :nth(-last)?-of-type(...)
+ if ( diff === false ) {
+ // Use the same loop as above to seek `elem` from the start
+ while ( (node = ++nodeIndex && node && node[ dir ] ||
+ (diff = nodeIndex = 0) || start.pop()) ) {
+
+ if ( ( ofType ?
+ node.nodeName.toLowerCase() === name :
+ node.nodeType === 1 ) &&
+ ++diff ) {
+
+ // Cache the index of each encountered element
+ if ( useCache ) {
+ outerCache = node[ expando ] || (node[ expando ] = {});
+
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ node.uniqueID ] ||
+ (outerCache[ node.uniqueID ] = {});
+
+ uniqueCache[ type ] = [ dirruns, diff ];
+ }
+
+ if ( node === elem ) {
+ break;
+ }
}
}
}
@@ -1795,7 +1942,7 @@ Expr = Sizzle.selectors = {
matched = fn( seed, argument ),
i = matched.length;
while ( i-- ) {
- idx = indexOf.call( seed, matched[i] );
+ idx = indexOf( seed, matched[i] );
seed[ idx ] = !( matches[ idx ] = matched[i] );
}
}) :
@@ -1834,6 +1981,8 @@ Expr = Sizzle.selectors = {
function( elem, context, xml ) {
input[0] = elem;
matcher( input, null, xml, results );
+ // Don't keep the element (issue #299)
+ input[0] = null;
return !results.pop();
};
}),
@@ -1845,6 +1994,7 @@ Expr = Sizzle.selectors = {
}),
"contains": markFunction(function( text ) {
+ text = text.replace( runescape, funescape );
return function( elem ) {
return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
};
@@ -1893,13 +2043,8 @@ Expr = Sizzle.selectors = {
},
// Boolean properties
- "enabled": function( elem ) {
- return elem.disabled === false;
- },
-
- "disabled": function( elem ) {
- return elem.disabled === true;
- },
+ "enabled": createDisabledPseudo( false ),
+ "disabled": createDisabledPseudo( true ),
"checked": function( elem ) {
// In CSS3, :checked should return both checked and selected elements
@@ -2101,7 +2246,9 @@ function toSelector( tokens ) {
function addCombinator( matcher, combinator, base ) {
var dir = combinator.dir,
- checkNonElements = base && dir === "parentNode",
+ skip = combinator.next,
+ key = skip || dir,
+ checkNonElements = base && key === "parentNode",
doneName = done++;
return combinator.first ?
@@ -2112,14 +2259,15 @@ function addCombinator( matcher, combinator, base ) {
return matcher( elem, context, xml );
}
}
+ return false;
} :
// Check against all ancestor/preceding elements
function( elem, context, xml ) {
- var oldCache, outerCache,
+ var oldCache, uniqueCache, outerCache,
newCache = [ dirruns, doneName ];
- // We can't set arbitrary data on XML nodes, so they don't benefit from dir caching
+ // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching
if ( xml ) {
while ( (elem = elem[ dir ]) ) {
if ( elem.nodeType === 1 || checkNonElements ) {
@@ -2132,14 +2280,21 @@ function addCombinator( matcher, combinator, base ) {
while ( (elem = elem[ dir ]) ) {
if ( elem.nodeType === 1 || checkNonElements ) {
outerCache = elem[ expando ] || (elem[ expando ] = {});
- if ( (oldCache = outerCache[ dir ]) &&
+
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ elem.uniqueID ] || (outerCache[ elem.uniqueID ] = {});
+
+ if ( skip && skip === elem.nodeName.toLowerCase() ) {
+ elem = elem[ dir ] || elem;
+ } else if ( (oldCache = uniqueCache[ key ]) &&
oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
// Assign to newCache so results back-propagate to previous elements
return (newCache[ 2 ] = oldCache[ 2 ]);
} else {
// Reuse newcache so results back-propagate to previous elements
- outerCache[ dir ] = newCache;
+ uniqueCache[ key ] = newCache;
// A match means we're done; a fail means we have to keep checking
if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
@@ -2149,6 +2304,7 @@ function addCombinator( matcher, combinator, base ) {
}
}
}
+ return false;
};
}
@@ -2266,7 +2422,7 @@ function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postS
i = matcherOut.length;
while ( i-- ) {
if ( (elem = matcherOut[i]) &&
- (temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) {
+ (temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) {
seed[temp] = !(results[temp] = elem);
}
@@ -2301,13 +2457,16 @@ function matcherFromTokens( tokens ) {
return elem === checkContext;
}, implicitRelative, true ),
matchAnyContext = addCombinator( function( elem ) {
- return indexOf.call( checkContext, elem ) > -1;
+ return indexOf( checkContext, elem ) > -1;
}, implicitRelative, true ),
matchers = [ function( elem, context, xml ) {
- return ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
+ var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
(checkContext = context).nodeType ?
matchContext( elem, context, xml ) :
matchAnyContext( elem, context, xml ) );
+ // Avoid hanging onto element (issue #299)
+ checkContext = null;
+ return ret;
} ];
for ( ; i < len; i++ ) {
@@ -2361,18 +2520,21 @@ function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
len = elems.length;
if ( outermost ) {
- outermostContext = context !== document && context;
+ outermostContext = context === document || context || outermost;
}
// Add elements passing elementMatchers directly to results
- // Keep `i` a string if there are no elements so `matchedCount` will be "00" below
// Support: IE<9, Safari
// Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
if ( byElement && elem ) {
j = 0;
+ if ( !context && elem.ownerDocument !== document ) {
+ setDocument( elem );
+ xml = !documentIsHTML;
+ }
while ( (matcher = elementMatchers[j++]) ) {
- if ( matcher( elem, context, xml ) ) {
+ if ( matcher( elem, context || document, xml) ) {
results.push( elem );
break;
}
@@ -2396,8 +2558,17 @@ function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
}
}
- // Apply set filters to unmatched elements
+ // `i` is now the count of elements visited above, and adding it to `matchedCount`
+ // makes the latter nonnegative.
matchedCount += i;
+
+ // Apply set filters to unmatched elements
+ // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount`
+ // equals `i`), unless we didn't visit _any_ elements in the above loop because we have
+ // no element matchers and no seed.
+ // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that
+ // case, which will result in a "00" `matchedCount` that differs from `i` but is also
+ // numerically zero.
if ( bySet && i !== matchedCount ) {
j = 0;
while ( (matcher = setMatchers[j++]) ) {
@@ -2489,14 +2660,14 @@ select = Sizzle.select = function( selector, context, results, seed ) {
results = results || [];
- // Try to minimize operations if there is no seed and only one group
+ // Try to minimize operations if there is only one selector in the list and no seed
+ // (the latter of which guarantees us context)
if ( match.length === 1 ) {
- // Take a shortcut and set the context if the root selector is an ID
+ // Reduce context if the leading compound selector is an ID
tokens = match[0] = match[0].slice( 0 );
if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
- support.getById && context.nodeType === 9 && documentIsHTML &&
- Expr.relative[ tokens[1].type ] ) {
+ context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[1].type ] ) {
context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
if ( !context ) {
@@ -2547,7 +2718,7 @@ select = Sizzle.select = function( selector, context, results, seed ) {
context,
!documentIsHTML,
results,
- rsibling.test( selector ) && testContext( context.parentNode ) || context
+ !context || rsibling.test( selector ) && testContext( context.parentNode ) || context
);
return results;
};
@@ -2557,7 +2728,7 @@ select = Sizzle.select = function( selector, context, results, seed ) {
// Sort stability
support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
-// Support: Chrome<14
+// Support: Chrome 14-35+
// Always assume duplicates if they aren't passed to the comparison function
support.detectDuplicates = !!hasDuplicate;
@@ -2566,17 +2737,17 @@ setDocument();
// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
// Detached nodes confoundingly follow *each other*
-support.sortDetached = assert(function( div1 ) {
+support.sortDetached = assert(function( el ) {
// Should return 1, but returns 4 (following)
- return div1.compareDocumentPosition( document.createElement("div") ) & 1;
+ return el.compareDocumentPosition( document.createElement("fieldset") ) & 1;
});
// Support: IE<8
// Prevent attribute/property "interpolation"
-// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !assert(function( div ) {
- div.innerHTML = "<a href='#'></a>";
- return div.firstChild.getAttribute("href") === "#" ;
+// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !assert(function( el ) {
+ el.innerHTML = "<a href='#'></a>";
+ return el.firstChild.getAttribute("href") === "#" ;
}) ) {
addHandle( "type|href|height|width", function( elem, name, isXML ) {
if ( !isXML ) {
@@ -2587,10 +2758,10 @@ if ( !assert(function( div ) {
// Support: IE<9
// Use defaultValue in place of getAttribute("value")
-if ( !support.attributes || !assert(function( div ) {
- div.innerHTML = "<input/>";
- div.firstChild.setAttribute( "value", "" );
- return div.firstChild.getAttribute( "value" ) === "";
+if ( !support.attributes || !assert(function( el ) {
+ el.innerHTML = "<input/>";
+ el.firstChild.setAttribute( "value", "" );
+ return el.firstChild.getAttribute( "value" ) === "";
}) ) {
addHandle( "value", function( elem, name, isXML ) {
if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
@@ -2601,8 +2772,8 @@ if ( !support.attributes || !assert(function( div ) {
// Support: IE<9
// Use getAttributeNode to fetch booleans when getAttribute lies
-if ( !assert(function( div ) {
- return div.getAttribute("disabled") == null;
+if ( !assert(function( el ) {
+ return el.getAttribute("disabled") == null;
}) ) {
addHandle( booleans, function( elem, name, isXML ) {
var val;
@@ -2623,50 +2794,94 @@ return Sizzle;
jQuery.find = Sizzle;
jQuery.expr = Sizzle.selectors;
-jQuery.expr[":"] = jQuery.expr.pseudos;
-jQuery.unique = Sizzle.uniqueSort;
+
+// Deprecated
+jQuery.expr[ ":" ] = jQuery.expr.pseudos;
+jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort;
jQuery.text = Sizzle.getText;
jQuery.isXMLDoc = Sizzle.isXML;
jQuery.contains = Sizzle.contains;
+jQuery.escapeSelector = Sizzle.escape;
-var rneedsContext = jQuery.expr.match.needsContext;
-var rsingleTag = (/^<(\w+)\s*\/?>(?:<\/\1>|)$/);
+var dir = function( elem, dir, until ) {
+ var matched = [],
+ truncate = until !== undefined;
+ while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) {
+ if ( elem.nodeType === 1 ) {
+ if ( truncate && jQuery( elem ).is( until ) ) {
+ break;
+ }
+ matched.push( elem );
+ }
+ }
+ return matched;
+};
-var risSimple = /^.[^:#\[\.,]*$/;
+var siblings = function( n, elem ) {
+ var matched = [];
-// Implement the identical functionality for filter and not
-function winnow( elements, qualifier, not ) {
- if ( jQuery.isFunction( qualifier ) ) {
+ for ( ; n; n = n.nextSibling ) {
+ if ( n.nodeType === 1 && n !== elem ) {
+ matched.push( n );
+ }
+ }
+
+ return matched;
+};
+
+
+var rneedsContext = jQuery.expr.match.needsContext;
+
+
+
+function nodeName( elem, name ) {
+
+ return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+
+};
+var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i );
+
+
+
+var risSimple = /^.[^:#\[\.,]*$/;
+
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, not ) {
+ if ( jQuery.isFunction( qualifier ) ) {
return jQuery.grep( elements, function( elem, i ) {
- /* jshint -W018 */
return !!qualifier.call( elem, i, elem ) !== not;
- });
-
+ } );
}
+ // Single element
if ( qualifier.nodeType ) {
return jQuery.grep( elements, function( elem ) {
return ( elem === qualifier ) !== not;
- });
-
+ } );
}
- if ( typeof qualifier === "string" ) {
- if ( risSimple.test( qualifier ) ) {
- return jQuery.filter( qualifier, elements, not );
- }
+ // Arraylike of elements (jQuery, arguments, Array)
+ if ( typeof qualifier !== "string" ) {
+ return jQuery.grep( elements, function( elem ) {
+ return ( indexOf.call( qualifier, elem ) > -1 ) !== not;
+ } );
+ }
- qualifier = jQuery.filter( qualifier, elements );
+ // Simple selector that can be filtered directly, removing non-Elements
+ if ( risSimple.test( qualifier ) ) {
+ return jQuery.filter( qualifier, elements, not );
}
+ // Complex selector, compare the two sets, removing non-Elements
+ qualifier = jQuery.filter( qualifier, elements );
return jQuery.grep( elements, function( elem ) {
- return ( jQuery.inArray( elem, qualifier ) >= 0 ) !== not;
- });
+ return ( indexOf.call( qualifier, elem ) > -1 ) !== not && elem.nodeType === 1;
+ } );
}
jQuery.filter = function( expr, elems, not ) {
@@ -2676,44 +2891,44 @@ jQuery.filter = function( expr, elems, not ) {
expr = ":not(" + expr + ")";
}
- return elems.length === 1 && elem.nodeType === 1 ?
- jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] :
- jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
- return elem.nodeType === 1;
- }));
+ if ( elems.length === 1 && elem.nodeType === 1 ) {
+ return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [];
+ }
+
+ return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
+ return elem.nodeType === 1;
+ } ) );
};
-jQuery.fn.extend({
+jQuery.fn.extend( {
find: function( selector ) {
- var i,
- ret = [],
- self = this,
- len = self.length;
+ var i, ret,
+ len = this.length,
+ self = this;
if ( typeof selector !== "string" ) {
- return this.pushStack( jQuery( selector ).filter(function() {
+ return this.pushStack( jQuery( selector ).filter( function() {
for ( i = 0; i < len; i++ ) {
if ( jQuery.contains( self[ i ], this ) ) {
return true;
}
}
- }) );
+ } ) );
}
+ ret = this.pushStack( [] );
+
for ( i = 0; i < len; i++ ) {
jQuery.find( selector, self[ i ], ret );
}
- // Needed because $( selector, context ) becomes $( context ).find( selector )
- ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret );
- ret.selector = this.selector ? this.selector + " " + selector : selector;
- return ret;
+ return len > 1 ? jQuery.uniqueSort( ret ) : ret;
},
filter: function( selector ) {
- return this.pushStack( winnow(this, selector || [], false) );
+ return this.pushStack( winnow( this, selector || [], false ) );
},
not: function( selector ) {
- return this.pushStack( winnow(this, selector || [], true) );
+ return this.pushStack( winnow( this, selector || [], true ) );
},
is: function( selector ) {
return !!winnow(
@@ -2727,7 +2942,7 @@ jQuery.fn.extend({
false
).length;
}
-});
+} );
// Initialize a jQuery object
@@ -2736,15 +2951,13 @@ jQuery.fn.extend({
// A central reference to the root jQuery(document)
var rootjQuery,
- // Use the correct document accordingly with window argument (sandbox)
- document = window.document,
-
// A simple way to check for HTML strings
// Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
// Strict HTML recognition (#11290: must start with <)
- rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,
+ // Shortcut simple #id case for speed
+ rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/,
- init = jQuery.fn.init = function( selector, context ) {
+ init = jQuery.fn.init = function( selector, context, root ) {
var match, elem;
// HANDLE: $(""), $(null), $(undefined), $(false)
@@ -2752,9 +2965,16 @@ var rootjQuery,
return this;
}
+ // Method init() accepts an alternate rootjQuery
+ // so migrate can support jQuery.sub (gh-2101)
+ root = root || rootjQuery;
+
// Handle HTML strings
if ( typeof selector === "string" ) {
- if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
+ if ( selector[ 0 ] === "<" &&
+ selector[ selector.length - 1 ] === ">" &&
+ selector.length >= 3 ) {
+
// Assume that strings that start and end with <> are HTML and skip the regex check
match = [ null, selector, null ];
@@ -2763,23 +2983,24 @@ var rootjQuery,
}
// Match html or make sure no context is specified for #id
- if ( match && (match[1] || !context) ) {
+ if ( match && ( match[ 1 ] || !context ) ) {
// HANDLE: $(html) -> $(array)
- if ( match[1] ) {
- context = context instanceof jQuery ? context[0] : context;
+ if ( match[ 1 ] ) {
+ context = context instanceof jQuery ? context[ 0 ] : context;
- // scripts is true for back-compat
+ // Option to run scripts is true for back-compat
// Intentionally let the error be thrown if parseHTML is not present
jQuery.merge( this, jQuery.parseHTML(
- match[1],
+ match[ 1 ],
context && context.nodeType ? context.ownerDocument || context : document,
true
) );
// HANDLE: $(html, props)
- if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) {
+ if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) {
for ( match in context ) {
+
// Properties of context are called as methods if possible
if ( jQuery.isFunction( this[ match ] ) ) {
this[ match ]( context[ match ] );
@@ -2795,30 +3016,20 @@ var rootjQuery,
// HANDLE: $(#id)
} else {
- elem = document.getElementById( match[2] );
-
- // Check parentNode to catch when Blackberry 4.6 returns
- // nodes that are no longer in the document #6963
- if ( elem && elem.parentNode ) {
- // Handle the case where IE and Opera return items
- // by name instead of ID
- if ( elem.id !== match[2] ) {
- return rootjQuery.find( selector );
- }
+ elem = document.getElementById( match[ 2 ] );
- // Otherwise, we inject the element directly into the jQuery object
+ if ( elem ) {
+
+ // Inject the element directly into the jQuery object
+ this[ 0 ] = elem;
this.length = 1;
- this[0] = elem;
}
-
- this.context = document;
- this.selector = selector;
return this;
}
// HANDLE: $(expr, $(...))
} else if ( !context || context.jquery ) {
- return ( context || rootjQuery ).find( selector );
+ return ( context || root ).find( selector );
// HANDLE: $(expr, context)
// (which is just equivalent to: $(context).find(expr)
@@ -2828,24 +3039,20 @@ var rootjQuery,
// HANDLE: $(DOMElement)
} else if ( selector.nodeType ) {
- this.context = this[0] = selector;
+ this[ 0 ] = selector;
this.length = 1;
return this;
// HANDLE: $(function)
// Shortcut for document ready
} else if ( jQuery.isFunction( selector ) ) {
- return typeof rootjQuery.ready !== "undefined" ?
- rootjQuery.ready( selector ) :
+ return root.ready !== undefined ?
+ root.ready( selector ) :
+
// Execute immediately if ready is not present
selector( jQuery );
}
- if ( selector.selector !== undefined ) {
- this.selector = selector.selector;
- this.context = selector.context;
- }
-
return jQuery.makeArray( selector, this );
};
@@ -2857,7 +3064,8 @@ rootjQuery = jQuery( document );
var rparentsprev = /^(?:parents|prev(?:Until|All))/,
- // methods guaranteed to produce a unique set when starting from a unique set
+
+ // Methods guaranteed to produce a unique set when starting from a unique set
guaranteedUnique = {
children: true,
contents: true,
@@ -2865,46 +3073,19 @@ var rparentsprev = /^(?:parents|prev(?:Until|All))/,
prev: true
};
-jQuery.extend({
- dir: function( elem, dir, until ) {
- var matched = [],
- cur = elem[ dir ];
-
- while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
- if ( cur.nodeType === 1 ) {
- matched.push( cur );
- }
- cur = cur[dir];
- }
- return matched;
- },
-
- sibling: function( n, elem ) {
- var r = [];
-
- for ( ; n; n = n.nextSibling ) {
- if ( n.nodeType === 1 && n !== elem ) {
- r.push( n );
- }
- }
-
- return r;
- }
-});
-
-jQuery.fn.extend({
+jQuery.fn.extend( {
has: function( target ) {
- var i,
- targets = jQuery( target, this ),
- len = targets.length;
+ var targets = jQuery( target, this ),
+ l = targets.length;
- return this.filter(function() {
- for ( i = 0; i < len; i++ ) {
- if ( jQuery.contains( this, targets[i] ) ) {
+ return this.filter( function() {
+ var i = 0;
+ for ( ; i < l; i++ ) {
+ if ( jQuery.contains( this, targets[ i ] ) ) {
return true;
}
}
- });
+ } );
},
closest: function( selectors, context ) {
@@ -2912,52 +3093,55 @@ jQuery.fn.extend({
i = 0,
l = this.length,
matched = [],
- pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ?
- jQuery( selectors, context || this.context ) :
- 0;
+ targets = typeof selectors !== "string" && jQuery( selectors );
- for ( ; i < l; i++ ) {
- for ( cur = this[i]; cur && cur !== context; cur = cur.parentNode ) {
- // Always skip document fragments
- if ( cur.nodeType < 11 && (pos ?
- pos.index(cur) > -1 :
+ // Positional selectors never match, since there's no _selection_ context
+ if ( !rneedsContext.test( selectors ) ) {
+ for ( ; i < l; i++ ) {
+ for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) {
- // Don't pass non-elements to Sizzle
- cur.nodeType === 1 &&
- jQuery.find.matchesSelector(cur, selectors)) ) {
+ // Always skip document fragments
+ if ( cur.nodeType < 11 && ( targets ?
+ targets.index( cur ) > -1 :
- matched.push( cur );
- break;
+ // Don't pass non-elements to Sizzle
+ cur.nodeType === 1 &&
+ jQuery.find.matchesSelector( cur, selectors ) ) ) {
+
+ matched.push( cur );
+ break;
+ }
}
}
}
- return this.pushStack( matched.length > 1 ? jQuery.unique( matched ) : matched );
+ return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched );
},
- // Determine the position of an element within
- // the matched set of elements
+ // Determine the position of an element within the set
index: function( elem ) {
// No argument, return index in parent
if ( !elem ) {
- return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1;
+ return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1;
}
- // index in selector
+ // Index in selector
if ( typeof elem === "string" ) {
- return jQuery.inArray( this[0], jQuery( elem ) );
+ return indexOf.call( jQuery( elem ), this[ 0 ] );
}
// Locate the position of the desired element
- return jQuery.inArray(
+ return indexOf.call( this,
+
// If it receives a jQuery object, the first element is used
- elem.jquery ? elem[0] : elem, this );
+ elem.jquery ? elem[ 0 ] : elem
+ );
},
add: function( selector, context ) {
return this.pushStack(
- jQuery.unique(
+ jQuery.uniqueSort(
jQuery.merge( this.get(), jQuery( selector, context ) )
)
);
@@ -2965,29 +3149,26 @@ jQuery.fn.extend({
addBack: function( selector ) {
return this.add( selector == null ?
- this.prevObject : this.prevObject.filter(selector)
+ this.prevObject : this.prevObject.filter( selector )
);
}
-});
+} );
function sibling( cur, dir ) {
- do {
- cur = cur[ dir ];
- } while ( cur && cur.nodeType !== 1 );
-
+ while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {}
return cur;
}
-jQuery.each({
+jQuery.each( {
parent: function( elem ) {
var parent = elem.parentNode;
return parent && parent.nodeType !== 11 ? parent : null;
},
parents: function( elem ) {
- return jQuery.dir( elem, "parentNode" );
+ return dir( elem, "parentNode" );
},
parentsUntil: function( elem, i, until ) {
- return jQuery.dir( elem, "parentNode", until );
+ return dir( elem, "parentNode", until );
},
next: function( elem ) {
return sibling( elem, "nextSibling" );
@@ -2996,68 +3177,75 @@ jQuery.each({
return sibling( elem, "previousSibling" );
},
nextAll: function( elem ) {
- return jQuery.dir( elem, "nextSibling" );
+ return dir( elem, "nextSibling" );
},
prevAll: function( elem ) {
- return jQuery.dir( elem, "previousSibling" );
+ return dir( elem, "previousSibling" );
},
nextUntil: function( elem, i, until ) {
- return jQuery.dir( elem, "nextSibling", until );
+ return dir( elem, "nextSibling", until );
},
prevUntil: function( elem, i, until ) {
- return jQuery.dir( elem, "previousSibling", until );
+ return dir( elem, "previousSibling", until );
},
siblings: function( elem ) {
- return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
+ return siblings( ( elem.parentNode || {} ).firstChild, elem );
},
children: function( elem ) {
- return jQuery.sibling( elem.firstChild );
+ return siblings( elem.firstChild );
},
contents: function( elem ) {
- return jQuery.nodeName( elem, "iframe" ) ?
- elem.contentDocument || elem.contentWindow.document :
- jQuery.merge( [], elem.childNodes );
+ if ( nodeName( elem, "iframe" ) ) {
+ return elem.contentDocument;
+ }
+
+ // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only
+ // Treat the template element as a regular one in browsers that
+ // don't support it.
+ if ( nodeName( elem, "template" ) ) {
+ elem = elem.content || elem;
+ }
+
+ return jQuery.merge( [], elem.childNodes );
}
}, function( name, fn ) {
jQuery.fn[ name ] = function( until, selector ) {
- var ret = jQuery.map( this, fn, until );
+ var matched = jQuery.map( this, fn, until );
if ( name.slice( -5 ) !== "Until" ) {
selector = until;
}
if ( selector && typeof selector === "string" ) {
- ret = jQuery.filter( selector, ret );
+ matched = jQuery.filter( selector, matched );
}
if ( this.length > 1 ) {
+
// Remove duplicates
if ( !guaranteedUnique[ name ] ) {
- ret = jQuery.unique( ret );
+ jQuery.uniqueSort( matched );
}
// Reverse order for parents* and prev-derivatives
if ( rparentsprev.test( name ) ) {
- ret = ret.reverse();
+ matched.reverse();
}
}
- return this.pushStack( ret );
+ return this.pushStack( matched );
};
-});
-var rnotwhite = (/\S+/g);
-
+} );
+var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g );
-// String to Object options format cache
-var optionsCache = {};
-// Convert String-formatted options into Object-formatted ones and store in cache
+// Convert String-formatted options into Object-formatted ones
function createOptions( options ) {
- var object = optionsCache[ options ] = {};
- jQuery.each( options.match( rnotwhite ) || [], function( _, flag ) {
+ var object = {};
+ jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) {
object[ flag ] = true;
- });
+ } );
return object;
}
@@ -3088,156 +3276,186 @@ jQuery.Callbacks = function( options ) {
// Convert options from String-formatted to Object-formatted if needed
// (we check in cache first)
options = typeof options === "string" ?
- ( optionsCache[ options ] || createOptions( options ) ) :
+ createOptions( options ) :
jQuery.extend( {}, options );
var // Flag to know if list is currently firing
firing,
- // Last fire value (for non-forgettable lists)
+
+ // Last fire value for non-forgettable lists
memory,
+
// Flag to know if list was already fired
fired,
- // End of the loop when firing
- firingLength,
- // Index of currently firing callback (modified by remove if needed)
- firingIndex,
- // First callback to fire (used internally by add and fireWith)
- firingStart,
+
+ // Flag to prevent firing
+ locked,
+
// Actual callback list
list = [],
- // Stack of fire calls for repeatable lists
- stack = !options.once && [],
+
+ // Queue of execution data for repeatable lists
+ queue = [],
+
+ // Index of currently firing callback (modified by add/remove as needed)
+ firingIndex = -1,
+
// Fire callbacks
- fire = function( data ) {
- memory = options.memory && data;
- fired = true;
- firingIndex = firingStart || 0;
- firingStart = 0;
- firingLength = list.length;
- firing = true;
- for ( ; list && firingIndex < firingLength; firingIndex++ ) {
- if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) {
- memory = false; // To prevent further calls using add
- break;
+ fire = function() {
+
+ // Enforce single-firing
+ locked = locked || options.once;
+
+ // Execute callbacks for all pending executions,
+ // respecting firingIndex overrides and runtime changes
+ fired = firing = true;
+ for ( ; queue.length; firingIndex = -1 ) {
+ memory = queue.shift();
+ while ( ++firingIndex < list.length ) {
+
+ // Run callback and check for early termination
+ if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false &&
+ options.stopOnFalse ) {
+
+ // Jump to end and forget the data so .add doesn't re-fire
+ firingIndex = list.length;
+ memory = false;
+ }
}
}
+
+ // Forget the data if we're done with it
+ if ( !options.memory ) {
+ memory = false;
+ }
+
firing = false;
- if ( list ) {
- if ( stack ) {
- if ( stack.length ) {
- fire( stack.shift() );
- }
- } else if ( memory ) {
+
+ // Clean up if we're done firing for good
+ if ( locked ) {
+
+ // Keep an empty list if we have data for future add calls
+ if ( memory ) {
list = [];
+
+ // Otherwise, this object is spent
} else {
- self.disable();
+ list = "";
}
}
},
+
// Actual Callbacks object
self = {
+
// Add a callback or a collection of callbacks to the list
add: function() {
if ( list ) {
- // First, we save the current length
- var start = list.length;
- (function add( args ) {
+
+ // If we have memory from a past run, we should fire after adding
+ if ( memory && !firing ) {
+ firingIndex = list.length - 1;
+ queue.push( memory );
+ }
+
+ ( function add( args ) {
jQuery.each( args, function( _, arg ) {
- var type = jQuery.type( arg );
- if ( type === "function" ) {
+ if ( jQuery.isFunction( arg ) ) {
if ( !options.unique || !self.has( arg ) ) {
list.push( arg );
}
- } else if ( arg && arg.length && type !== "string" ) {
+ } else if ( arg && arg.length && jQuery.type( arg ) !== "string" ) {
+
// Inspect recursively
add( arg );
}
- });
- })( arguments );
- // Do we need to add the callbacks to the
- // current firing batch?
- if ( firing ) {
- firingLength = list.length;
- // With memory, if we're not firing then
- // we should call right away
- } else if ( memory ) {
- firingStart = start;
- fire( memory );
+ } );
+ } )( arguments );
+
+ if ( memory && !firing ) {
+ fire();
}
}
return this;
},
+
// Remove a callback from the list
remove: function() {
- if ( list ) {
- jQuery.each( arguments, function( _, arg ) {
- var index;
- while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
- list.splice( index, 1 );
- // Handle firing indexes
- if ( firing ) {
- if ( index <= firingLength ) {
- firingLength--;
- }
- if ( index <= firingIndex ) {
- firingIndex--;
- }
- }
+ jQuery.each( arguments, function( _, arg ) {
+ var index;
+ while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
+ list.splice( index, 1 );
+
+ // Handle firing indexes
+ if ( index <= firingIndex ) {
+ firingIndex--;
}
- });
- }
+ }
+ } );
return this;
},
+
// Check if a given callback is in the list.
// If no argument is given, return whether or not list has callbacks attached.
has: function( fn ) {
- return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length );
+ return fn ?
+ jQuery.inArray( fn, list ) > -1 :
+ list.length > 0;
},
+
// Remove all callbacks from the list
empty: function() {
- list = [];
- firingLength = 0;
+ if ( list ) {
+ list = [];
+ }
return this;
},
- // Have the list do nothing anymore
+
+ // Disable .fire and .add
+ // Abort any current/pending executions
+ // Clear all callbacks and values
disable: function() {
- list = stack = memory = undefined;
+ locked = queue = [];
+ list = memory = "";
return this;
},
- // Is it disabled?
disabled: function() {
return !list;
},
- // Lock the list in its current state
+
+ // Disable .fire
+ // Also disable .add unless we have memory (since it would have no effect)
+ // Abort any pending executions
lock: function() {
- stack = undefined;
- if ( !memory ) {
- self.disable();
+ locked = queue = [];
+ if ( !memory && !firing ) {
+ list = memory = "";
}
return this;
},
- // Is it locked?
locked: function() {
- return !stack;
+ return !!locked;
},
+
// Call all callbacks with the given context and arguments
fireWith: function( context, args ) {
- if ( list && ( !fired || stack ) ) {
+ if ( !locked ) {
args = args || [];
args = [ context, args.slice ? args.slice() : args ];
- if ( firing ) {
- stack.push( args );
- } else {
- fire( args );
+ queue.push( args );
+ if ( !firing ) {
+ fire();
}
}
return this;
},
+
// Call all the callbacks with the given arguments
fire: function() {
self.fireWith( this, arguments );
return this;
},
+
// To know if the callbacks have already been called at least once
fired: function() {
return !!fired;
@@ -3248,14 +3466,59 @@ jQuery.Callbacks = function( options ) {
};
-jQuery.extend({
+function Identity( v ) {
+ return v;
+}
+function Thrower( ex ) {
+ throw ex;
+}
+
+function adoptValue( value, resolve, reject, noValue ) {
+ var method;
+
+ try {
+
+ // Check for promise aspect first to privilege synchronous behavior
+ if ( value && jQuery.isFunction( ( method = value.promise ) ) ) {
+ method.call( value ).done( resolve ).fail( reject );
+
+ // Other thenables
+ } else if ( value && jQuery.isFunction( ( method = value.then ) ) ) {
+ method.call( value, resolve, reject );
+
+ // Other non-thenables
+ } else {
+
+ // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer:
+ // * false: [ value ].slice( 0 ) => resolve( value )
+ // * true: [ value ].slice( 1 ) => resolve()
+ resolve.apply( undefined, [ value ].slice( noValue ) );
+ }
+
+ // For Promises/A+, convert exceptions into rejections
+ // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in
+ // Deferred#then to conditionally suppress rejection.
+ } catch ( value ) {
+
+ // Support: Android 4.0 only
+ // Strict mode functions invoked without .call/.apply get global-object context
+ reject.apply( undefined, [ value ] );
+ }
+}
+
+jQuery.extend( {
Deferred: function( func ) {
var tuples = [
- // action, add listener, listener list, final state
- [ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ],
- [ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ],
- [ "notify", "progress", jQuery.Callbacks("memory") ]
+
+ // action, add listener, callbacks,
+ // ... .then handlers, argument index, [final state]
+ [ "notify", "progress", jQuery.Callbacks( "memory" ),
+ jQuery.Callbacks( "memory" ), 2 ],
+ [ "resolve", "done", jQuery.Callbacks( "once memory" ),
+ jQuery.Callbacks( "once memory" ), 0, "resolved" ],
+ [ "reject", "fail", jQuery.Callbacks( "once memory" ),
+ jQuery.Callbacks( "once memory" ), 1, "rejected" ]
],
state = "pending",
promise = {
@@ -3266,27 +3529,206 @@ jQuery.extend({
deferred.done( arguments ).fail( arguments );
return this;
},
- then: function( /* fnDone, fnFail, fnProgress */ ) {
+ "catch": function( fn ) {
+ return promise.then( null, fn );
+ },
+
+ // Keep pipe for back-compat
+ pipe: function( /* fnDone, fnFail, fnProgress */ ) {
var fns = arguments;
- return jQuery.Deferred(function( newDefer ) {
+
+ return jQuery.Deferred( function( newDefer ) {
jQuery.each( tuples, function( i, tuple ) {
- var fn = jQuery.isFunction( fns[ i ] ) && fns[ i ];
- // deferred[ done | fail | progress ] for forwarding actions to newDefer
- deferred[ tuple[1] ](function() {
+
+ // Map tuples (progress, done, fail) to arguments (done, fail, progress)
+ var fn = jQuery.isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ];
+
+ // deferred.progress(function() { bind to newDefer or newDefer.notify })
+ // deferred.done(function() { bind to newDefer or newDefer.resolve })
+ // deferred.fail(function() { bind to newDefer or newDefer.reject })
+ deferred[ tuple[ 1 ] ]( function() {
var returned = fn && fn.apply( this, arguments );
if ( returned && jQuery.isFunction( returned.promise ) ) {
returned.promise()
+ .progress( newDefer.notify )
.done( newDefer.resolve )
- .fail( newDefer.reject )
- .progress( newDefer.notify );
+ .fail( newDefer.reject );
} else {
- newDefer[ tuple[ 0 ] + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments );
+ newDefer[ tuple[ 0 ] + "With" ](
+ this,
+ fn ? [ returned ] : arguments
+ );
}
- });
- });
+ } );
+ } );
fns = null;
- }).promise();
+ } ).promise();
+ },
+ then: function( onFulfilled, onRejected, onProgress ) {
+ var maxDepth = 0;
+ function resolve( depth, deferred, handler, special ) {
+ return function() {
+ var that = this,
+ args = arguments,
+ mightThrow = function() {
+ var returned, then;
+
+ // Support: Promises/A+ section 2.3.3.3.3
+ // https://promisesaplus.com/#point-59
+ // Ignore double-resolution attempts
+ if ( depth < maxDepth ) {
+ return;
+ }
+
+ returned = handler.apply( that, args );
+
+ // Support: Promises/A+ section 2.3.1
+ // https://promisesaplus.com/#point-48
+ if ( returned === deferred.promise() ) {
+ throw new TypeError( "Thenable self-resolution" );
+ }
+
+ // Support: Promises/A+ sections 2.3.3.1, 3.5
+ // https://promisesaplus.com/#point-54
+ // https://promisesaplus.com/#point-75
+ // Retrieve `then` only once
+ then = returned &&
+
+ // Support: Promises/A+ section 2.3.4
+ // https://promisesaplus.com/#point-64
+ // Only check objects and functions for thenability
+ ( typeof returned === "object" ||
+ typeof returned === "function" ) &&
+ returned.then;
+
+ // Handle a returned thenable
+ if ( jQuery.isFunction( then ) ) {
+
+ // Special processors (notify) just wait for resolution
+ if ( special ) {
+ then.call(
+ returned,
+ resolve( maxDepth, deferred, Identity, special ),
+ resolve( maxDepth, deferred, Thrower, special )
+ );
+
+ // Normal processors (resolve) also hook into progress
+ } else {
+
+ // ...and disregard older resolution values
+ maxDepth++;
+
+ then.call(
+ returned,
+ resolve( maxDepth, deferred, Identity, special ),
+ resolve( maxDepth, deferred, Thrower, special ),
+ resolve( maxDepth, deferred, Identity,
+ deferred.notifyWith )
+ );
+ }
+
+ // Handle all other returned values
+ } else {
+
+ // Only substitute handlers pass on context
+ // and multiple values (non-spec behavior)
+ if ( handler !== Identity ) {
+ that = undefined;
+ args = [ returned ];
+ }
+
+ // Process the value(s)
+ // Default process is resolve
+ ( special || deferred.resolveWith )( that, args );
+ }
+ },
+
+ // Only normal processors (resolve) catch and reject exceptions
+ process = special ?
+ mightThrow :
+ function() {
+ try {
+ mightThrow();
+ } catch ( e ) {
+
+ if ( jQuery.Deferred.exceptionHook ) {
+ jQuery.Deferred.exceptionHook( e,
+ process.stackTrace );
+ }
+
+ // Support: Promises/A+ section 2.3.3.3.4.1
+ // https://promisesaplus.com/#point-61
+ // Ignore post-resolution exceptions
+ if ( depth + 1 >= maxDepth ) {
+
+ // Only substitute handlers pass on context
+ // and multiple values (non-spec behavior)
+ if ( handler !== Thrower ) {
+ that = undefined;
+ args = [ e ];
+ }
+
+ deferred.rejectWith( that, args );
+ }
+ }
+ };
+
+ // Support: Promises/A+ section 2.3.3.3.1
+ // https://promisesaplus.com/#point-57
+ // Re-resolve promises immediately to dodge false rejection from
+ // subsequent errors
+ if ( depth ) {
+ process();
+ } else {
+
+ // Call an optional hook to record the stack, in case of exception
+ // since it's otherwise lost when execution goes async
+ if ( jQuery.Deferred.getStackHook ) {
+ process.stackTrace = jQuery.Deferred.getStackHook();
+ }
+ window.setTimeout( process );
+ }
+ };
+ }
+
+ return jQuery.Deferred( function( newDefer ) {
+
+ // progress_handlers.add( ... )
+ tuples[ 0 ][ 3 ].add(
+ resolve(
+ 0,
+ newDefer,
+ jQuery.isFunction( onProgress ) ?
+ onProgress :
+ Identity,
+ newDefer.notifyWith
+ )
+ );
+
+ // fulfilled_handlers.add( ... )
+ tuples[ 1 ][ 3 ].add(
+ resolve(
+ 0,
+ newDefer,
+ jQuery.isFunction( onFulfilled ) ?
+ onFulfilled :
+ Identity
+ )
+ );
+
+ // rejected_handlers.add( ... )
+ tuples[ 2 ][ 3 ].add(
+ resolve(
+ 0,
+ newDefer,
+ jQuery.isFunction( onRejected ) ?
+ onRejected :
+ Thrower
+ )
+ );
+ } ).promise();
},
+
// Get a promise for this deferred
// If obj is provided, the promise aspect is added to the object
promise: function( obj ) {
@@ -3295,34 +3737,53 @@ jQuery.extend({
},
deferred = {};
- // Keep pipe for back-compat
- promise.pipe = promise.then;
-
// Add list-specific methods
jQuery.each( tuples, function( i, tuple ) {
var list = tuple[ 2 ],
- stateString = tuple[ 3 ];
+ stateString = tuple[ 5 ];
- // promise[ done | fail | progress ] = list.add
- promise[ tuple[1] ] = list.add;
+ // promise.progress = list.add
+ // promise.done = list.add
+ // promise.fail = list.add
+ promise[ tuple[ 1 ] ] = list.add;
// Handle state
if ( stateString ) {
- list.add(function() {
- // state = [ resolved | rejected ]
- state = stateString;
+ list.add(
+ function() {
+
+ // state = "resolved" (i.e., fulfilled)
+ // state = "rejected"
+ state = stateString;
+ },
- // [ reject_list | resolve_list ].disable; progress_list.lock
- }, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );
+ // rejected_callbacks.disable
+ // fulfilled_callbacks.disable
+ tuples[ 3 - i ][ 2 ].disable,
+
+ // progress_callbacks.lock
+ tuples[ 0 ][ 2 ].lock
+ );
}
- // deferred[ resolve | reject | notify ]
- deferred[ tuple[0] ] = function() {
- deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments );
+ // progress_handlers.fire
+ // fulfilled_handlers.fire
+ // rejected_handlers.fire
+ list.add( tuple[ 3 ].fire );
+
+ // deferred.notify = function() { deferred.notifyWith(...) }
+ // deferred.resolve = function() { deferred.resolveWith(...) }
+ // deferred.reject = function() { deferred.rejectWith(...) }
+ deferred[ tuple[ 0 ] ] = function() {
+ deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments );
return this;
};
- deferred[ tuple[0] + "With" ] = list.fireWith;
- });
+
+ // deferred.notifyWith = list.fireWith
+ // deferred.resolveWith = list.fireWith
+ // deferred.rejectWith = list.fireWith
+ deferred[ tuple[ 0 ] + "With" ] = list.fireWith;
+ } );
// Make the deferred a promise
promise.promise( deferred );
@@ -3337,71 +3798,101 @@ jQuery.extend({
},
// Deferred helper
- when: function( subordinate /* , ..., subordinateN */ ) {
- var i = 0,
- resolveValues = slice.call( arguments ),
- length = resolveValues.length,
+ when: function( singleValue ) {
+ var
- // the count of uncompleted subordinates
- remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,
+ // count of uncompleted subordinates
+ remaining = arguments.length,
- // the master Deferred. If resolveValues consist of only a single Deferred, just use that.
- deferred = remaining === 1 ? subordinate : jQuery.Deferred(),
+ // count of unprocessed arguments
+ i = remaining,
- // Update function for both resolve and progress values
- updateFunc = function( i, contexts, values ) {
- return function( value ) {
- contexts[ i ] = this;
- values[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
- if ( values === progressValues ) {
- deferred.notifyWith( contexts, values );
+ // subordinate fulfillment data
+ resolveContexts = Array( i ),
+ resolveValues = slice.call( arguments ),
+
+ // the master Deferred
+ master = jQuery.Deferred(),
- } else if ( !(--remaining) ) {
- deferred.resolveWith( contexts, values );
+ // subordinate callback factory
+ updateFunc = function( i ) {
+ return function( value ) {
+ resolveContexts[ i ] = this;
+ resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
+ if ( !( --remaining ) ) {
+ master.resolveWith( resolveContexts, resolveValues );
}
};
- },
+ };
- progressValues, progressContexts, resolveContexts;
+ // Single- and empty arguments are adopted like Promise.resolve
+ if ( remaining <= 1 ) {
+ adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject,
+ !remaining );
- // add listeners to Deferred subordinates; treat others as resolved
- if ( length > 1 ) {
- progressValues = new Array( length );
- progressContexts = new Array( length );
- resolveContexts = new Array( length );
- for ( ; i < length; i++ ) {
- if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {
- resolveValues[ i ].promise()
- .done( updateFunc( i, resolveContexts, resolveValues ) )
- .fail( deferred.reject )
- .progress( updateFunc( i, progressContexts, progressValues ) );
- } else {
- --remaining;
- }
+ // Use .then() to unwrap secondary thenables (cf. gh-3000)
+ if ( master.state() === "pending" ||
+ jQuery.isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) {
+
+ return master.then();
}
}
- // if we're not waiting on anything, resolve the master
- if ( !remaining ) {
- deferred.resolveWith( resolveContexts, resolveValues );
+ // Multiple arguments are aggregated like Promise.all array elements
+ while ( i-- ) {
+ adoptValue( resolveValues[ i ], updateFunc( i ), master.reject );
}
- return deferred.promise();
+ return master.promise();
}
-});
+} );
+
+
+// These usually indicate a programmer mistake during development,
+// warn about them ASAP rather than swallowing them by default.
+var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/;
+
+jQuery.Deferred.exceptionHook = function( error, stack ) {
+
+ // Support: IE 8 - 9 only
+ // Console exists when dev tools are open, which can happen at any time
+ if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) {
+ window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack );
+ }
+};
+
+
+
+
+jQuery.readyException = function( error ) {
+ window.setTimeout( function() {
+ throw error;
+ } );
+};
+
+
// The deferred used on DOM ready
-var readyList;
+var readyList = jQuery.Deferred();
jQuery.fn.ready = function( fn ) {
- // Add the callback
- jQuery.ready.promise().done( fn );
+
+ readyList
+ .then( fn )
+
+ // Wrap jQuery.readyException in a function so that the lookup
+ // happens at the time of error handling instead of callback
+ // registration.
+ .catch( function( error ) {
+ jQuery.readyException( error );
+ } );
return this;
};
-jQuery.extend({
+jQuery.extend( {
+
// Is the DOM ready to be used? Set to true once it occurs.
isReady: false,
@@ -3409,15 +3900,6 @@ jQuery.extend({
// the ready event fires. See #6781
readyWait: 1,
- // Hold (or release) the ready event
- holdReady: function( hold ) {
- if ( hold ) {
- jQuery.readyWait++;
- } else {
- jQuery.ready( true );
- }
- },
-
// Handle when the DOM is ready
ready: function( wait ) {
@@ -3426,11 +3908,6 @@ jQuery.extend({
return;
}
- // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
- if ( !document.body ) {
- return setTimeout( jQuery.ready );
- }
-
// Remember that the DOM is ready
jQuery.isReady = true;
@@ -3441,486 +3918,381 @@ jQuery.extend({
// If there are functions bound, to execute
readyList.resolveWith( document, [ jQuery ] );
-
- // Trigger any bound ready events
- if ( jQuery.fn.triggerHandler ) {
- jQuery( document ).triggerHandler( "ready" );
- jQuery( document ).off( "ready" );
- }
}
-});
-
-/**
- * Clean-up method for dom ready events
- */
-function detach() {
- if ( document.addEventListener ) {
- document.removeEventListener( "DOMContentLoaded", completed, false );
- window.removeEventListener( "load", completed, false );
+} );
- } else {
- document.detachEvent( "onreadystatechange", completed );
- window.detachEvent( "onload", completed );
- }
-}
+jQuery.ready.then = readyList.then;
-/**
- * The ready event handler and self cleanup method
- */
+// The ready event handler and self cleanup method
function completed() {
- // readyState === "complete" is good enough for us to call the dom ready in oldIE
- if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) {
- detach();
- jQuery.ready();
- }
+ document.removeEventListener( "DOMContentLoaded", completed );
+ window.removeEventListener( "load", completed );
+ jQuery.ready();
}
-jQuery.ready.promise = function( obj ) {
- if ( !readyList ) {
-
- readyList = jQuery.Deferred();
+// Catch cases where $(document).ready() is called
+// after the browser event has already occurred.
+// Support: IE <=9 - 10 only
+// Older IE sometimes signals "interactive" too soon
+if ( document.readyState === "complete" ||
+ ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) {
- // Catch cases where $(document).ready() is called after the browser event has already occurred.
- // we once tried to use readyState "interactive" here, but it caused issues like the one
- // discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15
- if ( document.readyState === "complete" ) {
- // Handle it asynchronously to allow scripts the opportunity to delay ready
- setTimeout( jQuery.ready );
+ // Handle it asynchronously to allow scripts the opportunity to delay ready
+ window.setTimeout( jQuery.ready );
- // Standards-based browsers support DOMContentLoaded
- } else if ( document.addEventListener ) {
- // Use the handy event callback
- document.addEventListener( "DOMContentLoaded", completed, false );
+} else {
- // A fallback to window.onload, that will always work
- window.addEventListener( "load", completed, false );
+ // Use the handy event callback
+ document.addEventListener( "DOMContentLoaded", completed );
- // If IE event model is used
- } else {
- // Ensure firing before onload, maybe late but safe also for iframes
- document.attachEvent( "onreadystatechange", completed );
-
- // A fallback to window.onload, that will always work
- window.attachEvent( "onload", completed );
-
- // If IE and not a frame
- // continually check to see if the document is ready
- var top = false;
+ // A fallback to window.onload, that will always work
+ window.addEventListener( "load", completed );
+}
- try {
- top = window.frameElement == null && document.documentElement;
- } catch(e) {}
- if ( top && top.doScroll ) {
- (function doScrollCheck() {
- if ( !jQuery.isReady ) {
- try {
- // Use the trick by Diego Perini
- // http://javascript.nwbox.com/IEContentLoaded/
- top.doScroll("left");
- } catch(e) {
- return setTimeout( doScrollCheck, 50 );
- }
- // detach all dom ready events
- detach();
+// Multifunctional method to get and set values of a collection
+// The value/s can optionally be executed if it's a function
+var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
+ var i = 0,
+ len = elems.length,
+ bulk = key == null;
- // and execute any waiting functions
- jQuery.ready();
- }
- })();
- }
+ // Sets many values
+ if ( jQuery.type( key ) === "object" ) {
+ chainable = true;
+ for ( i in key ) {
+ access( elems, fn, i, key[ i ], true, emptyGet, raw );
}
- }
- return readyList.promise( obj );
-};
+ // Sets one value
+ } else if ( value !== undefined ) {
+ chainable = true;
-var strundefined = typeof undefined;
+ if ( !jQuery.isFunction( value ) ) {
+ raw = true;
+ }
+ if ( bulk ) {
+ // Bulk operations run against the entire set
+ if ( raw ) {
+ fn.call( elems, value );
+ fn = null;
-// Support: IE<9
-// Iteration over object's inherited properties before its own
-var i;
-for ( i in jQuery( support ) ) {
- break;
-}
-support.ownLast = i !== "0";
+ // ...except when executing function values
+ } else {
+ bulk = fn;
+ fn = function( elem, key, value ) {
+ return bulk.call( jQuery( elem ), value );
+ };
+ }
+ }
-// Note: most support tests are defined in their respective modules.
-// false until the test is run
-support.inlineBlockNeedsLayout = false;
-
-// Execute ASAP in case we need to set body.style.zoom
-jQuery(function() {
- // Minified: var a,b,c,d
- var val, div, body, container;
-
- body = document.getElementsByTagName( "body" )[ 0 ];
- if ( !body || !body.style ) {
- // Return for frameset docs that don't have a body
- return;
- }
-
- // Setup
- div = document.createElement( "div" );
- container = document.createElement( "div" );
- container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
- body.appendChild( container ).appendChild( div );
-
- if ( typeof div.style.zoom !== strundefined ) {
- // Support: IE<8
- // Check if natively block-level elements act like inline-block
- // elements when setting their display to 'inline' and giving
- // them layout
- div.style.cssText = "display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1";
-
- support.inlineBlockNeedsLayout = val = div.offsetWidth === 3;
- if ( val ) {
- // Prevent IE 6 from affecting layout for positioned elements #11048
- // Prevent IE from shrinking the body in IE 7 mode #12869
- // Support: IE<8
- body.style.zoom = 1;
+ if ( fn ) {
+ for ( ; i < len; i++ ) {
+ fn(
+ elems[ i ], key, raw ?
+ value :
+ value.call( elems[ i ], i, fn( elems[ i ], key ) )
+ );
+ }
}
}
- body.removeChild( container );
-});
+ if ( chainable ) {
+ return elems;
+ }
+ // Gets
+ if ( bulk ) {
+ return fn.call( elems );
+ }
+ return len ? fn( elems[ 0 ], key ) : emptyGet;
+};
+var acceptData = function( owner ) {
+
+ // Accepts only:
+ // - Node
+ // - Node.ELEMENT_NODE
+ // - Node.DOCUMENT_NODE
+ // - Object
+ // - Any
+ return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType );
+};
-(function() {
- var div = document.createElement( "div" );
- // Execute the test only if not already executed in another module.
- if (support.deleteExpando == null) {
- // Support: IE<9
- support.deleteExpando = true;
- try {
- delete div.test;
- } catch( e ) {
- support.deleteExpando = false;
- }
- }
- // Null elements to avoid leaks in IE.
- div = null;
-})();
+function Data() {
+ this.expando = jQuery.expando + Data.uid++;
+}
+Data.uid = 1;
-/**
- * Determines whether an object can have data
- */
-jQuery.acceptData = function( elem ) {
- var noData = jQuery.noData[ (elem.nodeName + " ").toLowerCase() ],
- nodeType = +elem.nodeType || 1;
+Data.prototype = {
- // Do not set data on non-element DOM nodes because it will not be cleared (#8335).
- return nodeType !== 1 && nodeType !== 9 ?
- false :
+ cache: function( owner ) {
- // Nodes accept data unless otherwise specified; rejection can be conditional
- !noData || noData !== true && elem.getAttribute("classid") === noData;
-};
+ // Check if the owner object already has a cache
+ var value = owner[ this.expando ];
+ // If not, create one
+ if ( !value ) {
+ value = {};
-var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
- rmultiDash = /([A-Z])/g;
+ // We can accept data for non-element nodes in modern browsers,
+ // but we should not, see #8335.
+ // Always return an empty object.
+ if ( acceptData( owner ) ) {
-function dataAttr( elem, key, data ) {
- // If nothing was found internally, try to fetch any
- // data from the HTML5 data-* attribute
- if ( data === undefined && elem.nodeType === 1 ) {
+ // If it is a node unlikely to be stringify-ed or looped over
+ // use plain assignment
+ if ( owner.nodeType ) {
+ owner[ this.expando ] = value;
- var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
+ // Otherwise secure it in a non-enumerable property
+ // configurable must be true to allow the property to be
+ // deleted when data is removed
+ } else {
+ Object.defineProperty( owner, this.expando, {
+ value: value,
+ configurable: true
+ } );
+ }
+ }
+ }
- data = elem.getAttribute( name );
+ return value;
+ },
+ set: function( owner, data, value ) {
+ var prop,
+ cache = this.cache( owner );
+ // Handle: [ owner, key, value ] args
+ // Always use camelCase key (gh-2257)
if ( typeof data === "string" ) {
- try {
- data = data === "true" ? true :
- data === "false" ? false :
- data === "null" ? null :
- // Only convert to a number if it doesn't change the string
- +data + "" === data ? +data :
- rbrace.test( data ) ? jQuery.parseJSON( data ) :
- data;
- } catch( e ) {}
-
- // Make sure we set the data so it isn't changed later
- jQuery.data( elem, key, data );
+ cache[ jQuery.camelCase( data ) ] = value;
+ // Handle: [ owner, { properties } ] args
} else {
- data = undefined;
+
+ // Copy the properties one-by-one to the cache object
+ for ( prop in data ) {
+ cache[ jQuery.camelCase( prop ) ] = data[ prop ];
+ }
}
- }
+ return cache;
+ },
+ get: function( owner, key ) {
+ return key === undefined ?
+ this.cache( owner ) :
- return data;
-}
+ // Always use camelCase key (gh-2257)
+ owner[ this.expando ] && owner[ this.expando ][ jQuery.camelCase( key ) ];
+ },
+ access: function( owner, key, value ) {
-// checks a cache object for emptiness
-function isEmptyDataObject( obj ) {
- var name;
- for ( name in obj ) {
+ // In cases where either:
+ //
+ // 1. No key was specified
+ // 2. A string key was specified, but no value provided
+ //
+ // Take the "read" path and allow the get method to determine
+ // which value to return, respectively either:
+ //
+ // 1. The entire cache object
+ // 2. The data stored at the key
+ //
+ if ( key === undefined ||
+ ( ( key && typeof key === "string" ) && value === undefined ) ) {
- // if the public data object is empty, the private is still empty
- if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
- continue;
- }
- if ( name !== "toJSON" ) {
- return false;
+ return this.get( owner, key );
}
- }
- return true;
-}
-
-function internalData( elem, name, data, pvt /* Internal Use Only */ ) {
- if ( !jQuery.acceptData( elem ) ) {
- return;
- }
+ // When the key is not a string, or both a key and value
+ // are specified, set or extend (existing objects) with either:
+ //
+ // 1. An object of properties
+ // 2. A key and value
+ //
+ this.set( owner, key, value );
- var ret, thisCache,
- internalKey = jQuery.expando,
+ // Since the "set" path can have two possible entry points
+ // return the expected data based on which path was taken[*]
+ return value !== undefined ? value : key;
+ },
+ remove: function( owner, key ) {
+ var i,
+ cache = owner[ this.expando ];
- // We have to handle DOM nodes and JS objects differently because IE6-7
- // can't GC object references properly across the DOM-JS boundary
- isNode = elem.nodeType,
+ if ( cache === undefined ) {
+ return;
+ }
- // Only DOM nodes need the global jQuery cache; JS object data is
- // attached directly to the object so GC can occur automatically
- cache = isNode ? jQuery.cache : elem,
+ if ( key !== undefined ) {
- // Only defining an ID for JS objects if its cache already exists allows
- // the code to shortcut on the same path as a DOM node with no cache
- id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey;
+ // Support array or space separated string of keys
+ if ( Array.isArray( key ) ) {
- // Avoid doing any more work than we need to when trying to get data on an
- // object that has no data at all
- if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && data === undefined && typeof name === "string" ) {
- return;
- }
+ // If key is an array of keys...
+ // We always set camelCase keys, so remove that.
+ key = key.map( jQuery.camelCase );
+ } else {
+ key = jQuery.camelCase( key );
- if ( !id ) {
- // Only DOM nodes need a new unique ID for each element since their data
- // ends up in the global cache
- if ( isNode ) {
- id = elem[ internalKey ] = deletedIds.pop() || jQuery.guid++;
- } else {
- id = internalKey;
- }
- }
+ // If a key with the spaces exists, use it.
+ // Otherwise, create an array by matching non-whitespace
+ key = key in cache ?
+ [ key ] :
+ ( key.match( rnothtmlwhite ) || [] );
+ }
- if ( !cache[ id ] ) {
- // Avoid exposing jQuery metadata on plain JS objects when the object
- // is serialized using JSON.stringify
- cache[ id ] = isNode ? {} : { toJSON: jQuery.noop };
- }
+ i = key.length;
- // An object can be passed to jQuery.data instead of a key/value pair; this gets
- // shallow copied over onto the existing cache
- if ( typeof name === "object" || typeof name === "function" ) {
- if ( pvt ) {
- cache[ id ] = jQuery.extend( cache[ id ], name );
- } else {
- cache[ id ].data = jQuery.extend( cache[ id ].data, name );
+ while ( i-- ) {
+ delete cache[ key[ i ] ];
+ }
}
- }
- thisCache = cache[ id ];
+ // Remove the expando if there's no more data
+ if ( key === undefined || jQuery.isEmptyObject( cache ) ) {
- // jQuery data() is stored in a separate object inside the object's internal data
- // cache in order to avoid key collisions between internal data and user-defined
- // data.
- if ( !pvt ) {
- if ( !thisCache.data ) {
- thisCache.data = {};
+ // Support: Chrome <=35 - 45
+ // Webkit & Blink performance suffers when deleting properties
+ // from DOM nodes, so set to undefined instead
+ // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted)
+ if ( owner.nodeType ) {
+ owner[ this.expando ] = undefined;
+ } else {
+ delete owner[ this.expando ];
+ }
}
-
- thisCache = thisCache.data;
- }
-
- if ( data !== undefined ) {
- thisCache[ jQuery.camelCase( name ) ] = data;
+ },
+ hasData: function( owner ) {
+ var cache = owner[ this.expando ];
+ return cache !== undefined && !jQuery.isEmptyObject( cache );
}
+};
+var dataPriv = new Data();
- // Check for both converted-to-camel and non-converted data property names
- // If a data property was specified
- if ( typeof name === "string" ) {
+var dataUser = new Data();
- // First Try to find as-is property data
- ret = thisCache[ name ];
- // Test for null|undefined property data
- if ( ret == null ) {
- // Try to find the camelCased property
- ret = thisCache[ jQuery.camelCase( name ) ];
- }
- } else {
- ret = thisCache;
- }
+// Implementation Summary
+//
+// 1. Enforce API surface and semantic compatibility with 1.9.x branch
+// 2. Improve the module's maintainability by reducing the storage
+// paths to a single mechanism.
+// 3. Use the same single mechanism to support "private" and "user" data.
+// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData)
+// 5. Avoid exposing implementation details on user objects (eg. expando properties)
+// 6. Provide a clear path for implementation upgrade to WeakMap in 2014
- return ret;
-}
+var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
+ rmultiDash = /[A-Z]/g;
-function internalRemoveData( elem, name, pvt ) {
- if ( !jQuery.acceptData( elem ) ) {
- return;
+function getData( data ) {
+ if ( data === "true" ) {
+ return true;
}
- var thisCache, i,
- isNode = elem.nodeType,
-
- // See jQuery.data for more information
- cache = isNode ? jQuery.cache : elem,
- id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
-
- // If there is already no cache entry for this object, there is no
- // purpose in continuing
- if ( !cache[ id ] ) {
- return;
+ if ( data === "false" ) {
+ return false;
}
- if ( name ) {
-
- thisCache = pvt ? cache[ id ] : cache[ id ].data;
-
- if ( thisCache ) {
-
- // Support array or space separated string names for data keys
- if ( !jQuery.isArray( name ) ) {
-
- // try the string as a key before any manipulation
- if ( name in thisCache ) {
- name = [ name ];
- } else {
-
- // split the camel cased version by spaces unless a key with the spaces exists
- name = jQuery.camelCase( name );
- if ( name in thisCache ) {
- name = [ name ];
- } else {
- name = name.split(" ");
- }
- }
- } else {
- // If "name" is an array of keys...
- // When data is initially created, via ("key", "val") signature,
- // keys will be converted to camelCase.
- // Since there is no way to tell _how_ a key was added, remove
- // both plain key and camelCase key. #12786
- // This will only penalize the array argument path.
- name = name.concat( jQuery.map( name, jQuery.camelCase ) );
- }
+ if ( data === "null" ) {
+ return null;
+ }
- i = name.length;
- while ( i-- ) {
- delete thisCache[ name[i] ];
- }
+ // Only convert to a number if it doesn't change the string
+ if ( data === +data + "" ) {
+ return +data;
+ }
- // If there is no data left in the cache, we want to continue
- // and let the cache object itself get destroyed
- if ( pvt ? !isEmptyDataObject(thisCache) : !jQuery.isEmptyObject(thisCache) ) {
- return;
- }
- }
+ if ( rbrace.test( data ) ) {
+ return JSON.parse( data );
}
- // See jQuery.data for more information
- if ( !pvt ) {
- delete cache[ id ].data;
+ return data;
+}
- // Don't destroy the parent cache unless the internal data object
- // had been the only thing left in it
- if ( !isEmptyDataObject( cache[ id ] ) ) {
- return;
- }
- }
+function dataAttr( elem, key, data ) {
+ var name;
- // Destroy the cache
- if ( isNode ) {
- jQuery.cleanData( [ elem ], true );
+ // If nothing was found internally, try to fetch any
+ // data from the HTML5 data-* attribute
+ if ( data === undefined && elem.nodeType === 1 ) {
+ name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase();
+ data = elem.getAttribute( name );
- // Use delete when supported for expandos or `cache` is not a window per isWindow (#10080)
- /* jshint eqeqeq: false */
- } else if ( support.deleteExpando || cache != cache.window ) {
- /* jshint eqeqeq: true */
- delete cache[ id ];
+ if ( typeof data === "string" ) {
+ try {
+ data = getData( data );
+ } catch ( e ) {}
- // When all else fails, null
- } else {
- cache[ id ] = null;
+ // Make sure we set the data so it isn't changed later
+ dataUser.set( elem, key, data );
+ } else {
+ data = undefined;
+ }
}
+ return data;
}
-jQuery.extend({
- cache: {},
-
- // The following elements (space-suffixed to avoid Object.prototype collisions)
- // throw uncatchable exceptions if you attempt to set expando properties
- noData: {
- "applet ": true,
- "embed ": true,
- // ...but Flash objects (which have this classid) *can* handle expandos
- "object ": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
- },
-
+jQuery.extend( {
hasData: function( elem ) {
- elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
- return !!elem && !isEmptyDataObject( elem );
+ return dataUser.hasData( elem ) || dataPriv.hasData( elem );
},
data: function( elem, name, data ) {
- return internalData( elem, name, data );
+ return dataUser.access( elem, name, data );
},
removeData: function( elem, name ) {
- return internalRemoveData( elem, name );
+ dataUser.remove( elem, name );
},
- // For internal use only.
+ // TODO: Now that all calls to _data and _removeData have been replaced
+ // with direct calls to dataPriv methods, these can be deprecated.
_data: function( elem, name, data ) {
- return internalData( elem, name, data, true );
+ return dataPriv.access( elem, name, data );
},
_removeData: function( elem, name ) {
- return internalRemoveData( elem, name, true );
+ dataPriv.remove( elem, name );
}
-});
+} );
-jQuery.fn.extend({
+jQuery.fn.extend( {
data: function( key, value ) {
var i, name, data,
- elem = this[0],
+ elem = this[ 0 ],
attrs = elem && elem.attributes;
- // Special expections of .data basically thwart jQuery.access,
- // so implement the relevant behavior ourselves
-
// Gets all values
if ( key === undefined ) {
if ( this.length ) {
- data = jQuery.data( elem );
+ data = dataUser.get( elem );
- if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
+ if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) {
i = attrs.length;
while ( i-- ) {
- // Support: IE11+
+ // Support: IE 11 only
// The attrs elements can be null (#14894)
if ( attrs[ i ] ) {
name = attrs[ i ].name;
if ( name.indexOf( "data-" ) === 0 ) {
- name = jQuery.camelCase( name.slice(5) );
+ name = jQuery.camelCase( name.slice( 5 ) );
dataAttr( elem, name, data[ name ] );
}
}
}
- jQuery._data( elem, "parsedAttrs", true );
+ dataPriv.set( elem, "hasDataAttrs", true );
}
}
@@ -3929,43 +4301,68 @@ jQuery.fn.extend({
// Sets multiple values
if ( typeof key === "object" ) {
- return this.each(function() {
- jQuery.data( this, key );
- });
+ return this.each( function() {
+ dataUser.set( this, key );
+ } );
}
- return arguments.length > 1 ?
+ return access( this, function( value ) {
+ var data;
+
+ // The calling jQuery object (element matches) is not empty
+ // (and therefore has an element appears at this[ 0 ]) and the
+ // `value` parameter was not undefined. An empty jQuery object
+ // will result in `undefined` for elem = this[ 0 ] which will
+ // throw an exception if an attempt to read a data cache is made.
+ if ( elem && value === undefined ) {
+
+ // Attempt to get data from the cache
+ // The key will always be camelCased in Data
+ data = dataUser.get( elem, key );
+ if ( data !== undefined ) {
+ return data;
+ }
+
+ // Attempt to "discover" the data in
+ // HTML5 custom data-* attrs
+ data = dataAttr( elem, key );
+ if ( data !== undefined ) {
+ return data;
+ }
+
+ // We tried really hard, but the data doesn't exist.
+ return;
+ }
- // Sets one value
- this.each(function() {
- jQuery.data( this, key, value );
- }) :
+ // Set the data...
+ this.each( function() {
- // Gets one value
- // Try to fetch any internally stored data first
- elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : undefined;
+ // We always store the camelCased key
+ dataUser.set( this, key, value );
+ } );
+ }, null, value, arguments.length > 1, null, true );
},
removeData: function( key ) {
- return this.each(function() {
- jQuery.removeData( this, key );
- });
+ return this.each( function() {
+ dataUser.remove( this, key );
+ } );
}
-});
+} );
-jQuery.extend({
+jQuery.extend( {
queue: function( elem, type, data ) {
var queue;
if ( elem ) {
type = ( type || "fx" ) + "queue";
- queue = jQuery._data( elem, type );
+ queue = dataPriv.get( elem, type );
// Speed up dequeue by getting out quickly if this is just a lookup
if ( data ) {
- if ( !queue || jQuery.isArray(data) ) {
- queue = jQuery._data( elem, type, jQuery.makeArray(data) );
+ if ( !queue || Array.isArray( data ) ) {
+ queue = dataPriv.access( elem, type, jQuery.makeArray( data ) );
} else {
queue.push( data );
}
@@ -3999,7 +4396,7 @@ jQuery.extend({
queue.unshift( "inprogress" );
}
- // clear up the last queue stop function
+ // Clear up the last queue stop function
delete hooks.stop;
fn.call( elem, next, hooks );
}
@@ -4009,19 +4406,18 @@ jQuery.extend({
}
},
- // not intended for public consumption - generates a queueHooks object, or returns the current one
+ // Not public - generate a queueHooks object, or return the current one
_queueHooks: function( elem, type ) {
var key = type + "queueHooks";
- return jQuery._data( elem, key ) || jQuery._data( elem, key, {
- empty: jQuery.Callbacks("once memory").add(function() {
- jQuery._removeData( elem, type + "queue" );
- jQuery._removeData( elem, key );
- })
- });
+ return dataPriv.get( elem, key ) || dataPriv.access( elem, key, {
+ empty: jQuery.Callbacks( "once memory" ).add( function() {
+ dataPriv.remove( elem, [ type + "queue", key ] );
+ } )
+ } );
}
-});
+} );
-jQuery.fn.extend({
+jQuery.fn.extend( {
queue: function( type, data ) {
var setter = 2;
@@ -4032,30 +4428,31 @@ jQuery.fn.extend({
}
if ( arguments.length < setter ) {
- return jQuery.queue( this[0], type );
+ return jQuery.queue( this[ 0 ], type );
}
return data === undefined ?
this :
- this.each(function() {
+ this.each( function() {
var queue = jQuery.queue( this, type, data );
- // ensure a hooks for this queue
+ // Ensure a hooks for this queue
jQuery._queueHooks( this, type );
- if ( type === "fx" && queue[0] !== "inprogress" ) {
+ if ( type === "fx" && queue[ 0 ] !== "inprogress" ) {
jQuery.dequeue( this, type );
}
- });
+ } );
},
dequeue: function( type ) {
- return this.each(function() {
+ return this.each( function() {
jQuery.dequeue( this, type );
- });
+ } );
},
clearQueue: function( type ) {
return this.queue( type || "fx", [] );
},
+
// Get a promise resolved when queues of a certain type
// are emptied (fx is the type by default)
promise: function( type, obj ) {
@@ -4077,7 +4474,7 @@ jQuery.fn.extend({
type = type || "fx";
while ( i-- ) {
- tmp = jQuery._data( elements[ i ], type + "queueHooks" );
+ tmp = dataPriv.get( elements[ i ], type + "queueHooks" );
if ( tmp && tmp.empty ) {
count++;
tmp.empty.add( resolve );
@@ -4086,199 +4483,500 @@ jQuery.fn.extend({
resolve();
return defer.promise( obj );
}
-});
-var pnum = (/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/).source;
+} );
+var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source;
+
+var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" );
+
var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
-var isHidden = function( elem, el ) {
- // isHidden might be called from jQuery#filter function;
+var isHiddenWithinTree = function( elem, el ) {
+
+ // isHiddenWithinTree might be called from jQuery#filter function;
// in that case, element will be second argument
elem = el || elem;
- return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem );
- };
+ // Inline style trumps all
+ return elem.style.display === "none" ||
+ elem.style.display === "" &&
+ // Otherwise, check computed style
+ // Support: Firefox <=43 - 45
+ // Disconnected elements can have computed display: none, so first confirm that elem is
+ // in the document.
+ jQuery.contains( elem.ownerDocument, elem ) &&
-// Multifunctional method to get and set values of a collection
-// The value/s can optionally be executed if it's a function
-var access = jQuery.access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
- var i = 0,
- length = elems.length,
- bulk = key == null;
-
- // Sets many values
- if ( jQuery.type( key ) === "object" ) {
- chainable = true;
- for ( i in key ) {
- jQuery.access( elems, fn, i, key[i], true, emptyGet, raw );
- }
-
- // Sets one value
- } else if ( value !== undefined ) {
- chainable = true;
+ jQuery.css( elem, "display" ) === "none";
+ };
- if ( !jQuery.isFunction( value ) ) {
- raw = true;
- }
+var swap = function( elem, options, callback, args ) {
+ var ret, name,
+ old = {};
- if ( bulk ) {
- // Bulk operations run against the entire set
- if ( raw ) {
- fn.call( elems, value );
- fn = null;
+ // Remember the old values, and insert the new ones
+ for ( name in options ) {
+ old[ name ] = elem.style[ name ];
+ elem.style[ name ] = options[ name ];
+ }
- // ...except when executing function values
- } else {
- bulk = fn;
- fn = function( elem, key, value ) {
- return bulk.call( jQuery( elem ), value );
- };
- }
- }
+ ret = callback.apply( elem, args || [] );
- if ( fn ) {
- for ( ; i < length; i++ ) {
- fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) );
- }
- }
+ // Revert the old values
+ for ( name in options ) {
+ elem.style[ name ] = old[ name ];
}
- return chainable ?
- elems :
-
- // Gets
- bulk ?
- fn.call( elems ) :
- length ? fn( elems[0], key ) : emptyGet;
+ return ret;
};
-var rcheckableType = (/^(?:checkbox|radio)$/i);
-(function() {
- // Minified: var a,b,c
- var input = document.createElement( "input" ),
- div = document.createElement( "div" ),
- fragment = document.createDocumentFragment();
-
- // Setup
- div.innerHTML = " <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
- // IE strips leading whitespace when .innerHTML is used
- support.leadingWhitespace = div.firstChild.nodeType === 3;
+function adjustCSS( elem, prop, valueParts, tween ) {
+ var adjusted,
+ scale = 1,
+ maxIterations = 20,
+ currentValue = tween ?
+ function() {
+ return tween.cur();
+ } :
+ function() {
+ return jQuery.css( elem, prop, "" );
+ },
+ initial = currentValue(),
+ unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
- // Make sure that tbody elements aren't automatically inserted
- // IE will insert them into empty tables
- support.tbody = !div.getElementsByTagName( "tbody" ).length;
+ // Starting value computation is required for potential unit mismatches
+ initialInUnit = ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) &&
+ rcssNum.exec( jQuery.css( elem, prop ) );
- // Make sure that link elements get serialized correctly by innerHTML
- // This requires a wrapper element in IE
- support.htmlSerialize = !!div.getElementsByTagName( "link" ).length;
+ if ( initialInUnit && initialInUnit[ 3 ] !== unit ) {
- // Makes sure cloning an html5 element does not cause problems
- // Where outerHTML is undefined, this still works
- support.html5Clone =
- document.createElement( "nav" ).cloneNode( true ).outerHTML !== "<:nav></:nav>";
+ // Trust units reported by jQuery.css
+ unit = unit || initialInUnit[ 3 ];
- // Check if a disconnected checkbox will retain its checked
- // value of true after appended to the DOM (IE6/7)
- input.type = "checkbox";
- input.checked = true;
- fragment.appendChild( input );
- support.appendChecked = input.checked;
+ // Make sure we update the tween properties later on
+ valueParts = valueParts || [];
- // Make sure textarea (and checkbox) defaultValue is properly cloned
- // Support: IE6-IE11+
- div.innerHTML = "<textarea>x</textarea>";
- support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
+ // Iteratively approximate from a nonzero starting point
+ initialInUnit = +initial || 1;
- // #11217 - WebKit loses check when the name is after the checked attribute
- fragment.appendChild( div );
- div.innerHTML = "<input type='radio' checked='checked' name='t'/>";
+ do {
- // Support: Safari 5.1, iOS 5.1, Android 4.x, Android 2.3
- // old WebKit doesn't clone checked state correctly in fragments
- support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
+ // If previous iteration zeroed out, double until we get *something*.
+ // Use string for doubling so we don't accidentally see scale as unchanged below
+ scale = scale || ".5";
- // Support: IE<9
- // Opera does not clone events (and typeof div.attachEvent === undefined).
- // IE9-10 clones events bound via attachEvent, but they don't trigger with .click()
- support.noCloneEvent = true;
- if ( div.attachEvent ) {
- div.attachEvent( "onclick", function() {
- support.noCloneEvent = false;
- });
+ // Adjust and apply
+ initialInUnit = initialInUnit / scale;
+ jQuery.style( elem, prop, initialInUnit + unit );
- div.cloneNode( true ).click();
+ // Update scale, tolerating zero or NaN from tween.cur()
+ // Break the loop if scale is unchanged or perfect, or if we've just had enough.
+ } while (
+ scale !== ( scale = currentValue() / initial ) && scale !== 1 && --maxIterations
+ );
}
- // Execute the test only if not already executed in another module.
- if (support.deleteExpando == null) {
- // Support: IE<9
- support.deleteExpando = true;
- try {
- delete div.test;
- } catch( e ) {
- support.deleteExpando = false;
+ if ( valueParts ) {
+ initialInUnit = +initialInUnit || +initial || 0;
+
+ // Apply relative offset (+=/-=) if specified
+ adjusted = valueParts[ 1 ] ?
+ initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] :
+ +valueParts[ 2 ];
+ if ( tween ) {
+ tween.unit = unit;
+ tween.start = initialInUnit;
+ tween.end = adjusted;
}
}
-})();
+ return adjusted;
+}
-(function() {
- var i, eventName,
- div = document.createElement( "div" );
+var defaultDisplayMap = {};
- // Support: IE<9 (lack submit/change bubble), Firefox 23+ (lack focusin event)
- for ( i in { submit: true, change: true, focusin: true }) {
- eventName = "on" + i;
+function getDefaultDisplay( elem ) {
+ var temp,
+ doc = elem.ownerDocument,
+ nodeName = elem.nodeName,
+ display = defaultDisplayMap[ nodeName ];
- if ( !(support[ i + "Bubbles" ] = eventName in window) ) {
- // Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP)
- div.setAttribute( eventName, "t" );
- support[ i + "Bubbles" ] = div.attributes[ eventName ].expando === false;
- }
+ if ( display ) {
+ return display;
}
- // Null elements to avoid leaks in IE.
- div = null;
-})();
-
+ temp = doc.body.appendChild( doc.createElement( nodeName ) );
+ display = jQuery.css( temp, "display" );
-var rformElems = /^(?:input|select|textarea)$/i,
- rkeyEvent = /^key/,
- rmouseEvent = /^(?:mouse|pointer|contextmenu)|click/,
- rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
- rtypenamespace = /^([^.]*)(?:\.(.+)|)$/;
+ temp.parentNode.removeChild( temp );
-function returnTrue() {
- return true;
-}
+ if ( display === "none" ) {
+ display = "block";
+ }
+ defaultDisplayMap[ nodeName ] = display;
-function returnFalse() {
- return false;
+ return display;
}
-function safeActiveElement() {
- try {
- return document.activeElement;
- } catch ( err ) { }
-}
+function showHide( elements, show ) {
+ var display, elem,
+ values = [],
+ index = 0,
+ length = elements.length;
-/*
- * Helper functions for managing events -- not part of the public interface.
- * Props to Dean Edwards' addEvent library for many of the ideas.
- */
-jQuery.event = {
+ // Determine new display value for elements that need to change
+ for ( ; index < length; index++ ) {
+ elem = elements[ index ];
+ if ( !elem.style ) {
+ continue;
+ }
- global: {},
+ display = elem.style.display;
+ if ( show ) {
+
+ // Since we force visibility upon cascade-hidden elements, an immediate (and slow)
+ // check is required in this first loop unless we have a nonempty display value (either
+ // inline or about-to-be-restored)
+ if ( display === "none" ) {
+ values[ index ] = dataPriv.get( elem, "display" ) || null;
+ if ( !values[ index ] ) {
+ elem.style.display = "";
+ }
+ }
+ if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) {
+ values[ index ] = getDefaultDisplay( elem );
+ }
+ } else {
+ if ( display !== "none" ) {
+ values[ index ] = "none";
+
+ // Remember what we're overwriting
+ dataPriv.set( elem, "display", display );
+ }
+ }
+ }
+
+ // Set the display of the elements in a second loop to avoid constant reflow
+ for ( index = 0; index < length; index++ ) {
+ if ( values[ index ] != null ) {
+ elements[ index ].style.display = values[ index ];
+ }
+ }
+
+ return elements;
+}
+
+jQuery.fn.extend( {
+ show: function() {
+ return showHide( this, true );
+ },
+ hide: function() {
+ return showHide( this );
+ },
+ toggle: function( state ) {
+ if ( typeof state === "boolean" ) {
+ return state ? this.show() : this.hide();
+ }
+
+ return this.each( function() {
+ if ( isHiddenWithinTree( this ) ) {
+ jQuery( this ).show();
+ } else {
+ jQuery( this ).hide();
+ }
+ } );
+ }
+} );
+var rcheckableType = ( /^(?:checkbox|radio)$/i );
+
+var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]+)/i );
+
+var rscriptType = ( /^$|\/(?:java|ecma)script/i );
+
+
+
+// We have to close these tags to support XHTML (#13200)
+var wrapMap = {
+
+ // Support: IE <=9 only
+ option: [ 1, "<select multiple='multiple'>", "</select>" ],
+
+ // XHTML parsers do not magically insert elements in the
+ // same way that tag soup parsers do. So we cannot shorten
+ // this by omitting <tbody> or other required elements.
+ thead: [ 1, "<table>", "</table>" ],
+ col: [ 2, "<table><colgroup>", "</colgroup></table>" ],
+ tr: [ 2, "<table><tbody>", "</tbody></table>" ],
+ td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
+
+ _default: [ 0, "", "" ]
+};
+
+// Support: IE <=9 only
+wrapMap.optgroup = wrapMap.option;
+
+wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
+wrapMap.th = wrapMap.td;
+
+
+function getAll( context, tag ) {
+
+ // Support: IE <=9 - 11 only
+ // Use typeof to avoid zero-argument method invocation on host objects (#15151)
+ var ret;
+
+ if ( typeof context.getElementsByTagName !== "undefined" ) {
+ ret = context.getElementsByTagName( tag || "*" );
+
+ } else if ( typeof context.querySelectorAll !== "undefined" ) {
+ ret = context.querySelectorAll( tag || "*" );
+
+ } else {
+ ret = [];
+ }
+
+ if ( tag === undefined || tag && nodeName( context, tag ) ) {
+ return jQuery.merge( [ context ], ret );
+ }
+
+ return ret;
+}
+
+
+// Mark scripts as having already been evaluated
+function setGlobalEval( elems, refElements ) {
+ var i = 0,
+ l = elems.length;
+
+ for ( ; i < l; i++ ) {
+ dataPriv.set(
+ elems[ i ],
+ "globalEval",
+ !refElements || dataPriv.get( refElements[ i ], "globalEval" )
+ );
+ }
+}
+
+
+var rhtml = /<|&#?\w+;/;
+
+function buildFragment( elems, context, scripts, selection, ignored ) {
+ var elem, tmp, tag, wrap, contains, j,
+ fragment = context.createDocumentFragment(),
+ nodes = [],
+ i = 0,
+ l = elems.length;
+
+ for ( ; i < l; i++ ) {
+ elem = elems[ i ];
+
+ if ( elem || elem === 0 ) {
+
+ // Add nodes directly
+ if ( jQuery.type( elem ) === "object" ) {
+
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
+ jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
+
+ // Convert non-html into a text node
+ } else if ( !rhtml.test( elem ) ) {
+ nodes.push( context.createTextNode( elem ) );
+
+ // Convert html into DOM nodes
+ } else {
+ tmp = tmp || fragment.appendChild( context.createElement( "div" ) );
+
+ // Deserialize a standard representation
+ tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase();
+ wrap = wrapMap[ tag ] || wrapMap._default;
+ tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ];
+
+ // Descend through wrappers to the right content
+ j = wrap[ 0 ];
+ while ( j-- ) {
+ tmp = tmp.lastChild;
+ }
+
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
+ jQuery.merge( nodes, tmp.childNodes );
+
+ // Remember the top-level container
+ tmp = fragment.firstChild;
+
+ // Ensure the created nodes are orphaned (#12392)
+ tmp.textContent = "";
+ }
+ }
+ }
+
+ // Remove wrapper from fragment
+ fragment.textContent = "";
+
+ i = 0;
+ while ( ( elem = nodes[ i++ ] ) ) {
+
+ // Skip elements already in the context collection (trac-4087)
+ if ( selection && jQuery.inArray( elem, selection ) > -1 ) {
+ if ( ignored ) {
+ ignored.push( elem );
+ }
+ continue;
+ }
+
+ contains = jQuery.contains( elem.ownerDocument, elem );
+
+ // Append to fragment
+ tmp = getAll( fragment.appendChild( elem ), "script" );
+
+ // Preserve script evaluation history
+ if ( contains ) {
+ setGlobalEval( tmp );
+ }
+
+ // Capture executables
+ if ( scripts ) {
+ j = 0;
+ while ( ( elem = tmp[ j++ ] ) ) {
+ if ( rscriptType.test( elem.type || "" ) ) {
+ scripts.push( elem );
+ }
+ }
+ }
+ }
+
+ return fragment;
+}
+
+
+( function() {
+ var fragment = document.createDocumentFragment(),
+ div = fragment.appendChild( document.createElement( "div" ) ),
+ input = document.createElement( "input" );
+
+ // Support: Android 4.0 - 4.3 only
+ // Check state lost if the name is set (#11217)
+ // Support: Windows Web Apps (WWA)
+ // `name` and `type` must use .setAttribute for WWA (#14901)
+ input.setAttribute( "type", "radio" );
+ input.setAttribute( "checked", "checked" );
+ input.setAttribute( "name", "t" );
+
+ div.appendChild( input );
+
+ // Support: Android <=4.1 only
+ // Older WebKit doesn't clone checked state correctly in fragments
+ support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
+
+ // Support: IE <=11 only
+ // Make sure textarea (and checkbox) defaultValue is properly cloned
+ div.innerHTML = "<textarea>x</textarea>";
+ support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
+} )();
+var documentElement = document.documentElement;
+
+
+
+var
+ rkeyEvent = /^key/,
+ rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/,
+ rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
+
+function returnTrue() {
+ return true;
+}
+
+function returnFalse() {
+ return false;
+}
+
+// Support: IE <=9 only
+// See #13393 for more info
+function safeActiveElement() {
+ try {
+ return document.activeElement;
+ } catch ( err ) { }
+}
+
+function on( elem, types, selector, data, fn, one ) {
+ var origFn, type;
+
+ // Types can be a map of types/handlers
+ if ( typeof types === "object" ) {
+
+ // ( types-Object, selector, data )
+ if ( typeof selector !== "string" ) {
+
+ // ( types-Object, data )
+ data = data || selector;
+ selector = undefined;
+ }
+ for ( type in types ) {
+ on( elem, type, selector, data, types[ type ], one );
+ }
+ return elem;
+ }
+
+ if ( data == null && fn == null ) {
+
+ // ( types, fn )
+ fn = selector;
+ data = selector = undefined;
+ } else if ( fn == null ) {
+ if ( typeof selector === "string" ) {
+
+ // ( types, selector, fn )
+ fn = data;
+ data = undefined;
+ } else {
+
+ // ( types, data, fn )
+ fn = data;
+ data = selector;
+ selector = undefined;
+ }
+ }
+ if ( fn === false ) {
+ fn = returnFalse;
+ } else if ( !fn ) {
+ return elem;
+ }
+
+ if ( one === 1 ) {
+ origFn = fn;
+ fn = function( event ) {
+
+ // Can use an empty set, since event contains the info
+ jQuery().off( event );
+ return origFn.apply( this, arguments );
+ };
+
+ // Use same guid so caller can remove using origFn
+ fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
+ }
+ return elem.each( function() {
+ jQuery.event.add( this, types, fn, data, selector );
+ } );
+}
+
+/*
+ * Helper functions for managing events -- not part of the public interface.
+ * Props to Dean Edwards' addEvent library for many of the ideas.
+ */
+jQuery.event = {
+
+ global: {},
add: function( elem, types, handler, data, selector ) {
- var tmp, events, t, handleObjIn,
- special, eventHandle, handleObj,
- handlers, type, namespaces, origType,
- elemData = jQuery._data( elem );
+
+ var handleObjIn, eventHandle, tmp,
+ events, t, handleObj,
+ special, handlers, type, namespaces, origType,
+ elemData = dataPriv.get( elem );
// Don't attach events to noData or text/comment nodes (but allow plain objects)
if ( !elemData ) {
@@ -4292,34 +4990,38 @@ jQuery.event = {
selector = handleObjIn.selector;
}
+ // Ensure that invalid selectors throw exceptions at attach time
+ // Evaluate against documentElement in case elem is a non-element node (e.g., document)
+ if ( selector ) {
+ jQuery.find.matchesSelector( documentElement, selector );
+ }
+
// Make sure that the handler has a unique ID, used to find/remove it later
if ( !handler.guid ) {
handler.guid = jQuery.guid++;
}
// Init the element's event structure and main handler, if this is the first
- if ( !(events = elemData.events) ) {
+ if ( !( events = elemData.events ) ) {
events = elemData.events = {};
}
- if ( !(eventHandle = elemData.handle) ) {
+ if ( !( eventHandle = elemData.handle ) ) {
eventHandle = elemData.handle = function( e ) {
+
// Discard the second event of a jQuery.event.trigger() and
// when an event is called after a page has unloaded
- return typeof jQuery !== strundefined && (!e || jQuery.event.triggered !== e.type) ?
- jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
- undefined;
+ return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ?
+ jQuery.event.dispatch.apply( elem, arguments ) : undefined;
};
- // Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
- eventHandle.elem = elem;
}
// Handle multiple events separated by a space
- types = ( types || "" ).match( rnotwhite ) || [ "" ];
+ types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
t = types.length;
while ( t-- ) {
- tmp = rtypenamespace.exec( types[t] ) || [];
- type = origType = tmp[1];
- namespaces = ( tmp[2] || "" ).split( "." ).sort();
+ tmp = rtypenamespace.exec( types[ t ] ) || [];
+ type = origType = tmp[ 1 ];
+ namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
// There *must* be a type, no attaching namespace-only handlers
if ( !type ) {
@@ -4336,7 +5038,7 @@ jQuery.event = {
special = jQuery.event.special[ type ] || {};
// handleObj is passed to all event handlers
- handleObj = jQuery.extend({
+ handleObj = jQuery.extend( {
type: type,
origType: origType,
data: data,
@@ -4344,22 +5046,20 @@ jQuery.event = {
guid: handler.guid,
selector: selector,
needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
- namespace: namespaces.join(".")
+ namespace: namespaces.join( "." )
}, handleObjIn );
// Init the event handler queue if we're the first
- if ( !(handlers = events[ type ]) ) {
+ if ( !( handlers = events[ type ] ) ) {
handlers = events[ type ] = [];
handlers.delegateCount = 0;
- // Only use addEventListener/attachEvent if the special events handler returns false
- if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
- // Bind the global event handler to the element
- if ( elem.addEventListener ) {
- elem.addEventListener( type, eventHandle, false );
+ // Only use addEventListener if the special events handler returns false
+ if ( !special.setup ||
+ special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
- } else if ( elem.attachEvent ) {
- elem.attachEvent( "on" + type, eventHandle );
+ if ( elem.addEventListener ) {
+ elem.addEventListener( type, eventHandle );
}
}
}
@@ -4383,29 +5083,27 @@ jQuery.event = {
jQuery.event.global[ type ] = true;
}
- // Nullify elem to prevent memory leaks in IE
- elem = null;
},
// Detach an event or set of events from an element
remove: function( elem, types, handler, selector, mappedTypes ) {
- var j, handleObj, tmp,
- origCount, t, events,
- special, handlers, type,
- namespaces, origType,
- elemData = jQuery.hasData( elem ) && jQuery._data( elem );
- if ( !elemData || !(events = elemData.events) ) {
+ var j, origCount, tmp,
+ events, t, handleObj,
+ special, handlers, type, namespaces, origType,
+ elemData = dataPriv.hasData( elem ) && dataPriv.get( elem );
+
+ if ( !elemData || !( events = elemData.events ) ) {
return;
}
// Once for each type.namespace in types; type may be omitted
- types = ( types || "" ).match( rnotwhite ) || [ "" ];
+ types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
t = types.length;
while ( t-- ) {
- tmp = rtypenamespace.exec( types[t] ) || [];
- type = origType = tmp[1];
- namespaces = ( tmp[2] || "" ).split( "." ).sort();
+ tmp = rtypenamespace.exec( types[ t ] ) || [];
+ type = origType = tmp[ 1 ];
+ namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
// Unbind all events (on this namespace, if provided) for the element
if ( !type ) {
@@ -4418,7 +5116,8 @@ jQuery.event = {
special = jQuery.event.special[ type ] || {};
type = ( selector ? special.delegateType : special.bindType ) || type;
handlers = events[ type ] || [];
- tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" );
+ tmp = tmp[ 2 ] &&
+ new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" );
// Remove matching events
origCount = j = handlers.length;
@@ -4428,7 +5127,8 @@ jQuery.event = {
if ( ( mappedTypes || origType === handleObj.origType ) &&
( !handler || handler.guid === handleObj.guid ) &&
( !tmp || tmp.test( handleObj.namespace ) ) &&
- ( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
+ ( !selector || selector === handleObj.selector ||
+ selector === "**" && handleObj.selector ) ) {
handlers.splice( j, 1 );
if ( handleObj.selector ) {
@@ -4443,7 +5143,9 @@ jQuery.event = {
// Remove generic event handler if we removed something and no more handlers exist
// (avoids potential for endless recursion during removal of special event handlers)
if ( origCount && !handlers.length ) {
- if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+ if ( !special.teardown ||
+ special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+
jQuery.removeEvent( elem, type, elemData.handle );
}
@@ -4451,202 +5153,65 @@ jQuery.event = {
}
}
- // Remove the expando if it's no longer used
+ // Remove data and the expando if it's no longer used
if ( jQuery.isEmptyObject( events ) ) {
- delete elemData.handle;
-
- // removeData also checks for emptiness and clears the expando if empty
- // so use it instead of delete
- jQuery._removeData( elem, "events" );
+ dataPriv.remove( elem, "handle events" );
}
},
- trigger: function( event, data, elem, onlyHandlers ) {
- var handle, ontype, cur,
- bubbleType, special, tmp, i,
- eventPath = [ elem || document ],
- type = hasOwn.call( event, "type" ) ? event.type : event,
- namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : [];
+ dispatch: function( nativeEvent ) {
- cur = tmp = elem = elem || document;
+ // Make a writable jQuery.Event from the native event object
+ var event = jQuery.event.fix( nativeEvent );
- // Don't do events on text and comment nodes
- if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
- return;
- }
+ var i, j, ret, matched, handleObj, handlerQueue,
+ args = new Array( arguments.length ),
+ handlers = ( dataPriv.get( this, "events" ) || {} )[ event.type ] || [],
+ special = jQuery.event.special[ event.type ] || {};
- // focus/blur morphs to focusin/out; ensure we're not firing them right now
- if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
- return;
- }
+ // Use the fix-ed jQuery.Event rather than the (read-only) native event
+ args[ 0 ] = event;
- if ( type.indexOf(".") >= 0 ) {
- // Namespaced trigger; create a regexp to match event type in handle()
- namespaces = type.split(".");
- type = namespaces.shift();
- namespaces.sort();
+ for ( i = 1; i < arguments.length; i++ ) {
+ args[ i ] = arguments[ i ];
}
- ontype = type.indexOf(":") < 0 && "on" + type;
-
- // Caller can pass in a jQuery.Event object, Object, or just an event type string
- event = event[ jQuery.expando ] ?
- event :
- new jQuery.Event( type, typeof event === "object" && event );
- // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
- event.isTrigger = onlyHandlers ? 2 : 3;
- event.namespace = namespaces.join(".");
- event.namespace_re = event.namespace ?
- new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) :
- null;
+ event.delegateTarget = this;
- // Clean up the event in case it is being reused
- event.result = undefined;
- if ( !event.target ) {
- event.target = elem;
+ // Call the preDispatch hook for the mapped type, and let it bail if desired
+ if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
+ return;
}
- // Clone any incoming data and prepend the event, creating the handler arg list
- data = data == null ?
- [ event ] :
- jQuery.makeArray( data, [ event ] );
+ // Determine handlers
+ handlerQueue = jQuery.event.handlers.call( this, event, handlers );
- // Allow special events to draw outside the lines
- special = jQuery.event.special[ type ] || {};
- if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
- return;
- }
+ // Run delegates first; they may want to stop propagation beneath us
+ i = 0;
+ while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) {
+ event.currentTarget = matched.elem;
- // Determine event propagation path in advance, per W3C events spec (#9951)
- // Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
- if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
+ j = 0;
+ while ( ( handleObj = matched.handlers[ j++ ] ) &&
+ !event.isImmediatePropagationStopped() ) {
- bubbleType = special.delegateType || type;
- if ( !rfocusMorph.test( bubbleType + type ) ) {
- cur = cur.parentNode;
- }
- for ( ; cur; cur = cur.parentNode ) {
- eventPath.push( cur );
- tmp = cur;
- }
+ // Triggered event must either 1) have no namespace, or 2) have namespace(s)
+ // a subset or equal to those in the bound event (both can have no namespace).
+ if ( !event.rnamespace || event.rnamespace.test( handleObj.namespace ) ) {
- // Only add window if we got to document (e.g., not plain obj or detached DOM)
- if ( tmp === (elem.ownerDocument || document) ) {
- eventPath.push( tmp.defaultView || tmp.parentWindow || window );
- }
- }
-
- // Fire handlers on the event path
- i = 0;
- while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) {
-
- event.type = i > 1 ?
- bubbleType :
- special.bindType || type;
-
- // jQuery handler
- handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
- if ( handle ) {
- handle.apply( cur, data );
- }
-
- // Native handler
- handle = ontype && cur[ ontype ];
- if ( handle && handle.apply && jQuery.acceptData( cur ) ) {
- event.result = handle.apply( cur, data );
- if ( event.result === false ) {
- event.preventDefault();
- }
- }
- }
- event.type = type;
-
- // If nobody prevented the default action, do it now
- if ( !onlyHandlers && !event.isDefaultPrevented() ) {
-
- if ( (!special._default || special._default.apply( eventPath.pop(), data ) === false) &&
- jQuery.acceptData( elem ) ) {
-
- // Call a native DOM method on the target with the same name name as the event.
- // Can't use an .isFunction() check here because IE6/7 fails that test.
- // Don't do default actions on window, that's where global variables be (#6170)
- if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) {
-
- // Don't re-trigger an onFOO event when we call its FOO() method
- tmp = elem[ ontype ];
-
- if ( tmp ) {
- elem[ ontype ] = null;
- }
-
- // Prevent re-triggering of the same event, since we already bubbled it above
- jQuery.event.triggered = type;
- try {
- elem[ type ]();
- } catch ( e ) {
- // IE<9 dies on focus/blur to hidden element (#1486,#12518)
- // only reproducible on winXP IE8 native, not IE9 in IE8 mode
- }
- jQuery.event.triggered = undefined;
-
- if ( tmp ) {
- elem[ ontype ] = tmp;
- }
- }
- }
- }
-
- return event.result;
- },
-
- dispatch: function( event ) {
-
- // Make a writable jQuery.Event from the native event object
- event = jQuery.event.fix( event );
-
- var i, ret, handleObj, matched, j,
- handlerQueue = [],
- args = slice.call( arguments ),
- handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [],
- special = jQuery.event.special[ event.type ] || {};
-
- // Use the fix-ed jQuery.Event rather than the (read-only) native event
- args[0] = event;
- event.delegateTarget = this;
-
- // Call the preDispatch hook for the mapped type, and let it bail if desired
- if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
- return;
- }
-
- // Determine handlers
- handlerQueue = jQuery.event.handlers.call( this, event, handlers );
-
- // Run delegates first; they may want to stop propagation beneath us
- i = 0;
- while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) {
- event.currentTarget = matched.elem;
-
- j = 0;
- while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) {
-
- // Triggered event must either 1) have no namespace, or
- // 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
- if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) {
-
- event.handleObj = handleObj;
- event.data = handleObj.data;
-
- ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
- .apply( matched.elem, args );
-
- if ( ret !== undefined ) {
- if ( (event.result = ret) === false ) {
- event.preventDefault();
- event.stopPropagation();
- }
- }
- }
+ event.handleObj = handleObj;
+ event.data = handleObj.data;
+
+ ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle ||
+ handleObj.handler ).apply( matched.elem, args );
+
+ if ( ret !== undefined ) {
+ if ( ( event.result = ret ) === false ) {
+ event.preventDefault();
+ event.stopPropagation();
+ }
+ }
+ }
}
}
@@ -4659,167 +5224,110 @@ jQuery.event = {
},
handlers: function( event, handlers ) {
- var sel, handleObj, matches, i,
+ var i, handleObj, sel, matchedHandlers, matchedSelectors,
handlerQueue = [],
delegateCount = handlers.delegateCount,
cur = event.target;
// Find delegate handlers
- // Black-hole SVG <use> instance trees (#13180)
- // Avoid non-left-click bubbling in Firefox (#3861)
- if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) {
+ if ( delegateCount &&
+
+ // Support: IE <=9
+ // Black-hole SVG <use> instance trees (trac-13180)
+ cur.nodeType &&
- /* jshint eqeqeq: false */
- for ( ; cur != this; cur = cur.parentNode || this ) {
- /* jshint eqeqeq: true */
+ // Support: Firefox <=42
+ // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861)
+ // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click
+ // Support: IE 11 only
+ // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343)
+ !( event.type === "click" && event.button >= 1 ) ) {
+
+ for ( ; cur !== this; cur = cur.parentNode || this ) {
// Don't check non-elements (#13208)
// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
- if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) {
- matches = [];
+ if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) {
+ matchedHandlers = [];
+ matchedSelectors = {};
for ( i = 0; i < delegateCount; i++ ) {
handleObj = handlers[ i ];
// Don't conflict with Object.prototype properties (#13203)
sel = handleObj.selector + " ";
- if ( matches[ sel ] === undefined ) {
- matches[ sel ] = handleObj.needsContext ?
- jQuery( sel, this ).index( cur ) >= 0 :
+ if ( matchedSelectors[ sel ] === undefined ) {
+ matchedSelectors[ sel ] = handleObj.needsContext ?
+ jQuery( sel, this ).index( cur ) > -1 :
jQuery.find( sel, this, null, [ cur ] ).length;
}
- if ( matches[ sel ] ) {
- matches.push( handleObj );
+ if ( matchedSelectors[ sel ] ) {
+ matchedHandlers.push( handleObj );
}
}
- if ( matches.length ) {
- handlerQueue.push({ elem: cur, handlers: matches });
+ if ( matchedHandlers.length ) {
+ handlerQueue.push( { elem: cur, handlers: matchedHandlers } );
}
}
}
}
// Add the remaining (directly-bound) handlers
+ cur = this;
if ( delegateCount < handlers.length ) {
- handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) });
+ handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } );
}
return handlerQueue;
},
- fix: function( event ) {
- if ( event[ jQuery.expando ] ) {
- return event;
- }
-
- // Create a writable copy of the event object and normalize some properties
- var i, prop, copy,
- type = event.type,
- originalEvent = event,
- fixHook = this.fixHooks[ type ];
-
- if ( !fixHook ) {
- this.fixHooks[ type ] = fixHook =
- rmouseEvent.test( type ) ? this.mouseHooks :
- rkeyEvent.test( type ) ? this.keyHooks :
- {};
- }
- copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
-
- event = new jQuery.Event( originalEvent );
-
- i = copy.length;
- while ( i-- ) {
- prop = copy[ i ];
- event[ prop ] = originalEvent[ prop ];
- }
-
- // Support: IE<9
- // Fix target property (#1925)
- if ( !event.target ) {
- event.target = originalEvent.srcElement || document;
- }
-
- // Support: Chrome 23+, Safari?
- // Target should not be a text node (#504, #13143)
- if ( event.target.nodeType === 3 ) {
- event.target = event.target.parentNode;
- }
-
- // Support: IE<9
- // For mouse/key events, metaKey==false if it's undefined (#3368, #11328)
- event.metaKey = !!event.metaKey;
-
- return fixHook.filter ? fixHook.filter( event, originalEvent ) : event;
- },
-
- // Includes some event props shared by KeyEvent and MouseEvent
- props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
-
- fixHooks: {},
+ addProp: function( name, hook ) {
+ Object.defineProperty( jQuery.Event.prototype, name, {
+ enumerable: true,
+ configurable: true,
- keyHooks: {
- props: "char charCode key keyCode".split(" "),
- filter: function( event, original ) {
+ get: jQuery.isFunction( hook ) ?
+ function() {
+ if ( this.originalEvent ) {
+ return hook( this.originalEvent );
+ }
+ } :
+ function() {
+ if ( this.originalEvent ) {
+ return this.originalEvent[ name ];
+ }
+ },
- // Add which for key events
- if ( event.which == null ) {
- event.which = original.charCode != null ? original.charCode : original.keyCode;
+ set: function( value ) {
+ Object.defineProperty( this, name, {
+ enumerable: true,
+ configurable: true,
+ writable: true,
+ value: value
+ } );
}
-
- return event;
- }
+ } );
},
- mouseHooks: {
- props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
- filter: function( event, original ) {
- var body, eventDoc, doc,
- button = original.button,
- fromElement = original.fromElement;
-
- // Calculate pageX/Y if missing and clientX/Y available
- if ( event.pageX == null && original.clientX != null ) {
- eventDoc = event.target.ownerDocument || document;
- doc = eventDoc.documentElement;
- body = eventDoc.body;
-
- event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
- event.pageY = original.clientY + ( doc && doc.scrollTop || body && body.scrollTop || 0 ) - ( doc && doc.clientTop || body && body.clientTop || 0 );
- }
-
- // Add relatedTarget, if necessary
- if ( !event.relatedTarget && fromElement ) {
- event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
- }
-
- // Add which for click: 1 === left; 2 === middle; 3 === right
- // Note: button is not normalized, so don't use it
- if ( !event.which && button !== undefined ) {
- event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
- }
-
- return event;
- }
+ fix: function( originalEvent ) {
+ return originalEvent[ jQuery.expando ] ?
+ originalEvent :
+ new jQuery.Event( originalEvent );
},
special: {
load: {
+
// Prevent triggered image.load events from bubbling to window.load
noBubble: true
},
focus: {
+
// Fire native event if possible so blur/focus sequence is correct
trigger: function() {
if ( this !== safeActiveElement() && this.focus ) {
- try {
- this.focus();
- return false;
- } catch ( e ) {
- // Support: IE<9
- // If we error on focus to hidden element (#1486, #12518),
- // let .trigger() run the handlers
- }
+ this.focus();
+ return false;
}
},
delegateType: "focusin"
@@ -4834,9 +5342,10 @@ jQuery.event = {
delegateType: "focusout"
},
click: {
+
// For checkbox, fire native event so checked state will be right
trigger: function() {
- if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) {
+ if ( this.type === "checkbox" && this.click && nodeName( this, "input" ) ) {
this.click();
return false;
}
@@ -4844,7 +5353,7 @@ jQuery.event = {
// For cross-browser consistency, don't fire native .click() on links
_default: function( event ) {
- return jQuery.nodeName( event.target, "a" );
+ return nodeName( event.target, "a" );
}
},
@@ -4858,56 +5367,21 @@ jQuery.event = {
}
}
}
- },
-
- simulate: function( type, elem, event, bubble ) {
- // Piggyback on a donor event to simulate a different one.
- // Fake originalEvent to avoid donor's stopPropagation, but if the
- // simulated event prevents default then we do the same on the donor.
- var e = jQuery.extend(
- new jQuery.Event(),
- event,
- {
- type: type,
- isSimulated: true,
- originalEvent: {}
- }
- );
- if ( bubble ) {
- jQuery.event.trigger( e, null, elem );
- } else {
- jQuery.event.dispatch.call( elem, e );
- }
- if ( e.isDefaultPrevented() ) {
- event.preventDefault();
- }
}
};
-jQuery.removeEvent = document.removeEventListener ?
- function( elem, type, handle ) {
- if ( elem.removeEventListener ) {
- elem.removeEventListener( type, handle, false );
- }
- } :
- function( elem, type, handle ) {
- var name = "on" + type;
-
- if ( elem.detachEvent ) {
-
- // #8545, #7054, preventing memory leaks for custom events in IE6-8
- // detachEvent needed property on element, by name of that event, to properly expose it to GC
- if ( typeof elem[ name ] === strundefined ) {
- elem[ name ] = null;
- }
+jQuery.removeEvent = function( elem, type, handle ) {
- elem.detachEvent( name, handle );
- }
- };
+ // This "if" is needed for plain objects
+ if ( elem.removeEventListener ) {
+ elem.removeEventListener( type, handle );
+ }
+};
jQuery.Event = function( src, props ) {
+
// Allow instantiation without the 'new' keyword
- if ( !(this instanceof jQuery.Event) ) {
+ if ( !( this instanceof jQuery.Event ) ) {
return new jQuery.Event( src, props );
}
@@ -4920,11 +5394,22 @@ jQuery.Event = function( src, props ) {
// by a handler lower down the tree; reflect the correct value.
this.isDefaultPrevented = src.defaultPrevented ||
src.defaultPrevented === undefined &&
- // Support: IE < 9, Android < 4.0
+
+ // Support: Android <=2.3 only
src.returnValue === false ?
returnTrue :
returnFalse;
+ // Create target properties
+ // Support: Safari <=6 - 7 only
+ // Target should not be a text node (#504, #13143)
+ this.target = ( src.target && src.target.nodeType === 3 ) ?
+ src.target.parentNode :
+ src.target;
+
+ this.currentTarget = src.currentTarget;
+ this.relatedTarget = src.relatedTarget;
+
// Event type
} else {
this.type = src;
@@ -4943,52 +5428,38 @@ jQuery.Event = function( src, props ) {
};
// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
-// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
+// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
jQuery.Event.prototype = {
+ constructor: jQuery.Event,
isDefaultPrevented: returnFalse,
isPropagationStopped: returnFalse,
isImmediatePropagationStopped: returnFalse,
+ isSimulated: false,
preventDefault: function() {
var e = this.originalEvent;
this.isDefaultPrevented = returnTrue;
- if ( !e ) {
- return;
- }
- // If preventDefault exists, run it on the original event
- if ( e.preventDefault ) {
+ if ( e && !this.isSimulated ) {
e.preventDefault();
-
- // Support: IE
- // Otherwise set the returnValue property of the original event to false
- } else {
- e.returnValue = false;
}
},
stopPropagation: function() {
var e = this.originalEvent;
this.isPropagationStopped = returnTrue;
- if ( !e ) {
- return;
- }
- // If stopPropagation exists, run it on the original event
- if ( e.stopPropagation ) {
+
+ if ( e && !this.isSimulated ) {
e.stopPropagation();
}
-
- // Support: IE
- // Set the cancelBubble property of the original event to true
- e.cancelBubble = true;
},
stopImmediatePropagation: function() {
var e = this.originalEvent;
this.isImmediatePropagationStopped = returnTrue;
- if ( e && e.stopImmediatePropagation ) {
+ if ( e && !this.isSimulated ) {
e.stopImmediatePropagation();
}
@@ -4996,8 +5467,76 @@ jQuery.Event.prototype = {
}
};
+// Includes all common event props including KeyEvent and MouseEvent specific props
+jQuery.each( {
+ altKey: true,
+ bubbles: true,
+ cancelable: true,
+ changedTouches: true,
+ ctrlKey: true,
+ detail: true,
+ eventPhase: true,
+ metaKey: true,
+ pageX: true,
+ pageY: true,
+ shiftKey: true,
+ view: true,
+ "char": true,
+ charCode: true,
+ key: true,
+ keyCode: true,
+ button: true,
+ buttons: true,
+ clientX: true,
+ clientY: true,
+ offsetX: true,
+ offsetY: true,
+ pointerId: true,
+ pointerType: true,
+ screenX: true,
+ screenY: true,
+ targetTouches: true,
+ toElement: true,
+ touches: true,
+
+ which: function( event ) {
+ var button = event.button;
+
+ // Add which for key events
+ if ( event.which == null && rkeyEvent.test( event.type ) ) {
+ return event.charCode != null ? event.charCode : event.keyCode;
+ }
+
+ // Add which for click: 1 === left; 2 === middle; 3 === right
+ if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) {
+ if ( button & 1 ) {
+ return 1;
+ }
+
+ if ( button & 2 ) {
+ return 3;
+ }
+
+ if ( button & 4 ) {
+ return 2;
+ }
+
+ return 0;
+ }
+
+ return event.which;
+ }
+}, jQuery.event.addProp );
+
// Create mouseenter/leave events using mouseover/out and event-time checks
-jQuery.each({
+// so that event delegation works in jQuery.
+// Do the same for pointerenter/pointerleave and pointerover/pointerout
+//
+// Support: Safari 7 only
+// Safari sends mouseenter too often; see:
+// https://bugs.chromium.org/p/chromium/issues/detail?id=470258
+// for the description of the bug (it existed in older Chrome versions as well).
+jQuery.each( {
mouseenter: "mouseover",
mouseleave: "mouseout",
pointerenter: "pointerover",
@@ -5013,9 +5552,9 @@ jQuery.each({
related = event.relatedTarget,
handleObj = event.handleObj;
- // For mousenter/leave call the handler if related is outside the target.
+ // For mouseenter/leave call the handler if related is outside the target.
// NB: No relatedTarget if the mouse left/entered the browser window
- if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
+ if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) {
event.type = handleObj.origType;
ret = handleObj.handler.apply( this, arguments );
event.type = fix;
@@ -5023,490 +5562,281 @@ jQuery.each({
return ret;
}
};
-});
-
-// IE submit delegation
-if ( !support.submitBubbles ) {
+} );
- jQuery.event.special.submit = {
- setup: function() {
- // Only need this for delegated form submit events
- if ( jQuery.nodeName( this, "form" ) ) {
- return false;
- }
+jQuery.fn.extend( {
- // Lazy-add a submit handler when a descendant form may potentially be submitted
- jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
- // Node name check avoids a VML-related crash in IE (#9807)
- var elem = e.target,
- form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
- if ( form && !jQuery._data( form, "submitBubbles" ) ) {
- jQuery.event.add( form, "submit._submit", function( event ) {
- event._submit_bubble = true;
- });
- jQuery._data( form, "submitBubbles", true );
- }
- });
- // return undefined since we don't need an event listener
- },
+ on: function( types, selector, data, fn ) {
+ return on( this, types, selector, data, fn );
+ },
+ one: function( types, selector, data, fn ) {
+ return on( this, types, selector, data, fn, 1 );
+ },
+ off: function( types, selector, fn ) {
+ var handleObj, type;
+ if ( types && types.preventDefault && types.handleObj ) {
- postDispatch: function( event ) {
- // If form was submitted by the user, bubble the event up the tree
- if ( event._submit_bubble ) {
- delete event._submit_bubble;
- if ( this.parentNode && !event.isTrigger ) {
- jQuery.event.simulate( "submit", this.parentNode, event, true );
- }
- }
- },
+ // ( event ) dispatched jQuery.Event
+ handleObj = types.handleObj;
+ jQuery( types.delegateTarget ).off(
+ handleObj.namespace ?
+ handleObj.origType + "." + handleObj.namespace :
+ handleObj.origType,
+ handleObj.selector,
+ handleObj.handler
+ );
+ return this;
+ }
+ if ( typeof types === "object" ) {
- teardown: function() {
- // Only need this for delegated form submit events
- if ( jQuery.nodeName( this, "form" ) ) {
- return false;
+ // ( types-object [, selector] )
+ for ( type in types ) {
+ this.off( type, selector, types[ type ] );
}
+ return this;
+ }
+ if ( selector === false || typeof selector === "function" ) {
- // Remove delegated handlers; cleanData eventually reaps submit handlers attached above
- jQuery.event.remove( this, "._submit" );
+ // ( types [, fn] )
+ fn = selector;
+ selector = undefined;
}
- };
-}
+ if ( fn === false ) {
+ fn = returnFalse;
+ }
+ return this.each( function() {
+ jQuery.event.remove( this, types, fn, selector );
+ } );
+ }
+} );
-// IE change delegation and checkbox/radio fix
-if ( !support.changeBubbles ) {
- jQuery.event.special.change = {
+var
- setup: function() {
+ /* eslint-disable max-len */
- if ( rformElems.test( this.nodeName ) ) {
- // IE doesn't fire change on a check/radio until blur; trigger it on click
- // after a propertychange. Eat the blur-change in special.change.handle.
- // This still fires onchange a second time for check/radio after blur.
- if ( this.type === "checkbox" || this.type === "radio" ) {
- jQuery.event.add( this, "propertychange._change", function( event ) {
- if ( event.originalEvent.propertyName === "checked" ) {
- this._just_changed = true;
- }
- });
- jQuery.event.add( this, "click._change", function( event ) {
- if ( this._just_changed && !event.isTrigger ) {
- this._just_changed = false;
- }
- // Allow triggered, simulated change events (#11500)
- jQuery.event.simulate( "change", this, event, true );
- });
- }
- return false;
- }
- // Delegated event; lazy-add a change handler on descendant inputs
- jQuery.event.add( this, "beforeactivate._change", function( e ) {
- var elem = e.target;
+ // See https://github.com/eslint/eslint/issues/3229
+ rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi,
- if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) {
- jQuery.event.add( elem, "change._change", function( event ) {
- if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
- jQuery.event.simulate( "change", this.parentNode, event, true );
- }
- });
- jQuery._data( elem, "changeBubbles", true );
- }
- });
- },
+ /* eslint-enable */
- handle: function( event ) {
- var elem = event.target;
+ // Support: IE <=10 - 11, Edge 12 - 13
+ // In IE/Edge using regex groups here causes severe slowdowns.
+ // See https://connect.microsoft.com/IE/feedback/details/1736512/
+ rnoInnerhtml = /<script|<style|<link/i,
- // Swallow native change events from checkbox/radio, we already triggered them above
- if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
- return event.handleObj.handler.apply( this, arguments );
- }
- },
+ // checked="checked" or checked
+ rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
+ rscriptTypeMasked = /^true\/(.*)/,
+ rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g;
- teardown: function() {
- jQuery.event.remove( this, "._change" );
+// Prefer a tbody over its parent table for containing new rows
+function manipulationTarget( elem, content ) {
+ if ( nodeName( elem, "table" ) &&
+ nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) {
- return !rformElems.test( this.nodeName );
- }
- };
+ return jQuery( ">tbody", elem )[ 0 ] || elem;
+ }
+
+ return elem;
}
-// Create "bubbling" focus and blur events
-if ( !support.focusinBubbles ) {
- jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
+// Replace/restore the type attribute of script elements for safe DOM manipulation
+function disableScript( elem ) {
+ elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type;
+ return elem;
+}
+function restoreScript( elem ) {
+ var match = rscriptTypeMasked.exec( elem.type );
- // Attach a single capturing handler on the document while someone wants focusin/focusout
- var handler = function( event ) {
- jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
- };
+ if ( match ) {
+ elem.type = match[ 1 ];
+ } else {
+ elem.removeAttribute( "type" );
+ }
- jQuery.event.special[ fix ] = {
- setup: function() {
- var doc = this.ownerDocument || this,
- attaches = jQuery._data( doc, fix );
-
- if ( !attaches ) {
- doc.addEventListener( orig, handler, true );
- }
- jQuery._data( doc, fix, ( attaches || 0 ) + 1 );
- },
- teardown: function() {
- var doc = this.ownerDocument || this,
- attaches = jQuery._data( doc, fix ) - 1;
-
- if ( !attaches ) {
- doc.removeEventListener( orig, handler, true );
- jQuery._removeData( doc, fix );
- } else {
- jQuery._data( doc, fix, attaches );
- }
- }
- };
- });
+ return elem;
}
-jQuery.fn.extend({
+function cloneCopyEvent( src, dest ) {
+ var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events;
- on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
- var type, origFn;
+ if ( dest.nodeType !== 1 ) {
+ return;
+ }
- // Types can be a map of types/handlers
- if ( typeof types === "object" ) {
- // ( types-Object, selector, data )
- if ( typeof selector !== "string" ) {
- // ( types-Object, data )
- data = data || selector;
- selector = undefined;
- }
- for ( type in types ) {
- this.on( type, selector, data, types[ type ], one );
- }
- return this;
- }
+ // 1. Copy private data: events, handlers, etc.
+ if ( dataPriv.hasData( src ) ) {
+ pdataOld = dataPriv.access( src );
+ pdataCur = dataPriv.set( dest, pdataOld );
+ events = pdataOld.events;
- if ( data == null && fn == null ) {
- // ( types, fn )
- fn = selector;
- data = selector = undefined;
- } else if ( fn == null ) {
- if ( typeof selector === "string" ) {
- // ( types, selector, fn )
- fn = data;
- data = undefined;
- } else {
- // ( types, data, fn )
- fn = data;
- data = selector;
- selector = undefined;
- }
- }
- if ( fn === false ) {
- fn = returnFalse;
- } else if ( !fn ) {
- return this;
- }
+ if ( events ) {
+ delete pdataCur.handle;
+ pdataCur.events = {};
- if ( one === 1 ) {
- origFn = fn;
- fn = function( event ) {
- // Can use an empty set, since event contains the info
- jQuery().off( event );
- return origFn.apply( this, arguments );
- };
- // Use same guid so caller can remove using origFn
- fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
- }
- return this.each( function() {
- jQuery.event.add( this, types, fn, data, selector );
- });
- },
- one: function( types, selector, data, fn ) {
- return this.on( types, selector, data, fn, 1 );
- },
- off: function( types, selector, fn ) {
- var handleObj, type;
- if ( types && types.preventDefault && types.handleObj ) {
- // ( event ) dispatched jQuery.Event
- handleObj = types.handleObj;
- jQuery( types.delegateTarget ).off(
- handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
- handleObj.selector,
- handleObj.handler
- );
- return this;
- }
- if ( typeof types === "object" ) {
- // ( types-object [, selector] )
- for ( type in types ) {
- this.off( type, selector, types[ type ] );
+ for ( type in events ) {
+ for ( i = 0, l = events[ type ].length; i < l; i++ ) {
+ jQuery.event.add( dest, type, events[ type ][ i ] );
+ }
}
- return this;
- }
- if ( selector === false || typeof selector === "function" ) {
- // ( types [, fn] )
- fn = selector;
- selector = undefined;
- }
- if ( fn === false ) {
- fn = returnFalse;
}
- return this.each(function() {
- jQuery.event.remove( this, types, fn, selector );
- });
- },
+ }
- trigger: function( type, data ) {
- return this.each(function() {
- jQuery.event.trigger( type, data, this );
- });
- },
- triggerHandler: function( type, data ) {
- var elem = this[0];
- if ( elem ) {
- return jQuery.event.trigger( type, data, elem, true );
- }
+ // 2. Copy user data
+ if ( dataUser.hasData( src ) ) {
+ udataOld = dataUser.access( src );
+ udataCur = jQuery.extend( {}, udataOld );
+
+ dataUser.set( dest, udataCur );
}
-});
+}
+// Fix IE bugs, see support tests
+function fixInput( src, dest ) {
+ var nodeName = dest.nodeName.toLowerCase();
-function createSafeFragment( document ) {
- var list = nodeNames.split( "|" ),
- safeFrag = document.createDocumentFragment();
+ // Fails to persist the checked state of a cloned checkbox or radio button.
+ if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
+ dest.checked = src.checked;
- if ( safeFrag.createElement ) {
- while ( list.length ) {
- safeFrag.createElement(
- list.pop()
- );
- }
+ // Fails to return the selected option to the default selected state when cloning options
+ } else if ( nodeName === "input" || nodeName === "textarea" ) {
+ dest.defaultValue = src.defaultValue;
}
- return safeFrag;
}
-var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
- "header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
- rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g,
- rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
- rleadingWhitespace = /^\s+/,
- rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,
- rtagName = /<([\w:]+)/,
- rtbody = /<tbody/i,
- rhtml = /<|&#?\w+;/,
- rnoInnerhtml = /<(?:script|style|link)/i,
- // checked="checked" or checked
- rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
- rscriptType = /^$|\/(?:java|ecma)script/i,
- rscriptTypeMasked = /^true\/(.*)/,
- rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g,
-
- // We have to close these tags to support XHTML (#13200)
- wrapMap = {
- option: [ 1, "<select multiple='multiple'>", "</select>" ],
- legend: [ 1, "<fieldset>", "</fieldset>" ],
- area: [ 1, "<map>", "</map>" ],
- param: [ 1, "<object>", "</object>" ],
- thead: [ 1, "<table>", "</table>" ],
- tr: [ 2, "<table><tbody>", "</tbody></table>" ],
- col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
- td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
-
- // IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags,
- // unless wrapped in a div with non-breaking characters in front of it.
- _default: support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X<div>", "</div>" ]
- },
- safeFragment = createSafeFragment( document ),
- fragmentDiv = safeFragment.appendChild( document.createElement("div") );
+function domManip( collection, args, callback, ignored ) {
-wrapMap.optgroup = wrapMap.option;
-wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
-wrapMap.th = wrapMap.td;
+ // Flatten any nested arrays
+ args = concat.apply( [], args );
-function getAll( context, tag ) {
- var elems, elem,
+ var fragment, first, scripts, hasScripts, node, doc,
i = 0,
- found = typeof context.getElementsByTagName !== strundefined ? context.getElementsByTagName( tag || "*" ) :
- typeof context.querySelectorAll !== strundefined ? context.querySelectorAll( tag || "*" ) :
- undefined;
+ l = collection.length,
+ iNoClone = l - 1,
+ value = args[ 0 ],
+ isFunction = jQuery.isFunction( value );
- if ( !found ) {
- for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) {
- if ( !tag || jQuery.nodeName( elem, tag ) ) {
- found.push( elem );
- } else {
- jQuery.merge( found, getAll( elem, tag ) );
+ // We can't cloneNode fragments that contain checked, in WebKit
+ if ( isFunction ||
+ ( l > 1 && typeof value === "string" &&
+ !support.checkClone && rchecked.test( value ) ) ) {
+ return collection.each( function( index ) {
+ var self = collection.eq( index );
+ if ( isFunction ) {
+ args[ 0 ] = value.call( this, index, self.html() );
}
- }
- }
-
- return tag === undefined || tag && jQuery.nodeName( context, tag ) ?
- jQuery.merge( [ context ], found ) :
- found;
-}
-
-// Used in buildFragment, fixes the defaultChecked property
-function fixDefaultChecked( elem ) {
- if ( rcheckableType.test( elem.type ) ) {
- elem.defaultChecked = elem.checked;
+ domManip( self, args, callback, ignored );
+ } );
}
-}
-// Support: IE<8
-// Manipulating tables requires a tbody
-function manipulationTarget( elem, content ) {
- return jQuery.nodeName( elem, "table" ) &&
- jQuery.nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ?
-
- elem.getElementsByTagName("tbody")[0] ||
- elem.appendChild( elem.ownerDocument.createElement("tbody") ) :
- elem;
-}
+ if ( l ) {
+ fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored );
+ first = fragment.firstChild;
-// Replace/restore the type attribute of script elements for safe DOM manipulation
-function disableScript( elem ) {
- elem.type = (jQuery.find.attr( elem, "type" ) !== null) + "/" + elem.type;
- return elem;
-}
-function restoreScript( elem ) {
- var match = rscriptTypeMasked.exec( elem.type );
- if ( match ) {
- elem.type = match[1];
- } else {
- elem.removeAttribute("type");
- }
- return elem;
-}
+ if ( fragment.childNodes.length === 1 ) {
+ fragment = first;
+ }
-// Mark scripts as having already been evaluated
-function setGlobalEval( elems, refElements ) {
- var elem,
- i = 0;
- for ( ; (elem = elems[i]) != null; i++ ) {
- jQuery._data( elem, "globalEval", !refElements || jQuery._data( refElements[i], "globalEval" ) );
- }
-}
+ // Require either new content or an interest in ignored elements to invoke the callback
+ if ( first || ignored ) {
+ scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
+ hasScripts = scripts.length;
-function cloneCopyEvent( src, dest ) {
+ // Use the original fragment for the last item
+ // instead of the first because it can end up
+ // being emptied incorrectly in certain situations (#8070).
+ for ( ; i < l; i++ ) {
+ node = fragment;
- if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) {
- return;
- }
+ if ( i !== iNoClone ) {
+ node = jQuery.clone( node, true, true );
- var type, i, l,
- oldData = jQuery._data( src ),
- curData = jQuery._data( dest, oldData ),
- events = oldData.events;
+ // Keep references to cloned scripts for later restoration
+ if ( hasScripts ) {
- if ( events ) {
- delete curData.handle;
- curData.events = {};
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
+ jQuery.merge( scripts, getAll( node, "script" ) );
+ }
+ }
- for ( type in events ) {
- for ( i = 0, l = events[ type ].length; i < l; i++ ) {
- jQuery.event.add( dest, type, events[ type ][ i ] );
+ callback.call( collection[ i ], node, i );
}
- }
- }
-
- // make the cloned public data object a copy from the original
- if ( curData.data ) {
- curData.data = jQuery.extend( {}, curData.data );
- }
-}
-function fixCloneNodeIssues( src, dest ) {
- var nodeName, e, data;
+ if ( hasScripts ) {
+ doc = scripts[ scripts.length - 1 ].ownerDocument;
- // We do not need to do anything for non-Elements
- if ( dest.nodeType !== 1 ) {
- return;
- }
+ // Reenable scripts
+ jQuery.map( scripts, restoreScript );
- nodeName = dest.nodeName.toLowerCase();
+ // Evaluate executable scripts on first document insertion
+ for ( i = 0; i < hasScripts; i++ ) {
+ node = scripts[ i ];
+ if ( rscriptType.test( node.type || "" ) &&
+ !dataPriv.access( node, "globalEval" ) &&
+ jQuery.contains( doc, node ) ) {
- // IE6-8 copies events bound via attachEvent when using cloneNode.
- if ( !support.noCloneEvent && dest[ jQuery.expando ] ) {
- data = jQuery._data( dest );
+ if ( node.src ) {
- for ( e in data.events ) {
- jQuery.removeEvent( dest, e, data.handle );
+ // Optional AJAX dependency, but won't run scripts if not present
+ if ( jQuery._evalUrl ) {
+ jQuery._evalUrl( node.src );
+ }
+ } else {
+ DOMEval( node.textContent.replace( rcleanScript, "" ), doc );
+ }
+ }
+ }
+ }
}
-
- // Event data gets referenced instead of copied if the expando gets copied too
- dest.removeAttribute( jQuery.expando );
}
- // IE blanks contents when cloning scripts, and tries to evaluate newly-set text
- if ( nodeName === "script" && dest.text !== src.text ) {
- disableScript( dest ).text = src.text;
- restoreScript( dest );
+ return collection;
+}
- // IE6-10 improperly clones children of object elements using classid.
- // IE10 throws NoModificationAllowedError if parent is null, #12132.
- } else if ( nodeName === "object" ) {
- if ( dest.parentNode ) {
- dest.outerHTML = src.outerHTML;
- }
+function remove( elem, selector, keepData ) {
+ var node,
+ nodes = selector ? jQuery.filter( selector, elem ) : elem,
+ i = 0;
- // This path appears unavoidable for IE9. When cloning an object
- // element in IE9, the outerHTML strategy above is not sufficient.
- // If the src has innerHTML and the destination does not,
- // copy the src.innerHTML into the dest.innerHTML. #10324
- if ( support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) {
- dest.innerHTML = src.innerHTML;
+ for ( ; ( node = nodes[ i ] ) != null; i++ ) {
+ if ( !keepData && node.nodeType === 1 ) {
+ jQuery.cleanData( getAll( node ) );
}
- } else if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
- // IE6-8 fails to persist the checked state of a cloned checkbox
- // or radio button. Worse, IE6-7 fail to give the cloned element
- // a checked appearance if the defaultChecked value isn't also set
-
- dest.defaultChecked = dest.checked = src.checked;
-
- // IE6-7 get confused and end up setting the value of a cloned
- // checkbox/radio button to an empty string instead of "on"
- if ( dest.value !== src.value ) {
- dest.value = src.value;
+ if ( node.parentNode ) {
+ if ( keepData && jQuery.contains( node.ownerDocument, node ) ) {
+ setGlobalEval( getAll( node, "script" ) );
+ }
+ node.parentNode.removeChild( node );
}
-
- // IE6-8 fails to return the selected option to the default selected
- // state when cloning options
- } else if ( nodeName === "option" ) {
- dest.defaultSelected = dest.selected = src.defaultSelected;
-
- // IE6-8 fails to set the defaultValue to the correct value when
- // cloning other types of input fields
- } else if ( nodeName === "input" || nodeName === "textarea" ) {
- dest.defaultValue = src.defaultValue;
}
+
+ return elem;
}
-jQuery.extend({
+jQuery.extend( {
+ htmlPrefilter: function( html ) {
+ return html.replace( rxhtmlTag, "<$1></$2>" );
+ },
+
clone: function( elem, dataAndEvents, deepDataAndEvents ) {
- var destElements, node, clone, i, srcElements,
+ var i, l, srcElements, destElements,
+ clone = elem.cloneNode( true ),
inPage = jQuery.contains( elem.ownerDocument, elem );
- if ( support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) {
- clone = elem.cloneNode( true );
-
- // IE<=8 does not properly clone detached, unknown element nodes
- } else {
- fragmentDiv.innerHTML = elem.outerHTML;
- fragmentDiv.removeChild( clone = fragmentDiv.firstChild );
- }
-
- if ( (!support.noCloneEvent || !support.noCloneChecked) &&
- (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
+ // Fix IE cloning issues
+ if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) &&
+ !jQuery.isXMLDoc( elem ) ) {
- // We eschew Sizzle here for performance reasons: http://jsperf.com/getall-vs-sizzle/2
+ // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2
destElements = getAll( clone );
srcElements = getAll( elem );
- // Fix all IE cloning issues
- for ( i = 0; (node = srcElements[i]) != null; ++i ) {
- // Ensure that the destination node is not null; Fixes #9587
- if ( destElements[i] ) {
- fixCloneNodeIssues( node, destElements[i] );
- }
+ for ( i = 0, l = srcElements.length; i < l; i++ ) {
+ fixInput( srcElements[ i ], destElements[ i ] );
}
}
@@ -5516,8 +5846,8 @@ jQuery.extend({
srcElements = srcElements || getAll( elem );
destElements = destElements || getAll( clone );
- for ( i = 0; (node = srcElements[i]) != null; i++ ) {
- cloneCopyEvent( node, destElements[i] );
+ for ( i = 0, l = srcElements.length; i < l; i++ ) {
+ cloneCopyEvent( srcElements[ i ], destElements[ i ] );
}
} else {
cloneCopyEvent( elem, clone );
@@ -5530,154 +5860,18 @@ jQuery.extend({
setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
}
- destElements = srcElements = node = null;
-
// Return the cloned set
return clone;
},
- buildFragment: function( elems, context, scripts, selection ) {
- var j, elem, contains,
- tmp, tag, tbody, wrap,
- l = elems.length,
-
- // Ensure a safe fragment
- safe = createSafeFragment( context ),
-
- nodes = [],
+ cleanData: function( elems ) {
+ var data, elem, type,
+ special = jQuery.event.special,
i = 0;
- for ( ; i < l; i++ ) {
- elem = elems[ i ];
-
- if ( elem || elem === 0 ) {
-
- // Add nodes directly
- if ( jQuery.type( elem ) === "object" ) {
- jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
-
- // Convert non-html into a text node
- } else if ( !rhtml.test( elem ) ) {
- nodes.push( context.createTextNode( elem ) );
-
- // Convert html into DOM nodes
- } else {
- tmp = tmp || safe.appendChild( context.createElement("div") );
-
- // Deserialize a standard representation
- tag = (rtagName.exec( elem ) || [ "", "" ])[ 1 ].toLowerCase();
- wrap = wrapMap[ tag ] || wrapMap._default;
-
- tmp.innerHTML = wrap[1] + elem.replace( rxhtmlTag, "<$1></$2>" ) + wrap[2];
-
- // Descend through wrappers to the right content
- j = wrap[0];
- while ( j-- ) {
- tmp = tmp.lastChild;
- }
-
- // Manually add leading whitespace removed by IE
- if ( !support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
- nodes.push( context.createTextNode( rleadingWhitespace.exec( elem )[0] ) );
- }
-
- // Remove IE's autoinserted <tbody> from table fragments
- if ( !support.tbody ) {
-
- // String was a <table>, *may* have spurious <tbody>
- elem = tag === "table" && !rtbody.test( elem ) ?
- tmp.firstChild :
-
- // String was a bare <thead> or <tfoot>
- wrap[1] === "<table>" && !rtbody.test( elem ) ?
- tmp :
- 0;
-
- j = elem && elem.childNodes.length;
- while ( j-- ) {
- if ( jQuery.nodeName( (tbody = elem.childNodes[j]), "tbody" ) && !tbody.childNodes.length ) {
- elem.removeChild( tbody );
- }
- }
- }
-
- jQuery.merge( nodes, tmp.childNodes );
-
- // Fix #12392 for WebKit and IE > 9
- tmp.textContent = "";
-
- // Fix #12392 for oldIE
- while ( tmp.firstChild ) {
- tmp.removeChild( tmp.firstChild );
- }
-
- // Remember the top-level container for proper cleanup
- tmp = safe.lastChild;
- }
- }
- }
-
- // Fix #11356: Clear elements from fragment
- if ( tmp ) {
- safe.removeChild( tmp );
- }
-
- // Reset defaultChecked for any radios and checkboxes
- // about to be appended to the DOM in IE 6/7 (#8060)
- if ( !support.appendChecked ) {
- jQuery.grep( getAll( nodes, "input" ), fixDefaultChecked );
- }
-
- i = 0;
- while ( (elem = nodes[ i++ ]) ) {
-
- // #4087 - If origin and destination elements are the same, and this is
- // that element, do not do anything
- if ( selection && jQuery.inArray( elem, selection ) !== -1 ) {
- continue;
- }
-
- contains = jQuery.contains( elem.ownerDocument, elem );
-
- // Append to fragment
- tmp = getAll( safe.appendChild( elem ), "script" );
-
- // Preserve script evaluation history
- if ( contains ) {
- setGlobalEval( tmp );
- }
-
- // Capture executables
- if ( scripts ) {
- j = 0;
- while ( (elem = tmp[ j++ ]) ) {
- if ( rscriptType.test( elem.type || "" ) ) {
- scripts.push( elem );
- }
- }
- }
- }
-
- tmp = null;
-
- return safe;
- },
-
- cleanData: function( elems, /* internal */ acceptData ) {
- var elem, type, id, data,
- i = 0,
- internalKey = jQuery.expando,
- cache = jQuery.cache,
- deleteExpando = support.deleteExpando,
- special = jQuery.event.special;
-
- for ( ; (elem = elems[i]) != null; i++ ) {
- if ( acceptData || jQuery.acceptData( elem ) ) {
-
- id = elem[ internalKey ];
- data = id && cache[ id ];
-
- if ( data ) {
+ for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) {
+ if ( acceptData( elem ) ) {
+ if ( ( data = elem[ dataPriv.expando ] ) ) {
if ( data.events ) {
for ( type in data.events ) {
if ( special[ type ] ) {
@@ -5690,129 +5884,101 @@ jQuery.extend({
}
}
- // Remove cache only if it was not already removed by jQuery.event.remove
- if ( cache[ id ] ) {
-
- delete cache[ id ];
-
- // IE does not allow us to delete expando properties from nodes,
- // nor does it have a removeAttribute function on Document nodes;
- // we must handle all of these cases
- if ( deleteExpando ) {
- delete elem[ internalKey ];
-
- } else if ( typeof elem.removeAttribute !== strundefined ) {
- elem.removeAttribute( internalKey );
-
- } else {
- elem[ internalKey ] = null;
- }
+ // Support: Chrome <=35 - 45+
+ // Assign undefined instead of using delete, see Data#remove
+ elem[ dataPriv.expando ] = undefined;
+ }
+ if ( elem[ dataUser.expando ] ) {
- deletedIds.push( id );
- }
+ // Support: Chrome <=35 - 45+
+ // Assign undefined instead of using delete, see Data#remove
+ elem[ dataUser.expando ] = undefined;
}
}
}
}
-});
+} );
+
+jQuery.fn.extend( {
+ detach: function( selector ) {
+ return remove( this, selector, true );
+ },
+
+ remove: function( selector ) {
+ return remove( this, selector );
+ },
-jQuery.fn.extend({
text: function( value ) {
return access( this, function( value ) {
return value === undefined ?
jQuery.text( this ) :
- this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
+ this.empty().each( function() {
+ if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+ this.textContent = value;
+ }
+ } );
}, null, value, arguments.length );
},
append: function() {
- return this.domManip( arguments, function( elem ) {
+ return domManip( this, arguments, function( elem ) {
if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
var target = manipulationTarget( this, elem );
target.appendChild( elem );
}
- });
+ } );
},
prepend: function() {
- return this.domManip( arguments, function( elem ) {
+ return domManip( this, arguments, function( elem ) {
if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
var target = manipulationTarget( this, elem );
target.insertBefore( elem, target.firstChild );
}
- });
+ } );
},
before: function() {
- return this.domManip( arguments, function( elem ) {
+ return domManip( this, arguments, function( elem ) {
if ( this.parentNode ) {
this.parentNode.insertBefore( elem, this );
}
- });
+ } );
},
after: function() {
- return this.domManip( arguments, function( elem ) {
+ return domManip( this, arguments, function( elem ) {
if ( this.parentNode ) {
this.parentNode.insertBefore( elem, this.nextSibling );
}
- });
+ } );
},
- remove: function( selector, keepData /* Internal Use Only */ ) {
+ empty: function() {
var elem,
- elems = selector ? jQuery.filter( selector, this ) : this,
i = 0;
- for ( ; (elem = elems[i]) != null; i++ ) {
+ for ( ; ( elem = this[ i ] ) != null; i++ ) {
+ if ( elem.nodeType === 1 ) {
- if ( !keepData && elem.nodeType === 1 ) {
- jQuery.cleanData( getAll( elem ) );
- }
+ // Prevent memory leaks
+ jQuery.cleanData( getAll( elem, false ) );
- if ( elem.parentNode ) {
- if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) {
- setGlobalEval( getAll( elem, "script" ) );
- }
- elem.parentNode.removeChild( elem );
+ // Remove any remaining nodes
+ elem.textContent = "";
}
}
return this;
},
- empty: function() {
- var elem,
- i = 0;
+ clone: function( dataAndEvents, deepDataAndEvents ) {
+ dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
+ deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
- for ( ; (elem = this[i]) != null; i++ ) {
- // Remove element nodes and prevent memory leaks
- if ( elem.nodeType === 1 ) {
- jQuery.cleanData( getAll( elem, false ) );
- }
-
- // Remove any remaining nodes
- while ( elem.firstChild ) {
- elem.removeChild( elem.firstChild );
- }
-
- // If this is a select, ensure that it displays empty (#12336)
- // Support: IE<9
- if ( elem.options && jQuery.nodeName( elem, "select" ) ) {
- elem.options.length = 0;
- }
- }
-
- return this;
- },
-
- clone: function( dataAndEvents, deepDataAndEvents ) {
- dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
- deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
-
- return this.map(function() {
+ return this.map( function() {
return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
- });
+ } );
},
html: function( value ) {
@@ -5821,24 +5987,21 @@ jQuery.fn.extend({
i = 0,
l = this.length;
- if ( value === undefined ) {
- return elem.nodeType === 1 ?
- elem.innerHTML.replace( rinlinejQuery, "" ) :
- undefined;
+ if ( value === undefined && elem.nodeType === 1 ) {
+ return elem.innerHTML;
}
// See if we can take a shortcut and just use innerHTML
if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
- ( support.htmlSerialize || !rnoshimcache.test( value ) ) &&
- ( support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
- !wrapMap[ (rtagName.exec( value ) || [ "", "" ])[ 1 ].toLowerCase() ] ) {
+ !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) {
- value = value.replace( rxhtmlTag, "<$1></$2>" );
+ value = jQuery.htmlPrefilter( value );
try {
- for (; i < l; i++ ) {
+ for ( ; i < l; i++ ) {
+ elem = this[ i ] || {};
+
// Remove element nodes and prevent memory leaks
- elem = this[i] || {};
if ( elem.nodeType === 1 ) {
jQuery.cleanData( getAll( elem, false ) );
elem.innerHTML = value;
@@ -5848,7 +6011,7 @@ jQuery.fn.extend({
elem = 0;
// If using innerHTML throws an exception, use the fallback method
- } catch(e) {}
+ } catch ( e ) {}
}
if ( elem ) {
@@ -5858,117 +6021,25 @@ jQuery.fn.extend({
},
replaceWith: function() {
- var arg = arguments[ 0 ];
-
- // Make the changes, replacing each context element with the new content
- this.domManip( arguments, function( elem ) {
- arg = this.parentNode;
-
- jQuery.cleanData( getAll( this ) );
-
- if ( arg ) {
- arg.replaceChild( elem, this );
- }
- });
-
- // Force removal if there was no new content (e.g., from empty arguments)
- return arg && (arg.length || arg.nodeType) ? this : this.remove();
- },
-
- detach: function( selector ) {
- return this.remove( selector, true );
- },
-
- domManip: function( args, callback ) {
-
- // Flatten any nested arrays
- args = concat.apply( [], args );
-
- var first, node, hasScripts,
- scripts, doc, fragment,
- i = 0,
- l = this.length,
- set = this,
- iNoClone = l - 1,
- value = args[0],
- isFunction = jQuery.isFunction( value );
-
- // We can't cloneNode fragments that contain checked, in WebKit
- if ( isFunction ||
- ( l > 1 && typeof value === "string" &&
- !support.checkClone && rchecked.test( value ) ) ) {
- return this.each(function( index ) {
- var self = set.eq( index );
- if ( isFunction ) {
- args[0] = value.call( this, index, self.html() );
- }
- self.domManip( args, callback );
- });
- }
-
- if ( l ) {
- fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this );
- first = fragment.firstChild;
-
- if ( fragment.childNodes.length === 1 ) {
- fragment = first;
- }
-
- if ( first ) {
- scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
- hasScripts = scripts.length;
-
- // Use the original fragment for the last item instead of the first because it can end up
- // being emptied incorrectly in certain situations (#8070).
- for ( ; i < l; i++ ) {
- node = fragment;
-
- if ( i !== iNoClone ) {
- node = jQuery.clone( node, true, true );
-
- // Keep references to cloned scripts for later restoration
- if ( hasScripts ) {
- jQuery.merge( scripts, getAll( node, "script" ) );
- }
- }
-
- callback.call( this[i], node, i );
- }
+ var ignored = [];
- if ( hasScripts ) {
- doc = scripts[ scripts.length - 1 ].ownerDocument;
+ // Make the changes, replacing each non-ignored context element with the new content
+ return domManip( this, arguments, function( elem ) {
+ var parent = this.parentNode;
- // Reenable scripts
- jQuery.map( scripts, restoreScript );
-
- // Evaluate executable scripts on first document insertion
- for ( i = 0; i < hasScripts; i++ ) {
- node = scripts[ i ];
- if ( rscriptType.test( node.type || "" ) &&
- !jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) {
-
- if ( node.src ) {
- // Optional AJAX dependency, but won't run scripts if not present
- if ( jQuery._evalUrl ) {
- jQuery._evalUrl( node.src );
- }
- } else {
- jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) );
- }
- }
- }
+ if ( jQuery.inArray( this, ignored ) < 0 ) {
+ jQuery.cleanData( getAll( this ) );
+ if ( parent ) {
+ parent.replaceChild( elem, this );
}
-
- // Fix #11809: Avoid leaking memory
- fragment = first = null;
}
- }
- return this;
+ // Force callback invocation
+ }, ignored );
}
-});
+} );
-jQuery.each({
+jQuery.each( {
appendTo: "append",
prependTo: "prepend",
insertBefore: "before",
@@ -5977,570 +6048,289 @@ jQuery.each({
}, function( name, original ) {
jQuery.fn[ name ] = function( selector ) {
var elems,
- i = 0,
ret = [],
insert = jQuery( selector ),
- last = insert.length - 1;
+ last = insert.length - 1,
+ i = 0;
for ( ; i <= last; i++ ) {
- elems = i === last ? this : this.clone(true);
- jQuery( insert[i] )[ original ]( elems );
+ elems = i === last ? this : this.clone( true );
+ jQuery( insert[ i ] )[ original ]( elems );
- // Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get()
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // .get() because push.apply(_, arraylike) throws on ancient WebKit
push.apply( ret, elems.get() );
}
return this.pushStack( ret );
};
-});
-
-
-var iframe,
- elemdisplay = {};
-
-/**
- * Retrieve the actual display of a element
- * @param {String} name nodeName of the element
- * @param {Object} doc Document object
- */
-// Called only from within defaultDisplay
-function actualDisplay( name, doc ) {
- var style,
- elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ),
-
- // getDefaultComputedStyle might be reliably used only on attached element
- display = window.getDefaultComputedStyle && ( style = window.getDefaultComputedStyle( elem[ 0 ] ) ) ?
+} );
+var rmargin = ( /^margin/ );
- // Use of this method is a temporary fix (more like optmization) until something better comes along,
- // since it was removed from specification and supported only in FF
- style.display : jQuery.css( elem[ 0 ], "display" );
-
- // We don't have any data stored on the element,
- // so use "detach" method as fast way to get rid of the element
- elem.detach();
-
- return display;
-}
-
-/**
- * Try to determine the default display value of an element
- * @param {String} nodeName
- */
-function defaultDisplay( nodeName ) {
- var doc = document,
- display = elemdisplay[ nodeName ];
-
- if ( !display ) {
- display = actualDisplay( nodeName, doc );
-
- // If the simple way fails, read from inside an iframe
- if ( display === "none" || !display ) {
-
- // Use the already-created iframe if possible
- iframe = (iframe || jQuery( "<iframe frameborder='0' width='0' height='0'/>" )).appendTo( doc.documentElement );
+var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
- // Always write a new HTML skeleton so Webkit and Firefox don't choke on reuse
- doc = ( iframe[ 0 ].contentWindow || iframe[ 0 ].contentDocument ).document;
+var getStyles = function( elem ) {
- // Support: IE
- doc.write();
- doc.close();
+ // Support: IE <=11 only, Firefox <=30 (#15098, #14150)
+ // IE throws on elements created in popups
+ // FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
+ var view = elem.ownerDocument.defaultView;
- display = actualDisplay( nodeName, doc );
- iframe.detach();
+ if ( !view || !view.opener ) {
+ view = window;
}
- // Store the correct default display
- elemdisplay[ nodeName ] = display;
- }
-
- return display;
-}
-
+ return view.getComputedStyle( elem );
+ };
-(function() {
- var shrinkWrapBlocksVal;
- support.shrinkWrapBlocks = function() {
- if ( shrinkWrapBlocksVal != null ) {
- return shrinkWrapBlocksVal;
- }
- // Will be changed later if needed.
- shrinkWrapBlocksVal = false;
+( function() {
- // Minified: var b,c,d
- var div, body, container;
+ // Executing both pixelPosition & boxSizingReliable tests require only one layout
+ // so they're executed at the same time to save the second computation.
+ function computeStyleTests() {
- body = document.getElementsByTagName( "body" )[ 0 ];
- if ( !body || !body.style ) {
- // Test fired too early or in an unsupported environment, exit.
+ // This is a singleton, we need to execute it only once
+ if ( !div ) {
return;
}
- // Setup
- div = document.createElement( "div" );
- container = document.createElement( "div" );
- container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
- body.appendChild( container ).appendChild( div );
-
- // Support: IE6
- // Check if elements with layout shrink-wrap their children
- if ( typeof div.style.zoom !== strundefined ) {
- // Reset CSS: box-sizing; display; margin; border
- div.style.cssText =
- // Support: Firefox<29, Android 2.3
- // Vendor-prefix box-sizing
- "-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
- "box-sizing:content-box;display:block;margin:0;border:0;" +
- "padding:1px;width:1px;zoom:1";
- div.appendChild( document.createElement( "div" ) ).style.width = "5px";
- shrinkWrapBlocksVal = div.offsetWidth !== 3;
- }
-
- body.removeChild( container );
-
- return shrinkWrapBlocksVal;
- };
-
-})();
-var rmargin = (/^margin/);
-
-var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
-
+ div.style.cssText =
+ "box-sizing:border-box;" +
+ "position:relative;display:block;" +
+ "margin:auto;border:1px;padding:1px;" +
+ "top:1%;width:50%";
+ div.innerHTML = "";
+ documentElement.appendChild( container );
+ var divStyle = window.getComputedStyle( div );
+ pixelPositionVal = divStyle.top !== "1%";
-var getStyles, curCSS,
- rposition = /^(top|right|bottom|left)$/;
+ // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44
+ reliableMarginLeftVal = divStyle.marginLeft === "2px";
+ boxSizingReliableVal = divStyle.width === "4px";
-if ( window.getComputedStyle ) {
- getStyles = function( elem ) {
- return elem.ownerDocument.defaultView.getComputedStyle( elem, null );
- };
+ // Support: Android 4.0 - 4.3 only
+ // Some styles come back with percentage values, even though they shouldn't
+ div.style.marginRight = "50%";
+ pixelMarginRightVal = divStyle.marginRight === "4px";
- curCSS = function( elem, name, computed ) {
- var width, minWidth, maxWidth, ret,
- style = elem.style;
+ documentElement.removeChild( container );
- computed = computed || getStyles( elem );
+ // Nullify the div so it wouldn't be stored in the memory and
+ // it will also be a sign that checks already performed
+ div = null;
+ }
- // getPropertyValue is only needed for .css('filter') in IE9, see #12537
- ret = computed ? computed.getPropertyValue( name ) || computed[ name ] : undefined;
+ var pixelPositionVal, boxSizingReliableVal, pixelMarginRightVal, reliableMarginLeftVal,
+ container = document.createElement( "div" ),
+ div = document.createElement( "div" );
- if ( computed ) {
+ // Finish early in limited (non-browser) environments
+ if ( !div.style ) {
+ return;
+ }
- if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
- ret = jQuery.style( elem, name );
- }
+ // Support: IE <=9 - 11 only
+ // Style of cloned element affects source element cloned (#8908)
+ div.style.backgroundClip = "content-box";
+ div.cloneNode( true ).style.backgroundClip = "";
+ support.clearCloneStyle = div.style.backgroundClip === "content-box";
- // A tribute to the "awesome hack by Dean Edwards"
- // Chrome < 17 and Safari 5.0 uses "computed value" instead of "used value" for margin-right
- // Safari 5.1.7 (at least) returns percentage for a larger set of values, but width seems to be reliably pixels
- // this is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values
- if ( rnumnonpx.test( ret ) && rmargin.test( name ) ) {
+ container.style.cssText = "border:0;width:8px;height:0;top:0;left:-9999px;" +
+ "padding:0;margin-top:1px;position:absolute";
+ container.appendChild( div );
- // Remember the original values
- width = style.width;
- minWidth = style.minWidth;
- maxWidth = style.maxWidth;
+ jQuery.extend( support, {
+ pixelPosition: function() {
+ computeStyleTests();
+ return pixelPositionVal;
+ },
+ boxSizingReliable: function() {
+ computeStyleTests();
+ return boxSizingReliableVal;
+ },
+ pixelMarginRight: function() {
+ computeStyleTests();
+ return pixelMarginRightVal;
+ },
+ reliableMarginLeft: function() {
+ computeStyleTests();
+ return reliableMarginLeftVal;
+ }
+ } );
+} )();
- // Put in the new values to get a computed value out
- style.minWidth = style.maxWidth = style.width = ret;
- ret = computed.width;
- // Revert the changed values
- style.width = width;
- style.minWidth = minWidth;
- style.maxWidth = maxWidth;
- }
- }
+function curCSS( elem, name, computed ) {
+ var width, minWidth, maxWidth, ret,
- // Support: IE
- // IE returns zIndex value as an integer.
- return ret === undefined ?
- ret :
- ret + "";
- };
-} else if ( document.documentElement.currentStyle ) {
- getStyles = function( elem ) {
- return elem.currentStyle;
- };
+ // Support: Firefox 51+
+ // Retrieving style before computed somehow
+ // fixes an issue with getting wrong values
+ // on detached elements
+ style = elem.style;
- curCSS = function( elem, name, computed ) {
- var left, rs, rsLeft, ret,
- style = elem.style;
+ computed = computed || getStyles( elem );
- computed = computed || getStyles( elem );
- ret = computed ? computed[ name ] : undefined;
+ // getPropertyValue is needed for:
+ // .css('filter') (IE 9 only, #12537)
+ // .css('--customProperty) (#3144)
+ if ( computed ) {
+ ret = computed.getPropertyValue( name ) || computed[ name ];
- // Avoid setting ret to empty string here
- // so we don't default to auto
- if ( ret == null && style && style[ name ] ) {
- ret = style[ name ];
+ if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
+ ret = jQuery.style( elem, name );
}
- // From the awesome hack by Dean Edwards
- // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
-
- // If we're not dealing with a regular pixel number
- // but a number that has a weird ending, we need to convert it to pixels
- // but not position css attributes, as those are proportional to the parent element instead
- // and we can't measure the parent instead because it might trigger a "stacking dolls" problem
- if ( rnumnonpx.test( ret ) && !rposition.test( name ) ) {
+ // A tribute to the "awesome hack by Dean Edwards"
+ // Android Browser returns percentage for some values,
+ // but width seems to be reliably pixels.
+ // This is against the CSSOM draft spec:
+ // https://drafts.csswg.org/cssom/#resolved-values
+ if ( !support.pixelMarginRight() && rnumnonpx.test( ret ) && rmargin.test( name ) ) {
// Remember the original values
- left = style.left;
- rs = elem.runtimeStyle;
- rsLeft = rs && rs.left;
+ width = style.width;
+ minWidth = style.minWidth;
+ maxWidth = style.maxWidth;
// Put in the new values to get a computed value out
- if ( rsLeft ) {
- rs.left = elem.currentStyle.left;
- }
- style.left = name === "fontSize" ? "1em" : ret;
- ret = style.pixelLeft + "px";
+ style.minWidth = style.maxWidth = style.width = ret;
+ ret = computed.width;
// Revert the changed values
- style.left = left;
- if ( rsLeft ) {
- rs.left = rsLeft;
- }
+ style.width = width;
+ style.minWidth = minWidth;
+ style.maxWidth = maxWidth;
}
+ }
+
+ return ret !== undefined ?
- // Support: IE
+ // Support: IE <=9 - 11 only
// IE returns zIndex value as an integer.
- return ret === undefined ?
- ret :
- ret + "" || "auto";
- };
+ ret + "" :
+ ret;
}
-
-
function addGetHookIf( conditionFn, hookFn ) {
+
// Define the hook, we'll check on the first run if it's really needed.
return {
get: function() {
- var condition = conditionFn();
-
- if ( condition == null ) {
- // The test was not ready at this point; screw the hook this time
- // but check again when needed next time.
- return;
- }
+ if ( conditionFn() ) {
- if ( condition ) {
- // Hook not needed (or it's not possible to use it due to missing dependency),
- // remove it.
- // Since there are no other hooks for marginRight, remove the whole object.
+ // Hook not needed (or it's not possible to use it due
+ // to missing dependency), remove it.
delete this.get;
return;
}
// Hook needed; redefine it so that the support test is not executed again.
-
- return (this.get = hookFn).apply( this, arguments );
+ return ( this.get = hookFn ).apply( this, arguments );
}
};
}
-(function() {
- // Minified: var b,c,d,e,f,g, h,i
- var div, style, a, pixelPositionVal, boxSizingReliableVal,
- reliableHiddenOffsetsVal, reliableMarginRightVal;
-
- // Setup
- div = document.createElement( "div" );
- div.innerHTML = " <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
- a = div.getElementsByTagName( "a" )[ 0 ];
- style = a && a.style;
-
- // Finish early in limited (non-browser) environments
- if ( !style ) {
- return;
- }
-
- style.cssText = "float:left;opacity:.5";
-
- // Support: IE<9
- // Make sure that element opacity exists (as opposed to filter)
- support.opacity = style.opacity === "0.5";
-
- // Verify style float existence
- // (IE uses styleFloat instead of cssFloat)
- support.cssFloat = !!style.cssFloat;
-
- div.style.backgroundClip = "content-box";
- div.cloneNode( true ).style.backgroundClip = "";
- support.clearCloneStyle = div.style.backgroundClip === "content-box";
-
- // Support: Firefox<29, Android 2.3
- // Vendor-prefix box-sizing
- support.boxSizing = style.boxSizing === "" || style.MozBoxSizing === "" ||
- style.WebkitBoxSizing === "";
-
- jQuery.extend(support, {
- reliableHiddenOffsets: function() {
- if ( reliableHiddenOffsetsVal == null ) {
- computeStyleTests();
- }
- return reliableHiddenOffsetsVal;
- },
-
- boxSizingReliable: function() {
- if ( boxSizingReliableVal == null ) {
- computeStyleTests();
- }
- return boxSizingReliableVal;
- },
-
- pixelPosition: function() {
- if ( pixelPositionVal == null ) {
- computeStyleTests();
- }
- return pixelPositionVal;
- },
-
- // Support: Android 2.3
- reliableMarginRight: function() {
- if ( reliableMarginRightVal == null ) {
- computeStyleTests();
- }
- return reliableMarginRightVal;
- }
- });
-
- function computeStyleTests() {
- // Minified: var b,c,d,j
- var div, body, container, contents;
-
- body = document.getElementsByTagName( "body" )[ 0 ];
- if ( !body || !body.style ) {
- // Test fired too early or in an unsupported environment, exit.
- return;
- }
-
- // Setup
- div = document.createElement( "div" );
- container = document.createElement( "div" );
- container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
- body.appendChild( container ).appendChild( div );
-
- div.style.cssText =
- // Support: Firefox<29, Android 2.3
- // Vendor-prefix box-sizing
- "-webkit-box-sizing:border-box;-moz-box-sizing:border-box;" +
- "box-sizing:border-box;display:block;margin-top:1%;top:1%;" +
- "border:1px;padding:1px;width:4px;position:absolute";
-
- // Support: IE<9
- // Assume reasonable values in the absence of getComputedStyle
- pixelPositionVal = boxSizingReliableVal = false;
- reliableMarginRightVal = true;
-
- // Check for getComputedStyle so that this code is not run in IE<9.
- if ( window.getComputedStyle ) {
- pixelPositionVal = ( window.getComputedStyle( div, null ) || {} ).top !== "1%";
- boxSizingReliableVal =
- ( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px";
-
- // Support: Android 2.3
- // Div with explicit width and no margin-right incorrectly
- // gets computed margin-right based on width of container (#3333)
- // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
- contents = div.appendChild( document.createElement( "div" ) );
-
- // Reset CSS: box-sizing; display; margin; border; padding
- contents.style.cssText = div.style.cssText =
- // Support: Firefox<29, Android 2.3
- // Vendor-prefix box-sizing
- "-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
- "box-sizing:content-box;display:block;margin:0;border:0;padding:0";
- contents.style.marginRight = contents.style.width = "0";
- div.style.width = "1px";
-
- reliableMarginRightVal =
- !parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight );
- }
-
- // Support: IE8
- // Check if table cells still have offsetWidth/Height when they are set
- // to display:none and there are still other visible table cells in a
- // table row; if so, offsetWidth/Height are not reliable for use when
- // determining if an element has been hidden directly using
- // display:none (it is still safe to use offsets if a parent element is
- // hidden; don safety goggles and see bug #4512 for more information).
- div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
- contents = div.getElementsByTagName( "td" );
- contents[ 0 ].style.cssText = "margin:0;border:0;padding:0;display:none";
- reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
- if ( reliableHiddenOffsetsVal ) {
- contents[ 0 ].style.display = "";
- contents[ 1 ].style.display = "none";
- reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
- }
-
- body.removeChild( container );
- }
-
-})();
-
-
-// A method for quickly swapping in/out CSS properties to get correct calculations.
-jQuery.swap = function( elem, options, callback, args ) {
- var ret, name,
- old = {};
-
- // Remember the old values, and insert the new ones
- for ( name in options ) {
- old[ name ] = elem.style[ name ];
- elem.style[ name ] = options[ name ];
- }
-
- ret = callback.apply( elem, args || [] );
-
- // Revert the old values
- for ( name in options ) {
- elem.style[ name ] = old[ name ];
- }
-
- return ret;
-};
-
-
var
- ralpha = /alpha\([^)]*\)/i,
- ropacity = /opacity\s*=\s*([^)]*)/,
- // swappable if display is none or starts with table except "table", "table-cell", or "table-caption"
- // see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
+ // Swappable if display is none or starts with table
+ // except "table", "table-cell", or "table-caption"
+ // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
rdisplayswap = /^(none|table(?!-c[ea]).+)/,
- rnumsplit = new RegExp( "^(" + pnum + ")(.*)$", "i" ),
- rrelNum = new RegExp( "^([+-])=(" + pnum + ")", "i" ),
-
+ rcustomProp = /^--/,
cssShow = { position: "absolute", visibility: "hidden", display: "block" },
cssNormalTransform = {
letterSpacing: "0",
fontWeight: "400"
},
- cssPrefixes = [ "Webkit", "O", "Moz", "ms" ];
-
+ cssPrefixes = [ "Webkit", "Moz", "ms" ],
+ emptyStyle = document.createElement( "div" ).style;
-// return a css property mapped to a potentially vendor prefixed property
-function vendorPropName( style, name ) {
+// Return a css property mapped to a potentially vendor prefixed property
+function vendorPropName( name ) {
- // shortcut for names that are not vendor prefixed
- if ( name in style ) {
+ // Shortcut for names that are not vendor prefixed
+ if ( name in emptyStyle ) {
return name;
}
- // check for vendor prefixed names
- var capName = name.charAt(0).toUpperCase() + name.slice(1),
- origName = name,
+ // Check for vendor prefixed names
+ var capName = name[ 0 ].toUpperCase() + name.slice( 1 ),
i = cssPrefixes.length;
while ( i-- ) {
name = cssPrefixes[ i ] + capName;
- if ( name in style ) {
+ if ( name in emptyStyle ) {
return name;
}
}
-
- return origName;
}
-function showHide( elements, show ) {
- var display, elem, hidden,
- values = [],
- index = 0,
- length = elements.length;
-
- for ( ; index < length; index++ ) {
- elem = elements[ index ];
- if ( !elem.style ) {
- continue;
- }
-
- values[ index ] = jQuery._data( elem, "olddisplay" );
- display = elem.style.display;
- if ( show ) {
- // Reset the inline display of this element to learn if it is
- // being hidden by cascaded rules or not
- if ( !values[ index ] && display === "none" ) {
- elem.style.display = "";
- }
-
- // Set elements which have been overridden with display: none
- // in a stylesheet to whatever the default browser style is
- // for such an element
- if ( elem.style.display === "" && isHidden( elem ) ) {
- values[ index ] = jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) );
- }
- } else {
- hidden = isHidden( elem );
-
- if ( display && display !== "none" || !hidden ) {
- jQuery._data( elem, "olddisplay", hidden ? display : jQuery.css( elem, "display" ) );
- }
- }
- }
-
- // Set the display of most of the elements in a second loop
- // to avoid the constant reflow
- for ( index = 0; index < length; index++ ) {
- elem = elements[ index ];
- if ( !elem.style ) {
- continue;
- }
- if ( !show || elem.style.display === "none" || elem.style.display === "" ) {
- elem.style.display = show ? values[ index ] || "" : "none";
- }
+// Return a property mapped along what jQuery.cssProps suggests or to
+// a vendor prefixed property.
+function finalPropName( name ) {
+ var ret = jQuery.cssProps[ name ];
+ if ( !ret ) {
+ ret = jQuery.cssProps[ name ] = vendorPropName( name ) || name;
}
-
- return elements;
+ return ret;
}
function setPositiveNumber( elem, value, subtract ) {
- var matches = rnumsplit.exec( value );
+
+ // Any relative (+/-) values have already been
+ // normalized at this point
+ var matches = rcssNum.exec( value );
return matches ?
+
// Guard against undefined "subtract", e.g., when used as in cssHooks
- Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) :
+ Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) :
value;
}
function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
- var i = extra === ( isBorderBox ? "border" : "content" ) ?
- // If we already have the right measurement, avoid augmentation
- 4 :
- // Otherwise initialize for horizontal or vertical properties
- name === "width" ? 1 : 0,
-
+ var i,
val = 0;
+ // If we already have the right measurement, avoid augmentation
+ if ( extra === ( isBorderBox ? "border" : "content" ) ) {
+ i = 4;
+
+ // Otherwise initialize for horizontal or vertical properties
+ } else {
+ i = name === "width" ? 1 : 0;
+ }
+
for ( ; i < 4; i += 2 ) {
- // both box models exclude margin, so add it if we want it
+
+ // Both box models exclude margin, so add it if we want it
if ( extra === "margin" ) {
val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
}
if ( isBorderBox ) {
+
// border-box includes padding, so remove it if we want content
if ( extra === "content" ) {
val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
}
- // at this point, extra isn't border nor margin, so remove border
+ // At this point, extra isn't border nor margin, so remove border
if ( extra !== "margin" ) {
val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
}
} else {
- // at this point, extra isn't content, so add padding
+
+ // At this point, extra isn't content, so add padding
val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
- // at this point, extra isn't content nor padding, so add border
+ // At this point, extra isn't content nor padding, so add border
if ( extra !== "padding" ) {
val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
}
@@ -6552,36 +6342,32 @@ function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
function getWidthOrHeight( elem, name, extra ) {
- // Start with offset property, which is equivalent to the border-box value
- var valueIsBorderBox = true,
- val = name === "width" ? elem.offsetWidth : elem.offsetHeight,
+ // Start with computed style
+ var valueIsBorderBox,
styles = getStyles( elem ),
- isBorderBox = support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
-
- // some non-html elements return undefined for offsetWidth, so check for null/undefined
- // svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285
- // MathML - https://bugzilla.mozilla.org/show_bug.cgi?id=491668
- if ( val <= 0 || val == null ) {
- // Fall back to computed then uncomputed css if necessary
- val = curCSS( elem, name, styles );
- if ( val < 0 || val == null ) {
- val = elem.style[ name ];
- }
+ val = curCSS( elem, name, styles ),
+ isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
- // Computed unit is not pixels. Stop here and return.
- if ( rnumnonpx.test(val) ) {
- return val;
- }
+ // Computed unit is not pixels. Stop here and return.
+ if ( rnumnonpx.test( val ) ) {
+ return val;
+ }
- // we need the check for style in case a browser which returns unreliable values
- // for getComputedStyle silently falls back to the reliable elem.style
- valueIsBorderBox = isBorderBox && ( support.boxSizingReliable() || val === elem.style[ name ] );
+ // Check for style in case a browser which returns unreliable values
+ // for getComputedStyle silently falls back to the reliable elem.style
+ valueIsBorderBox = isBorderBox &&
+ ( support.boxSizingReliable() || val === elem.style[ name ] );
- // Normalize "", auto, and prepare for extra
- val = parseFloat( val ) || 0;
+ // Fall back to offsetWidth/Height when value is "auto"
+ // This happens for inline elements with no explicit setting (gh-3571)
+ if ( val === "auto" ) {
+ val = elem[ "offset" + name[ 0 ].toUpperCase() + name.slice( 1 ) ];
}
- // use the active box-sizing model to add/subtract irrelevant styles
+ // Normalize "", auto, and prepare for extra
+ val = parseFloat( val ) || 0;
+
+ // Use the active box-sizing model to add/subtract irrelevant styles
return ( val +
augmentWidthOrHeight(
elem,
@@ -6593,13 +6379,15 @@ function getWidthOrHeight( elem, name, extra ) {
) + "px";
}
-jQuery.extend({
+jQuery.extend( {
+
// Add in style property hooks for overriding the default
// behavior of getting and setting a style property
cssHooks: {
opacity: {
get: function( elem, computed ) {
if ( computed ) {
+
// We should always get a number back from opacity
var ret = curCSS( elem, "opacity" );
return ret === "" ? "1" : ret;
@@ -6610,6 +6398,7 @@ jQuery.extend({
// Don't automatically add "px" to these possibly-unitless properties
cssNumber: {
+ "animationIterationCount": true,
"columnCount": true,
"fillOpacity": true,
"flexGrow": true,
@@ -6627,12 +6416,12 @@ jQuery.extend({
// Add in properties whose names you wish to fix before
// setting or getting the value
cssProps: {
- // normalize float css property
- "float": support.cssFloat ? "cssFloat" : "styleFloat"
+ "float": "cssFloat"
},
// Get and set the style property on a DOM Node
style: function( elem, name, value, extra ) {
+
// Don't set styles on text and comment nodes
if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
return;
@@ -6641,54 +6430,63 @@ jQuery.extend({
// Make sure that we're working with the right name
var ret, type, hooks,
origName = jQuery.camelCase( name ),
+ isCustomProp = rcustomProp.test( name ),
style = elem.style;
- name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) );
+ // Make sure that we're working with the right name. We don't
+ // want to query the value if it is a CSS custom property
+ // since they are user-defined.
+ if ( !isCustomProp ) {
+ name = finalPropName( origName );
+ }
- // gets hook for the prefixed version
- // followed by the unprefixed version
+ // Gets hook for the prefixed version, then unprefixed version
hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
// Check if we're setting a value
if ( value !== undefined ) {
type = typeof value;
- // convert relative number strings (+= or -=) to relative numbers. #7345
- if ( type === "string" && (ret = rrelNum.exec( value )) ) {
- value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) );
+ // Convert "+=" or "-=" to relative numbers (#7345)
+ if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) {
+ value = adjustCSS( elem, name, ret );
+
// Fixes bug #9237
type = "number";
}
- // Make sure that null and NaN values aren't set. See: #7116
+ // Make sure that null and NaN values aren't set (#7116)
if ( value == null || value !== value ) {
return;
}
- // If a number was passed in, add 'px' to the (except for certain CSS properties)
- if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
- value += "px";
+ // If a number was passed in, add the unit (except for certain CSS properties)
+ if ( type === "number" ) {
+ value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" );
}
- // Fixes #8908, it can be done more correctly by specifing setters in cssHooks,
- // but it would mean to define eight (for every problematic property) identical functions
- if ( !support.clearCloneStyle && value === "" && name.indexOf("background") === 0 ) {
+ // background-* props affect original clone's values
+ if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) {
style[ name ] = "inherit";
}
// If a hook was provided, use that value, otherwise just set the specified value
- if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) {
+ if ( !hooks || !( "set" in hooks ) ||
+ ( value = hooks.set( elem, value, extra ) ) !== undefined ) {
- // Support: IE
- // Swallow errors from 'invalid' CSS values (#5509)
- try {
+ if ( isCustomProp ) {
+ style.setProperty( name, value );
+ } else {
style[ name ] = value;
- } catch(e) {}
+ }
}
} else {
+
// If a hook was provided get the non-computed value from there
- if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
+ if ( hooks && "get" in hooks &&
+ ( ret = hooks.get( elem, false, extra ) ) !== undefined ) {
+
return ret;
}
@@ -6698,14 +6496,18 @@ jQuery.extend({
},
css: function( elem, name, extra, styles ) {
- var num, val, hooks,
- origName = jQuery.camelCase( name );
+ var val, num, hooks,
+ origName = jQuery.camelCase( name ),
+ isCustomProp = rcustomProp.test( name );
- // Make sure that we're working with the right name
- name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) );
+ // Make sure that we're working with the right name. We don't
+ // want to modify the value if it is a CSS custom property
+ // since they are user-defined.
+ if ( !isCustomProp ) {
+ name = finalPropName( origName );
+ }
- // gets hook for the prefixed version
- // followed by the unprefixed version
+ // Try prefixed name followed by the unprefixed name
hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
// If a hook was provided get the computed value from there
@@ -6718,106 +6520,83 @@ jQuery.extend({
val = curCSS( elem, name, styles );
}
- //convert "normal" to computed value
+ // Convert "normal" to computed value
if ( val === "normal" && name in cssNormalTransform ) {
val = cssNormalTransform[ name ];
}
- // Return, converting to number if forced or a qualifier was provided and val looks numeric
+ // Make numeric if forced or a qualifier was provided and val looks numeric
if ( extra === "" || extra ) {
num = parseFloat( val );
- return extra === true || jQuery.isNumeric( num ) ? num || 0 : val;
+ return extra === true || isFinite( num ) ? num || 0 : val;
}
+
return val;
}
-});
+} );
-jQuery.each([ "height", "width" ], function( i, name ) {
+jQuery.each( [ "height", "width" ], function( i, name ) {
jQuery.cssHooks[ name ] = {
get: function( elem, computed, extra ) {
if ( computed ) {
- // certain elements can have dimension info if we invisibly show them
- // however, it must have a current display style that would benefit from this
- return rdisplayswap.test( jQuery.css( elem, "display" ) ) && elem.offsetWidth === 0 ?
- jQuery.swap( elem, cssShow, function() {
- return getWidthOrHeight( elem, name, extra );
- }) :
- getWidthOrHeight( elem, name, extra );
+
+ // Certain elements can have dimension info if we invisibly show them
+ // but it must have a current display style that would benefit
+ return rdisplayswap.test( jQuery.css( elem, "display" ) ) &&
+
+ // Support: Safari 8+
+ // Table columns in Safari have non-zero offsetWidth & zero
+ // getBoundingClientRect().width unless display is changed.
+ // Support: IE <=11 only
+ // Running getBoundingClientRect on a disconnected node
+ // in IE throws an error.
+ ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ?
+ swap( elem, cssShow, function() {
+ return getWidthOrHeight( elem, name, extra );
+ } ) :
+ getWidthOrHeight( elem, name, extra );
}
},
set: function( elem, value, extra ) {
- var styles = extra && getStyles( elem );
- return setPositiveNumber( elem, value, extra ?
- augmentWidthOrHeight(
+ var matches,
+ styles = extra && getStyles( elem ),
+ subtract = extra && augmentWidthOrHeight(
elem,
name,
extra,
- support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+ jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
styles
- ) : 0
- );
- }
- };
-});
-
-if ( !support.opacity ) {
- jQuery.cssHooks.opacity = {
- get: function( elem, computed ) {
- // IE uses filters for opacity
- return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ?
- ( 0.01 * parseFloat( RegExp.$1 ) ) + "" :
- computed ? "1" : "";
- },
-
- set: function( elem, value ) {
- var style = elem.style,
- currentStyle = elem.currentStyle,
- opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "",
- filter = currentStyle && currentStyle.filter || style.filter || "";
-
- // IE has trouble with opacity if it does not have layout
- // Force it by setting the zoom level
- style.zoom = 1;
-
- // if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652
- // if value === "", then remove inline opacity #12685
- if ( ( value >= 1 || value === "" ) &&
- jQuery.trim( filter.replace( ralpha, "" ) ) === "" &&
- style.removeAttribute ) {
+ );
- // Setting style.filter to null, "" & " " still leave "filter:" in the cssText
- // if "filter:" is present at all, clearType is disabled, we want to avoid this
- // style.removeAttribute is IE Only, but so apparently is this code path...
- style.removeAttribute( "filter" );
+ // Convert to pixels if value adjustment is needed
+ if ( subtract && ( matches = rcssNum.exec( value ) ) &&
+ ( matches[ 3 ] || "px" ) !== "px" ) {
- // if there is no filter style applied in a css rule or unset inline opacity, we are done
- if ( value === "" || currentStyle && !currentStyle.filter ) {
- return;
- }
+ elem.style[ name ] = value;
+ value = jQuery.css( elem, name );
}
- // otherwise, set new filter values
- style.filter = ralpha.test( filter ) ?
- filter.replace( ralpha, opacity ) :
- filter + " " + opacity;
+ return setPositiveNumber( elem, value, subtract );
}
};
-}
+} );
-jQuery.cssHooks.marginRight = addGetHookIf( support.reliableMarginRight,
+jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft,
function( elem, computed ) {
if ( computed ) {
- // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
- // Work around by temporarily setting element display to inline-block
- return jQuery.swap( elem, { "display": "inline-block" },
- curCSS, [ elem, "marginRight" ] );
+ return ( parseFloat( curCSS( elem, "marginLeft" ) ) ||
+ elem.getBoundingClientRect().left -
+ swap( elem, { marginLeft: 0 }, function() {
+ return elem.getBoundingClientRect().left;
+ } )
+ ) + "px";
}
}
);
// These hooks are used by animate to expand properties
-jQuery.each({
+jQuery.each( {
margin: "",
padding: "",
border: "Width"
@@ -6827,8 +6606,8 @@ jQuery.each({
var i = 0,
expanded = {},
- // assumes a single number if not a string
- parts = typeof value === "string" ? value.split(" ") : [ value ];
+ // Assumes a single number if not a string
+ parts = typeof value === "string" ? value.split( " " ) : [ value ];
for ( ; i < 4; i++ ) {
expanded[ prefix + cssExpand[ i ] + suffix ] =
@@ -6842,16 +6621,16 @@ jQuery.each({
if ( !rmargin.test( prefix ) ) {
jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
}
-});
+} );
-jQuery.fn.extend({
+jQuery.fn.extend( {
css: function( name, value ) {
return access( this, function( elem, name, value ) {
var styles, len,
map = {},
i = 0;
- if ( jQuery.isArray( name ) ) {
+ if ( Array.isArray( name ) ) {
styles = getStyles( elem );
len = name.length;
@@ -6866,27 +6645,8 @@ jQuery.fn.extend({
jQuery.style( elem, name, value ) :
jQuery.css( elem, name );
}, name, value, arguments.length > 1 );
- },
- show: function() {
- return showHide( this, true );
- },
- hide: function() {
- return showHide( this );
- },
- toggle: function( state ) {
- if ( typeof state === "boolean" ) {
- return state ? this.show() : this.hide();
- }
-
- return this.each(function() {
- if ( isHidden( this ) ) {
- jQuery( this ).show();
- } else {
- jQuery( this ).hide();
- }
- });
}
-});
+} );
function Tween( elem, options, prop, end, easing ) {
@@ -6899,7 +6659,7 @@ Tween.prototype = {
init: function( elem, options, prop, end, easing, unit ) {
this.elem = elem;
this.prop = prop;
- this.easing = easing || "swing";
+ this.easing = easing || jQuery.easing._default;
this.options = options;
this.start = this.now = this.cur();
this.end = end;
@@ -6945,25 +6705,32 @@ Tween.propHooks = {
get: function( tween ) {
var result;
- if ( tween.elem[ tween.prop ] != null &&
- (!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) {
+ // Use a property on the element directly when it is not a DOM element,
+ // or when there is no matching style property that exists.
+ if ( tween.elem.nodeType !== 1 ||
+ tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) {
return tween.elem[ tween.prop ];
}
- // passing an empty string as a 3rd parameter to .css will automatically
- // attempt a parseFloat and fallback to a string if the parse fails
- // so, simple values such as "10px" are parsed to Float.
- // complex values such as "rotate(1rad)" are returned as is.
+ // Passing an empty string as a 3rd parameter to .css will automatically
+ // attempt a parseFloat and fallback to a string if the parse fails.
+ // Simple values such as "10px" are parsed to Float;
+ // complex values such as "rotate(1rad)" are returned as-is.
result = jQuery.css( tween.elem, tween.prop, "" );
+
// Empty strings, null, undefined and "auto" are converted to 0.
return !result || result === "auto" ? 0 : result;
},
set: function( tween ) {
- // use step hook for back compat - use cssHook if its there - use .style if its
- // available and use plain properties where available
+
+ // Use step hook for back compat.
+ // Use cssHook if its there.
+ // Use .style if available and use plain properties where available.
if ( jQuery.fx.step[ tween.prop ] ) {
jQuery.fx.step[ tween.prop ]( tween );
- } else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) {
+ } else if ( tween.elem.nodeType === 1 &&
+ ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null ||
+ jQuery.cssHooks[ tween.prop ] ) ) {
jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
} else {
tween.elem[ tween.prop ] = tween.now;
@@ -6972,9 +6739,8 @@ Tween.propHooks = {
}
};
-// Support: IE <=9
+// Support: IE <=9 only
// Panic based approach to setting things on disconnected nodes
-
Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
set: function( tween ) {
if ( tween.elem.nodeType && tween.elem.parentNode ) {
@@ -6989,92 +6755,53 @@ jQuery.easing = {
},
swing: function( p ) {
return 0.5 - Math.cos( p * Math.PI ) / 2;
- }
+ },
+ _default: "swing"
};
jQuery.fx = Tween.prototype.init;
-// Back Compat <1.8 extension point
+// Back compat <1.8 extension point
jQuery.fx.step = {};
var
- fxNow, timerId,
+ fxNow, inProgress,
rfxtypes = /^(?:toggle|show|hide)$/,
- rfxnum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ),
- rrun = /queueHooks$/,
- animationPrefilters = [ defaultPrefilter ],
- tweeners = {
- "*": [ function( prop, value ) {
- var tween = this.createTween( prop, value ),
- target = tween.cur(),
- parts = rfxnum.exec( value ),
- unit = parts && parts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
-
- // Starting value computation is required for potential unit mismatches
- start = ( jQuery.cssNumber[ prop ] || unit !== "px" && +target ) &&
- rfxnum.exec( jQuery.css( tween.elem, prop ) ),
- scale = 1,
- maxIterations = 20;
-
- if ( start && start[ 3 ] !== unit ) {
- // Trust units reported by jQuery.css
- unit = unit || start[ 3 ];
-
- // Make sure we update the tween properties later on
- parts = parts || [];
-
- // Iteratively approximate from a nonzero starting point
- start = +target || 1;
-
- do {
- // If previous iteration zeroed out, double until we get *something*
- // Use a string for doubling factor so we don't accidentally see scale as unchanged below
- scale = scale || ".5";
+ rrun = /queueHooks$/;
- // Adjust and apply
- start = start / scale;
- jQuery.style( tween.elem, prop, start + unit );
-
- // Update scale, tolerating zero or NaN from tween.cur()
- // And breaking the loop if scale is unchanged or perfect, or if we've just had enough
- } while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations );
- }
-
- // Update tween properties
- if ( parts ) {
- start = tween.start = +start || +target || 0;
- tween.unit = unit;
- // If a +=/-= token was provided, we're doing a relative animation
- tween.end = parts[ 1 ] ?
- start + ( parts[ 1 ] + 1 ) * parts[ 2 ] :
- +parts[ 2 ];
- }
+function schedule() {
+ if ( inProgress ) {
+ if ( document.hidden === false && window.requestAnimationFrame ) {
+ window.requestAnimationFrame( schedule );
+ } else {
+ window.setTimeout( schedule, jQuery.fx.interval );
+ }
- return tween;
- } ]
- };
+ jQuery.fx.tick();
+ }
+}
// Animations created synchronously will run synchronously
function createFxNow() {
- setTimeout(function() {
+ window.setTimeout( function() {
fxNow = undefined;
- });
+ } );
return ( fxNow = jQuery.now() );
}
// Generate parameters to create a standard animation
function genFx( type, includeWidth ) {
var which,
- attrs = { height: type },
- i = 0;
+ i = 0,
+ attrs = { height: type };
- // if we include width, step value is 1 to do all cssExpand values,
- // if we don't include width, step value is 2 to skip over Left and Right
+ // If we include width, step value is 1 to do all cssExpand values,
+ // otherwise step value is 2 to skip over Left and Right
includeWidth = includeWidth ? 1 : 0;
- for ( ; i < 4 ; i += 2 - includeWidth ) {
+ for ( ; i < 4; i += 2 - includeWidth ) {
which = cssExpand[ i ];
attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
}
@@ -7088,28 +6815,28 @@ function genFx( type, includeWidth ) {
function createTween( value, prop, animation ) {
var tween,
- collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ),
+ collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ),
index = 0,
length = collection.length;
for ( ; index < length; index++ ) {
- if ( (tween = collection[ index ].call( animation, prop, value )) ) {
+ if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) {
- // we're done with this property
+ // We're done with this property
return tween;
}
}
}
function defaultPrefilter( elem, props, opts ) {
- /* jshint validthis: true */
- var prop, value, toggle, tween, hooks, oldfire, display, checkDisplay,
+ var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display,
+ isBox = "width" in props || "height" in props,
anim = this,
orig = {},
style = elem.style,
- hidden = elem.nodeType && isHidden( elem ),
- dataShow = jQuery._data( elem, "fxshow" );
+ hidden = elem.nodeType && isHiddenWithinTree( elem ),
+ dataShow = dataPriv.get( elem, "fxshow" );
- // handle queue: false promises
+ // Queue-skipping animations hijack the fx hooks
if ( !opts.queue ) {
hooks = jQuery._queueHooks( elem, "fx" );
if ( hooks.unqueued == null ) {
@@ -7123,122 +6850,151 @@ function defaultPrefilter( elem, props, opts ) {
}
hooks.unqueued++;
- anim.always(function() {
- // doing this makes sure that the complete handler will be called
- // before this completes
- anim.always(function() {
+ anim.always( function() {
+
+ // Ensure the complete handler is called before this completes
+ anim.always( function() {
hooks.unqueued--;
if ( !jQuery.queue( elem, "fx" ).length ) {
hooks.empty.fire();
}
- });
- });
- }
-
- // height/width overflow pass
- if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) {
- // Make sure that nothing sneaks out
- // Record all 3 overflow attributes because IE does not
- // change the overflow attribute when overflowX and
- // overflowY are set to the same value
- opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
-
- // Set display property to inline-block for height/width
- // animations on inline elements that are having width/height animated
- display = jQuery.css( elem, "display" );
-
- // Test default display if display is currently "none"
- checkDisplay = display === "none" ?
- jQuery._data( elem, "olddisplay" ) || defaultDisplay( elem.nodeName ) : display;
-
- if ( checkDisplay === "inline" && jQuery.css( elem, "float" ) === "none" ) {
-
- // inline-level elements accept inline-block;
- // block-level elements need to be inline with layout
- if ( !support.inlineBlockNeedsLayout || defaultDisplay( elem.nodeName ) === "inline" ) {
- style.display = "inline-block";
- } else {
- style.zoom = 1;
- }
- }
- }
-
- if ( opts.overflow ) {
- style.overflow = "hidden";
- if ( !support.shrinkWrapBlocks() ) {
- anim.always(function() {
- style.overflow = opts.overflow[ 0 ];
- style.overflowX = opts.overflow[ 1 ];
- style.overflowY = opts.overflow[ 2 ];
- });
- }
+ } );
+ } );
}
- // show/hide pass
+ // Detect show/hide animations
for ( prop in props ) {
value = props[ prop ];
- if ( rfxtypes.exec( value ) ) {
+ if ( rfxtypes.test( value ) ) {
delete props[ prop ];
toggle = toggle || value === "toggle";
if ( value === ( hidden ? "hide" : "show" ) ) {
- // If there is dataShow left over from a stopped hide or show and we are going to proceed with show, we should pretend to be hidden
+ // Pretend to be hidden if this is a "show" and
+ // there is still data from a stopped show/hide
if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
hidden = true;
+
+ // Ignore all other no-op show/hide data
} else {
continue;
}
}
orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
-
- // Any non-fx value stops us from restoring the original display value
- } else {
- display = undefined;
}
}
- if ( !jQuery.isEmptyObject( orig ) ) {
- if ( dataShow ) {
- if ( "hidden" in dataShow ) {
- hidden = dataShow.hidden;
- }
- } else {
- dataShow = jQuery._data( elem, "fxshow", {} );
- }
+ // Bail out if this is a no-op like .hide().hide()
+ propTween = !jQuery.isEmptyObject( props );
+ if ( !propTween && jQuery.isEmptyObject( orig ) ) {
+ return;
+ }
+
+ // Restrict "overflow" and "display" styles during box animations
+ if ( isBox && elem.nodeType === 1 ) {
- // store state if its toggle - enables .stop().toggle() to "reverse"
- if ( toggle ) {
- dataShow.hidden = !hidden;
+ // Support: IE <=9 - 11, Edge 12 - 13
+ // Record all 3 overflow attributes because IE does not infer the shorthand
+ // from identically-valued overflowX and overflowY
+ opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
+
+ // Identify a display type, preferring old show/hide data over the CSS cascade
+ restoreDisplay = dataShow && dataShow.display;
+ if ( restoreDisplay == null ) {
+ restoreDisplay = dataPriv.get( elem, "display" );
}
- if ( hidden ) {
- jQuery( elem ).show();
- } else {
- anim.done(function() {
- jQuery( elem ).hide();
- });
+ display = jQuery.css( elem, "display" );
+ if ( display === "none" ) {
+ if ( restoreDisplay ) {
+ display = restoreDisplay;
+ } else {
+
+ // Get nonempty value(s) by temporarily forcing visibility
+ showHide( [ elem ], true );
+ restoreDisplay = elem.style.display || restoreDisplay;
+ display = jQuery.css( elem, "display" );
+ showHide( [ elem ] );
+ }
}
- anim.done(function() {
- var prop;
- jQuery._removeData( elem, "fxshow" );
- for ( prop in orig ) {
- jQuery.style( elem, prop, orig[ prop ] );
+
+ // Animate inline elements as inline-block
+ if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) {
+ if ( jQuery.css( elem, "float" ) === "none" ) {
+
+ // Restore the original display value at the end of pure show/hide animations
+ if ( !propTween ) {
+ anim.done( function() {
+ style.display = restoreDisplay;
+ } );
+ if ( restoreDisplay == null ) {
+ display = style.display;
+ restoreDisplay = display === "none" ? "" : display;
+ }
+ }
+ style.display = "inline-block";
}
- });
- for ( prop in orig ) {
- tween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
+ }
+ }
- if ( !( prop in dataShow ) ) {
- dataShow[ prop ] = tween.start;
- if ( hidden ) {
- tween.end = tween.start;
- tween.start = prop === "width" || prop === "height" ? 1 : 0;
+ if ( opts.overflow ) {
+ style.overflow = "hidden";
+ anim.always( function() {
+ style.overflow = opts.overflow[ 0 ];
+ style.overflowX = opts.overflow[ 1 ];
+ style.overflowY = opts.overflow[ 2 ];
+ } );
+ }
+
+ // Implement show/hide animations
+ propTween = false;
+ for ( prop in orig ) {
+
+ // General show/hide setup for this element animation
+ if ( !propTween ) {
+ if ( dataShow ) {
+ if ( "hidden" in dataShow ) {
+ hidden = dataShow.hidden;
}
+ } else {
+ dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } );
+ }
+
+ // Store hidden/visible for toggle so `.stop().toggle()` "reverses"
+ if ( toggle ) {
+ dataShow.hidden = !hidden;
+ }
+
+ // Show elements before animating them
+ if ( hidden ) {
+ showHide( [ elem ], true );
}
+
+ /* eslint-disable no-loop-func */
+
+ anim.done( function() {
+
+ /* eslint-enable no-loop-func */
+
+ // The final step of a "hide" animation is actually hiding the element
+ if ( !hidden ) {
+ showHide( [ elem ] );
+ }
+ dataPriv.remove( elem, "fxshow" );
+ for ( prop in orig ) {
+ jQuery.style( elem, prop, orig[ prop ] );
+ }
+ } );
}
- // If this is a noop like .hide().hide(), restore an overwritten display value
- } else if ( (display === "none" ? defaultDisplay( elem.nodeName ) : display) === "inline" ) {
- style.display = display;
+ // Per-property setup
+ propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
+ if ( !( prop in dataShow ) ) {
+ dataShow[ prop ] = propTween.start;
+ if ( hidden ) {
+ propTween.end = propTween.start;
+ propTween.start = 0;
+ }
+ }
}
}
@@ -7250,7 +7006,7 @@ function propFilter( props, specialEasing ) {
name = jQuery.camelCase( index );
easing = specialEasing[ name ];
value = props[ index ];
- if ( jQuery.isArray( value ) ) {
+ if ( Array.isArray( value ) ) {
easing = value[ 1 ];
value = props[ index ] = value[ 0 ];
}
@@ -7265,8 +7021,8 @@ function propFilter( props, specialEasing ) {
value = hooks.expand( value );
delete props[ name ];
- // not quite $.extend, this wont overwrite keys already present.
- // also - reusing 'index' from above because we have the correct "name"
+ // Not quite $.extend, this won't overwrite existing keys.
+ // Reusing 'index' because we have the correct "name"
for ( index in value ) {
if ( !( index in props ) ) {
props[ index ] = value[ index ];
@@ -7283,40 +7039,53 @@ function Animation( elem, properties, options ) {
var result,
stopped,
index = 0,
- length = animationPrefilters.length,
+ length = Animation.prefilters.length,
deferred = jQuery.Deferred().always( function() {
- // don't match elem in the :animated selector
+
+ // Don't match elem in the :animated selector
delete tick.elem;
- }),
+ } ),
tick = function() {
if ( stopped ) {
return false;
}
var currentTime = fxNow || createFxNow(),
remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
- // archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497)
+
+ // Support: Android 2.3 only
+ // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497)
temp = remaining / animation.duration || 0,
percent = 1 - temp,
index = 0,
length = animation.tweens.length;
- for ( ; index < length ; index++ ) {
+ for ( ; index < length; index++ ) {
animation.tweens[ index ].run( percent );
}
- deferred.notifyWith( elem, [ animation, percent, remaining ]);
+ deferred.notifyWith( elem, [ animation, percent, remaining ] );
+ // If there's more to do, yield
if ( percent < 1 && length ) {
return remaining;
- } else {
- deferred.resolveWith( elem, [ animation ] );
- return false;
}
+
+ // If this was an empty animation, synthesize a final progress notification
+ if ( !length ) {
+ deferred.notifyWith( elem, [ animation, 1, 0 ] );
+ }
+
+ // Resolve the animation and report its conclusion
+ deferred.resolveWith( elem, [ animation ] );
+ return false;
},
- animation = deferred.promise({
+ animation = deferred.promise( {
elem: elem,
props: jQuery.extend( {}, properties ),
- opts: jQuery.extend( true, { specialEasing: {} }, options ),
+ opts: jQuery.extend( true, {
+ specialEasing: {},
+ easing: jQuery.easing._default
+ }, options ),
originalProperties: properties,
originalOptions: options,
startTime: fxNow || createFxNow(),
@@ -7330,34 +7099,39 @@ function Animation( elem, properties, options ) {
},
stop: function( gotoEnd ) {
var index = 0,
- // if we are going to the end, we want to run all the tweens
+
+ // If we are going to the end, we want to run all the tweens
// otherwise we skip this part
length = gotoEnd ? animation.tweens.length : 0;
if ( stopped ) {
return this;
}
stopped = true;
- for ( ; index < length ; index++ ) {
+ for ( ; index < length; index++ ) {
animation.tweens[ index ].run( 1 );
}
- // resolve when we played the last frame
- // otherwise, reject
+ // Resolve when we played the last frame; otherwise, reject
if ( gotoEnd ) {
+ deferred.notifyWith( elem, [ animation, 1, 0 ] );
deferred.resolveWith( elem, [ animation, gotoEnd ] );
} else {
deferred.rejectWith( elem, [ animation, gotoEnd ] );
}
return this;
}
- }),
+ } ),
props = animation.props;
propFilter( props, animation.opts.specialEasing );
- for ( ; index < length ; index++ ) {
- result = animationPrefilters[ index ].call( animation, elem, props, animation.opts );
+ for ( ; index < length; index++ ) {
+ result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts );
if ( result ) {
+ if ( jQuery.isFunction( result.stop ) ) {
+ jQuery._queueHooks( animation.elem, animation.opts.queue ).stop =
+ jQuery.proxy( result.stop, result );
+ }
return result;
}
}
@@ -7368,49 +7142,63 @@ function Animation( elem, properties, options ) {
animation.opts.start.call( elem, animation );
}
+ // Attach callbacks from options
+ animation
+ .progress( animation.opts.progress )
+ .done( animation.opts.done, animation.opts.complete )
+ .fail( animation.opts.fail )
+ .always( animation.opts.always );
+
jQuery.fx.timer(
jQuery.extend( tick, {
elem: elem,
anim: animation,
queue: animation.opts.queue
- })
+ } )
);
- // attach callbacks from options
- return animation.progress( animation.opts.progress )
- .done( animation.opts.done, animation.opts.complete )
- .fail( animation.opts.fail )
- .always( animation.opts.always );
+ return animation;
}
jQuery.Animation = jQuery.extend( Animation, {
+
+ tweeners: {
+ "*": [ function( prop, value ) {
+ var tween = this.createTween( prop, value );
+ adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween );
+ return tween;
+ } ]
+ },
+
tweener: function( props, callback ) {
if ( jQuery.isFunction( props ) ) {
callback = props;
props = [ "*" ];
} else {
- props = props.split(" ");
+ props = props.match( rnothtmlwhite );
}
var prop,
index = 0,
length = props.length;
- for ( ; index < length ; index++ ) {
+ for ( ; index < length; index++ ) {
prop = props[ index ];
- tweeners[ prop ] = tweeners[ prop ] || [];
- tweeners[ prop ].unshift( callback );
+ Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || [];
+ Animation.tweeners[ prop ].unshift( callback );
}
},
+ prefilters: [ defaultPrefilter ],
+
prefilter: function( callback, prepend ) {
if ( prepend ) {
- animationPrefilters.unshift( callback );
+ Animation.prefilters.unshift( callback );
} else {
- animationPrefilters.push( callback );
+ Animation.prefilters.push( callback );
}
}
-});
+} );
jQuery.speed = function( speed, easing, fn ) {
var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
@@ -7420,10 +7208,22 @@ jQuery.speed = function( speed, easing, fn ) {
easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
};
- opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
- opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
+ // Go to the end state if fx are off
+ if ( jQuery.fx.off ) {
+ opt.duration = 0;
- // normalize opt.queue - true/undefined/null -> "fx"
+ } else {
+ if ( typeof opt.duration !== "number" ) {
+ if ( opt.duration in jQuery.fx.speeds ) {
+ opt.duration = jQuery.fx.speeds[ opt.duration ];
+
+ } else {
+ opt.duration = jQuery.fx.speeds._default;
+ }
+ }
+ }
+
+ // Normalize opt.queue - true/undefined/null -> "fx"
if ( opt.queue == null || opt.queue === true ) {
opt.queue = "fx";
}
@@ -7444,24 +7244,25 @@ jQuery.speed = function( speed, easing, fn ) {
return opt;
};
-jQuery.fn.extend({
+jQuery.fn.extend( {
fadeTo: function( speed, to, easing, callback ) {
- // show any hidden elements after setting opacity to 0
- return this.filter( isHidden ).css( "opacity", 0 ).show()
+ // Show any hidden elements after setting opacity to 0
+ return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show()
- // animate to the value specified
- .end().animate({ opacity: to }, speed, easing, callback );
+ // Animate to the value specified
+ .end().animate( { opacity: to }, speed, easing, callback );
},
animate: function( prop, speed, easing, callback ) {
var empty = jQuery.isEmptyObject( prop ),
optall = jQuery.speed( speed, easing, callback ),
doAnimation = function() {
+
// Operate on a copy of prop so per-property easing won't be lost
var anim = Animation( this, jQuery.extend( {}, prop ), optall );
// Empty animations, or finishing resolves immediately
- if ( empty || jQuery._data( this, "finish" ) ) {
+ if ( empty || dataPriv.get( this, "finish" ) ) {
anim.stop( true );
}
};
@@ -7487,11 +7288,11 @@ jQuery.fn.extend({
this.queue( type || "fx", [] );
}
- return this.each(function() {
+ return this.each( function() {
var dequeue = true,
index = type != null && type + "queueHooks",
timers = jQuery.timers,
- data = jQuery._data( this );
+ data = dataPriv.get( this );
if ( index ) {
if ( data[ index ] && data[ index ].stop ) {
@@ -7506,44 +7307,46 @@ jQuery.fn.extend({
}
for ( index = timers.length; index--; ) {
- if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
+ if ( timers[ index ].elem === this &&
+ ( type == null || timers[ index ].queue === type ) ) {
+
timers[ index ].anim.stop( gotoEnd );
dequeue = false;
timers.splice( index, 1 );
}
}
- // start the next in the queue if the last step wasn't forced
- // timers currently will call their complete callbacks, which will dequeue
- // but only if they were gotoEnd
+ // Start the next in the queue if the last step wasn't forced.
+ // Timers currently will call their complete callbacks, which
+ // will dequeue but only if they were gotoEnd.
if ( dequeue || !gotoEnd ) {
jQuery.dequeue( this, type );
}
- });
+ } );
},
finish: function( type ) {
if ( type !== false ) {
type = type || "fx";
}
- return this.each(function() {
+ return this.each( function() {
var index,
- data = jQuery._data( this ),
+ data = dataPriv.get( this ),
queue = data[ type + "queue" ],
hooks = data[ type + "queueHooks" ],
timers = jQuery.timers,
length = queue ? queue.length : 0;
- // enable finishing flag on private data
+ // Enable finishing flag on private data
data.finish = true;
- // empty the queue first
+ // Empty the queue first
jQuery.queue( this, type, [] );
if ( hooks && hooks.stop ) {
hooks.stop.call( this, true );
}
- // look for any active animations, and finish them
+ // Look for any active animations, and finish them
for ( index = timers.length; index--; ) {
if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
timers[ index ].anim.stop( true );
@@ -7551,33 +7354,33 @@ jQuery.fn.extend({
}
}
- // look for any animations in the old queue and finish them
+ // Look for any animations in the old queue and finish them
for ( index = 0; index < length; index++ ) {
if ( queue[ index ] && queue[ index ].finish ) {
queue[ index ].finish.call( this );
}
}
- // turn off finishing flag
+ // Turn off finishing flag
delete data.finish;
- });
+ } );
}
-});
+} );
-jQuery.each([ "toggle", "show", "hide" ], function( i, name ) {
+jQuery.each( [ "toggle", "show", "hide" ], function( i, name ) {
var cssFn = jQuery.fn[ name ];
jQuery.fn[ name ] = function( speed, easing, callback ) {
return speed == null || typeof speed === "boolean" ?
cssFn.apply( this, arguments ) :
this.animate( genFx( name, true ), speed, easing, callback );
};
-});
+} );
// Generate shortcuts for custom animations
-jQuery.each({
- slideDown: genFx("show"),
- slideUp: genFx("hide"),
- slideToggle: genFx("toggle"),
+jQuery.each( {
+ slideDown: genFx( "show" ),
+ slideUp: genFx( "hide" ),
+ slideToggle: genFx( "toggle" ),
fadeIn: { opacity: "show" },
fadeOut: { opacity: "hide" },
fadeToggle: { opacity: "toggle" }
@@ -7585,19 +7388,20 @@ jQuery.each({
jQuery.fn[ name ] = function( speed, easing, callback ) {
return this.animate( props, speed, easing, callback );
};
-});
+} );
jQuery.timers = [];
jQuery.fx.tick = function() {
var timer,
- timers = jQuery.timers,
- i = 0;
+ i = 0,
+ timers = jQuery.timers;
fxNow = jQuery.now();
for ( ; i < timers.length; i++ ) {
timer = timers[ i ];
- // Checks the timer has not already been removed
+
+ // Run the timer and safely remove it when done (allowing for external removal)
if ( !timer() && timers[ i ] === timer ) {
timers.splice( i--, 1 );
}
@@ -7611,383 +7415,138 @@ jQuery.fx.tick = function() {
jQuery.fx.timer = function( timer ) {
jQuery.timers.push( timer );
- if ( timer() ) {
- jQuery.fx.start();
- } else {
- jQuery.timers.pop();
- }
+ jQuery.fx.start();
};
jQuery.fx.interval = 13;
-
jQuery.fx.start = function() {
- if ( !timerId ) {
- timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval );
+ if ( inProgress ) {
+ return;
}
+
+ inProgress = true;
+ schedule();
};
jQuery.fx.stop = function() {
- clearInterval( timerId );
- timerId = null;
+ inProgress = null;
};
jQuery.fx.speeds = {
slow: 600,
fast: 200,
+
// Default speed
_default: 400
};
// Based off of the plugin by Clint Helfers, with permission.
-// http://blindsignals.com/index.php/2009/07/jquery-delay/
+// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/
jQuery.fn.delay = function( time, type ) {
time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
type = type || "fx";
return this.queue( type, function( next, hooks ) {
- var timeout = setTimeout( next, time );
+ var timeout = window.setTimeout( next, time );
hooks.stop = function() {
- clearTimeout( timeout );
+ window.clearTimeout( timeout );
};
- });
+ } );
};
-(function() {
- // Minified: var a,b,c,d,e
- var input, div, select, a, opt;
-
- // Setup
- div = document.createElement( "div" );
- div.setAttribute( "className", "t" );
- div.innerHTML = " <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
- a = div.getElementsByTagName("a")[ 0 ];
-
- // First batch of tests.
- select = document.createElement("select");
- opt = select.appendChild( document.createElement("option") );
- input = div.getElementsByTagName("input")[ 0 ];
-
- a.style.cssText = "top:1px";
-
- // Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
- support.getSetAttribute = div.className !== "t";
-
- // Get the style information from getAttribute
- // (IE uses .cssText instead)
- support.style = /top/.test( a.getAttribute("style") );
+( function() {
+ var input = document.createElement( "input" ),
+ select = document.createElement( "select" ),
+ opt = select.appendChild( document.createElement( "option" ) );
- // Make sure that URLs aren't manipulated
- // (IE normalizes it by default)
- support.hrefNormalized = a.getAttribute("href") === "/a";
+ input.type = "checkbox";
- // Check the default checkbox/radio value ("" on WebKit; "on" elsewhere)
- support.checkOn = !!input.value;
+ // Support: Android <=4.3 only
+ // Default value for a checkbox should be "on"
+ support.checkOn = input.value !== "";
- // Make sure that a selected-by-default option has a working selected property.
- // (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
+ // Support: IE <=11 only
+ // Must access selectedIndex to make default options select
support.optSelected = opt.selected;
- // Tests for enctype support on a form (#6743)
- support.enctype = !!document.createElement("form").enctype;
-
- // Make sure that the options inside disabled selects aren't marked as disabled
- // (WebKit marks them as disabled)
- select.disabled = true;
- support.optDisabled = !opt.disabled;
-
- // Support: IE8 only
- // Check if we can trust getAttribute("value")
+ // Support: IE <=11 only
+ // An input loses its value after becoming a radio
input = document.createElement( "input" );
- input.setAttribute( "value", "" );
- support.input = input.getAttribute( "value" ) === "";
-
- // Check if an input maintains its value after becoming a radio
input.value = "t";
- input.setAttribute( "type", "radio" );
+ input.type = "radio";
support.radioValue = input.value === "t";
-})();
-
-
-var rreturn = /\r/g;
+} )();
-jQuery.fn.extend({
- val: function( value ) {
- var hooks, ret, isFunction,
- elem = this[0];
- if ( !arguments.length ) {
- if ( elem ) {
- hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+var boolHook,
+ attrHandle = jQuery.expr.attrHandle;
- if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
- return ret;
- }
+jQuery.fn.extend( {
+ attr: function( name, value ) {
+ return access( this, jQuery.attr, name, value, arguments.length > 1 );
+ },
- ret = elem.value;
+ removeAttr: function( name ) {
+ return this.each( function() {
+ jQuery.removeAttr( this, name );
+ } );
+ }
+} );
- return typeof ret === "string" ?
- // handle most common string cases
- ret.replace(rreturn, "") :
- // handle cases where value is null/undef or number
- ret == null ? "" : ret;
- }
+jQuery.extend( {
+ attr: function( elem, name, value ) {
+ var ret, hooks,
+ nType = elem.nodeType;
+ // Don't get/set attributes on text, comment and attribute nodes
+ if ( nType === 3 || nType === 8 || nType === 2 ) {
return;
}
- isFunction = jQuery.isFunction( value );
+ // Fallback to prop when attributes are not supported
+ if ( typeof elem.getAttribute === "undefined" ) {
+ return jQuery.prop( elem, name, value );
+ }
- return this.each(function( i ) {
- var val;
+ // Attribute hooks are determined by the lowercase version
+ // Grab necessary hook if one is defined
+ if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+ hooks = jQuery.attrHooks[ name.toLowerCase() ] ||
+ ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined );
+ }
- if ( this.nodeType !== 1 ) {
+ if ( value !== undefined ) {
+ if ( value === null ) {
+ jQuery.removeAttr( elem, name );
return;
}
- if ( isFunction ) {
- val = value.call( this, i, jQuery( this ).val() );
- } else {
- val = value;
+ if ( hooks && "set" in hooks &&
+ ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
+ return ret;
}
- // Treat null/undefined as ""; convert numbers to string
- if ( val == null ) {
- val = "";
- } else if ( typeof val === "number" ) {
- val += "";
- } else if ( jQuery.isArray( val ) ) {
- val = jQuery.map( val, function( value ) {
- return value == null ? "" : value + "";
- });
- }
+ elem.setAttribute( name, value + "" );
+ return value;
+ }
- hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
+ if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
+ return ret;
+ }
- // If set returns undefined, fall back to normal setting
- if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
- this.value = val;
- }
- });
- }
-});
+ ret = jQuery.find.attr( elem, name );
-jQuery.extend({
- valHooks: {
- option: {
- get: function( elem ) {
- var val = jQuery.find.attr( elem, "value" );
- return val != null ?
- val :
- // Support: IE10-11+
- // option.text throws exceptions (#14686, #14858)
- jQuery.trim( jQuery.text( elem ) );
- }
- },
- select: {
- get: function( elem ) {
- var value, option,
- options = elem.options,
- index = elem.selectedIndex,
- one = elem.type === "select-one" || index < 0,
- values = one ? null : [],
- max = one ? index + 1 : options.length,
- i = index < 0 ?
- max :
- one ? index : 0;
-
- // Loop through all the selected options
- for ( ; i < max; i++ ) {
- option = options[ i ];
-
- // oldIE doesn't update selected after form reset (#2551)
- if ( ( option.selected || i === index ) &&
- // Don't return options that are disabled or in a disabled optgroup
- ( support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) &&
- ( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) {
-
- // Get the specific value for the option
- value = jQuery( option ).val();
-
- // We don't need an array for one selects
- if ( one ) {
- return value;
- }
-
- // Multi-Selects return an array
- values.push( value );
- }
- }
-
- return values;
- },
-
- set: function( elem, value ) {
- var optionSet, option,
- options = elem.options,
- values = jQuery.makeArray( value ),
- i = options.length;
-
- while ( i-- ) {
- option = options[ i ];
-
- if ( jQuery.inArray( jQuery.valHooks.option.get( option ), values ) >= 0 ) {
-
- // Support: IE6
- // When new option element is added to select box we need to
- // force reflow of newly added node in order to workaround delay
- // of initialization properties
- try {
- option.selected = optionSet = true;
-
- } catch ( _ ) {
-
- // Will be executed only in IE6
- option.scrollHeight;
- }
-
- } else {
- option.selected = false;
- }
- }
-
- // Force browsers to behave consistently when non-matching value is set
- if ( !optionSet ) {
- elem.selectedIndex = -1;
- }
-
- return options;
- }
- }
- }
-});
-
-// Radios and checkboxes getter/setter
-jQuery.each([ "radio", "checkbox" ], function() {
- jQuery.valHooks[ this ] = {
- set: function( elem, value ) {
- if ( jQuery.isArray( value ) ) {
- return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
- }
- }
- };
- if ( !support.checkOn ) {
- jQuery.valHooks[ this ].get = function( elem ) {
- // Support: Webkit
- // "" is returned instead of "on" if a value isn't specified
- return elem.getAttribute("value") === null ? "on" : elem.value;
- };
- }
-});
-
-
-
-
-var nodeHook, boolHook,
- attrHandle = jQuery.expr.attrHandle,
- ruseDefault = /^(?:checked|selected)$/i,
- getSetAttribute = support.getSetAttribute,
- getSetInput = support.input;
-
-jQuery.fn.extend({
- attr: function( name, value ) {
- return access( this, jQuery.attr, name, value, arguments.length > 1 );
- },
-
- removeAttr: function( name ) {
- return this.each(function() {
- jQuery.removeAttr( this, name );
- });
- }
-});
-
-jQuery.extend({
- attr: function( elem, name, value ) {
- var hooks, ret,
- nType = elem.nodeType;
-
- // don't get/set attributes on text, comment and attribute nodes
- if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
- return;
- }
-
- // Fallback to prop when attributes are not supported
- if ( typeof elem.getAttribute === strundefined ) {
- return jQuery.prop( elem, name, value );
- }
-
- // All attributes are lowercase
- // Grab necessary hook if one is defined
- if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
- name = name.toLowerCase();
- hooks = jQuery.attrHooks[ name ] ||
- ( jQuery.expr.match.bool.test( name ) ? boolHook : nodeHook );
- }
-
- if ( value !== undefined ) {
-
- if ( value === null ) {
- jQuery.removeAttr( elem, name );
-
- } else if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
- return ret;
-
- } else {
- elem.setAttribute( name, value + "" );
- return value;
- }
-
- } else if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
- return ret;
-
- } else {
- ret = jQuery.find.attr( elem, name );
-
- // Non-existent attributes return null, we normalize to undefined
- return ret == null ?
- undefined :
- ret;
- }
- },
-
- removeAttr: function( elem, value ) {
- var name, propName,
- i = 0,
- attrNames = value && value.match( rnotwhite );
-
- if ( attrNames && elem.nodeType === 1 ) {
- while ( (name = attrNames[i++]) ) {
- propName = jQuery.propFix[ name ] || name;
-
- // Boolean attributes get special treatment (#10870)
- if ( jQuery.expr.match.bool.test( name ) ) {
- // Set corresponding property to false
- if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
- elem[ propName ] = false;
- // Support: IE<9
- // Also clear defaultChecked/defaultSelected (if appropriate)
- } else {
- elem[ jQuery.camelCase( "default-" + name ) ] =
- elem[ propName ] = false;
- }
-
- // See #9699 for explanation of this approach (setting first, then removal)
- } else {
- jQuery.attr( elem, name, "" );
- }
-
- elem.removeAttribute( getSetAttribute ? name : propName );
- }
- }
+ // Non-existent attributes return null, we normalize to undefined
+ return ret == null ? undefined : ret;
},
attrHooks: {
type: {
set: function( elem, value ) {
- if ( !support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
- // Setting the type on a radio button after the value resets the value in IE6-9
- // Reset value to default in case type is set after value during creation
+ if ( !support.radioValue && value === "radio" &&
+ nodeName( elem, "input" ) ) {
var val = elem.value;
elem.setAttribute( "type", value );
if ( val ) {
@@ -7997,264 +7556,181 @@ jQuery.extend({
}
}
}
+ },
+
+ removeAttr: function( elem, value ) {
+ var name,
+ i = 0,
+
+ // Attribute names can contain non-HTML whitespace characters
+ // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2
+ attrNames = value && value.match( rnothtmlwhite );
+
+ if ( attrNames && elem.nodeType === 1 ) {
+ while ( ( name = attrNames[ i++ ] ) ) {
+ elem.removeAttribute( name );
+ }
+ }
}
-});
+} );
-// Hook for boolean attributes
+// Hooks for boolean attributes
boolHook = {
set: function( elem, value, name ) {
if ( value === false ) {
+
// Remove boolean attributes when set to false
jQuery.removeAttr( elem, name );
- } else if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
- // IE<8 needs the *property* name
- elem.setAttribute( !getSetAttribute && jQuery.propFix[ name ] || name, name );
-
- // Use defaultChecked and defaultSelected for oldIE
} else {
- elem[ jQuery.camelCase( "default-" + name ) ] = elem[ name ] = true;
+ elem.setAttribute( name, name );
}
-
return name;
}
};
-// Retrieve booleans specially
jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
-
var getter = attrHandle[ name ] || jQuery.find.attr;
- attrHandle[ name ] = getSetInput && getSetAttribute || !ruseDefault.test( name ) ?
- function( elem, name, isXML ) {
- var ret, handle;
- if ( !isXML ) {
- // Avoid an infinite loop by temporarily removing this function from the getter
- handle = attrHandle[ name ];
- attrHandle[ name ] = ret;
- ret = getter( elem, name, isXML ) != null ?
- name.toLowerCase() :
- null;
- attrHandle[ name ] = handle;
- }
- return ret;
- } :
- function( elem, name, isXML ) {
- if ( !isXML ) {
- return elem[ jQuery.camelCase( "default-" + name ) ] ?
- name.toLowerCase() :
- null;
- }
- };
-});
-
-// fix oldIE attroperties
-if ( !getSetInput || !getSetAttribute ) {
- jQuery.attrHooks.value = {
- set: function( elem, value, name ) {
- if ( jQuery.nodeName( elem, "input" ) ) {
- // Does not return so that setAttribute is also used
- elem.defaultValue = value;
- } else {
- // Use nodeHook if defined (#1954); otherwise setAttribute is fine
- return nodeHook && nodeHook.set( elem, value, name );
- }
- }
- };
-}
-
-// IE6/7 do not support getting/setting some attributes with get/setAttribute
-if ( !getSetAttribute ) {
-
- // Use this for any attribute in IE6/7
- // This fixes almost every IE6/7 issue
- nodeHook = {
- set: function( elem, value, name ) {
- // Set the existing or create a new attribute node
- var ret = elem.getAttributeNode( name );
- if ( !ret ) {
- elem.setAttributeNode(
- (ret = elem.ownerDocument.createAttribute( name ))
- );
- }
-
- ret.value = value += "";
-
- // Break association with cloned elements by also using setAttribute (#9646)
- if ( name === "value" || value === elem.getAttribute( name ) ) {
- return value;
- }
- }
- };
-
- // Some attributes are constructed with empty-string values when not defined
- attrHandle.id = attrHandle.name = attrHandle.coords =
- function( elem, name, isXML ) {
- var ret;
- if ( !isXML ) {
- return (ret = elem.getAttributeNode( name )) && ret.value !== "" ?
- ret.value :
- null;
- }
- };
-
- // Fixing value retrieval on a button requires this module
- jQuery.valHooks.button = {
- get: function( elem, name ) {
- var ret = elem.getAttributeNode( name );
- if ( ret && ret.specified ) {
- return ret.value;
- }
- },
- set: nodeHook.set
- };
-
- // Set contenteditable to false on removals(#10429)
- // Setting to empty string throws an error as an invalid value
- jQuery.attrHooks.contenteditable = {
- set: function( elem, value, name ) {
- nodeHook.set( elem, value === "" ? false : value, name );
- }
- };
+ attrHandle[ name ] = function( elem, name, isXML ) {
+ var ret, handle,
+ lowercaseName = name.toLowerCase();
- // Set width and height to auto instead of 0 on empty string( Bug #8150 )
- // This is for removals
- jQuery.each([ "width", "height" ], function( i, name ) {
- jQuery.attrHooks[ name ] = {
- set: function( elem, value ) {
- if ( value === "" ) {
- elem.setAttribute( name, "auto" );
- return value;
- }
- }
- };
- });
-}
+ if ( !isXML ) {
-if ( !support.style ) {
- jQuery.attrHooks.style = {
- get: function( elem ) {
- // Return undefined in the case of empty string
- // Note: IE uppercases css property names, but if we were to .toLowerCase()
- // .cssText, that would destroy case senstitivity in URL's, like in "background"
- return elem.style.cssText || undefined;
- },
- set: function( elem, value ) {
- return ( elem.style.cssText = value + "" );
+ // Avoid an infinite loop by temporarily removing this function from the getter
+ handle = attrHandle[ lowercaseName ];
+ attrHandle[ lowercaseName ] = ret;
+ ret = getter( elem, name, isXML ) != null ?
+ lowercaseName :
+ null;
+ attrHandle[ lowercaseName ] = handle;
}
+ return ret;
};
-}
+} );
-var rfocusable = /^(?:input|select|textarea|button|object)$/i,
+var rfocusable = /^(?:input|select|textarea|button)$/i,
rclickable = /^(?:a|area)$/i;
-jQuery.fn.extend({
+jQuery.fn.extend( {
prop: function( name, value ) {
return access( this, jQuery.prop, name, value, arguments.length > 1 );
},
removeProp: function( name ) {
- name = jQuery.propFix[ name ] || name;
- return this.each(function() {
- // try/catch handles cases where IE balks (such as removing a property on window)
- try {
- this[ name ] = undefined;
- delete this[ name ];
- } catch( e ) {}
- });
+ return this.each( function() {
+ delete this[ jQuery.propFix[ name ] || name ];
+ } );
}
-});
-
-jQuery.extend({
- propFix: {
- "for": "htmlFor",
- "class": "className"
- },
+} );
+jQuery.extend( {
prop: function( elem, name, value ) {
- var ret, hooks, notxml,
+ var ret, hooks,
nType = elem.nodeType;
- // don't get/set properties on text, comment and attribute nodes
- if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+ // Don't get/set properties on text, comment and attribute nodes
+ if ( nType === 3 || nType === 8 || nType === 2 ) {
return;
}
- notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
+ if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
- if ( notxml ) {
// Fix name and attach hooks
name = jQuery.propFix[ name ] || name;
hooks = jQuery.propHooks[ name ];
}
if ( value !== undefined ) {
- return hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ?
- ret :
- ( elem[ name ] = value );
+ if ( hooks && "set" in hooks &&
+ ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
+ return ret;
+ }
- } else {
- return hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ?
- ret :
- elem[ name ];
+ return ( elem[ name ] = value );
}
+
+ if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
+ return ret;
+ }
+
+ return elem[ name ];
},
propHooks: {
tabIndex: {
get: function( elem ) {
- // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
- // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
+
+ // Support: IE <=9 - 11 only
+ // elem.tabIndex doesn't always return the
+ // correct value when it hasn't been explicitly set
+ // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
// Use proper attribute retrieval(#12072)
var tabindex = jQuery.find.attr( elem, "tabindex" );
- return tabindex ?
- parseInt( tabindex, 10 ) :
- rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
- 0 :
- -1;
+ if ( tabindex ) {
+ return parseInt( tabindex, 10 );
+ }
+
+ if (
+ rfocusable.test( elem.nodeName ) ||
+ rclickable.test( elem.nodeName ) &&
+ elem.href
+ ) {
+ return 0;
+ }
+
+ return -1;
}
}
- }
-});
+ },
-// Some attributes require a special call on IE
-// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !support.hrefNormalized ) {
- // href/src property should get the full normalized URL (#10299/#12915)
- jQuery.each([ "href", "src" ], function( i, name ) {
- jQuery.propHooks[ name ] = {
- get: function( elem ) {
- return elem.getAttribute( name, 4 );
- }
- };
- });
-}
+ propFix: {
+ "for": "htmlFor",
+ "class": "className"
+ }
+} );
-// Support: Safari, IE9+
-// mis-reports the default selected property of an option
-// Accessing the parent's selectedIndex property fixes it
+// Support: IE <=11 only
+// Accessing the selectedIndex property
+// forces the browser to respect setting selected
+// on the option
+// The getter ensures a default option is selected
+// when in an optgroup
+// eslint rule "no-unused-expressions" is disabled for this code
+// since it considers such accessions noop
if ( !support.optSelected ) {
jQuery.propHooks.selected = {
get: function( elem ) {
+
+ /* eslint no-unused-expressions: "off" */
+
var parent = elem.parentNode;
+ if ( parent && parent.parentNode ) {
+ parent.parentNode.selectedIndex;
+ }
+ return null;
+ },
+ set: function( elem ) {
+
+ /* eslint no-unused-expressions: "off" */
+ var parent = elem.parentNode;
if ( parent ) {
parent.selectedIndex;
- // Make sure that it also works with optgroups, see #5701
if ( parent.parentNode ) {
parent.parentNode.selectedIndex;
}
}
- return null;
}
};
}
-jQuery.each([
+jQuery.each( [
"tabIndex",
"readOnly",
"maxLength",
@@ -8267,54 +7743,53 @@ jQuery.each([
"contentEditable"
], function() {
jQuery.propFix[ this.toLowerCase() ] = this;
-});
+} );
-// IE6/7 call enctype encoding
-if ( !support.enctype ) {
- jQuery.propFix.enctype = "encoding";
-}
+ // Strip and collapse whitespace according to HTML spec
+ // https://html.spec.whatwg.org/multipage/infrastructure.html#strip-and-collapse-whitespace
+ function stripAndCollapse( value ) {
+ var tokens = value.match( rnothtmlwhite ) || [];
+ return tokens.join( " " );
+ }
+
-var rclass = /[\t\r\n\f]/g;
+function getClass( elem ) {
+ return elem.getAttribute && elem.getAttribute( "class" ) || "";
+}
-jQuery.fn.extend({
+jQuery.fn.extend( {
addClass: function( value ) {
- var classes, elem, cur, clazz, j, finalValue,
- i = 0,
- len = this.length,
- proceed = typeof value === "string" && value;
+ var classes, elem, cur, curValue, clazz, j, finalValue,
+ i = 0;
if ( jQuery.isFunction( value ) ) {
- return this.each(function( j ) {
- jQuery( this ).addClass( value.call( this, j, this.className ) );
- });
+ return this.each( function( j ) {
+ jQuery( this ).addClass( value.call( this, j, getClass( this ) ) );
+ } );
}
- if ( proceed ) {
- // The disjunction here is for better compressibility (see removeClass)
- classes = ( value || "" ).match( rnotwhite ) || [];
+ if ( typeof value === "string" && value ) {
+ classes = value.match( rnothtmlwhite ) || [];
- for ( ; i < len; i++ ) {
- elem = this[ i ];
- cur = elem.nodeType === 1 && ( elem.className ?
- ( " " + elem.className + " " ).replace( rclass, " " ) :
- " "
- );
+ while ( ( elem = this[ i++ ] ) ) {
+ curValue = getClass( elem );
+ cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
if ( cur ) {
j = 0;
- while ( (clazz = classes[j++]) ) {
+ while ( ( clazz = classes[ j++ ] ) ) {
if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
cur += clazz + " ";
}
}
- // only assign if different to avoid unneeded rendering.
- finalValue = jQuery.trim( cur );
- if ( elem.className !== finalValue ) {
- elem.className = finalValue;
+ // Only assign if different to avoid unneeded rendering.
+ finalValue = stripAndCollapse( cur );
+ if ( curValue !== finalValue ) {
+ elem.setAttribute( "class", finalValue );
}
}
}
@@ -8324,40 +7799,42 @@ jQuery.fn.extend({
},
removeClass: function( value ) {
- var classes, elem, cur, clazz, j, finalValue,
- i = 0,
- len = this.length,
- proceed = arguments.length === 0 || typeof value === "string" && value;
+ var classes, elem, cur, curValue, clazz, j, finalValue,
+ i = 0;
if ( jQuery.isFunction( value ) ) {
- return this.each(function( j ) {
- jQuery( this ).removeClass( value.call( this, j, this.className ) );
- });
+ return this.each( function( j ) {
+ jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) );
+ } );
}
- if ( proceed ) {
- classes = ( value || "" ).match( rnotwhite ) || [];
- for ( ; i < len; i++ ) {
- elem = this[ i ];
+ if ( !arguments.length ) {
+ return this.attr( "class", "" );
+ }
+
+ if ( typeof value === "string" && value ) {
+ classes = value.match( rnothtmlwhite ) || [];
+
+ while ( ( elem = this[ i++ ] ) ) {
+ curValue = getClass( elem );
+
// This expression is here for better compressibility (see addClass)
- cur = elem.nodeType === 1 && ( elem.className ?
- ( " " + elem.className + " " ).replace( rclass, " " ) :
- ""
- );
+ cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
if ( cur ) {
j = 0;
- while ( (clazz = classes[j++]) ) {
+ while ( ( clazz = classes[ j++ ] ) ) {
+
// Remove *all* instances
- while ( cur.indexOf( " " + clazz + " " ) >= 0 ) {
+ while ( cur.indexOf( " " + clazz + " " ) > -1 ) {
cur = cur.replace( " " + clazz + " ", " " );
}
}
- // only assign if different to avoid unneeded rendering.
- finalValue = value ? jQuery.trim( cur ) : "";
- if ( elem.className !== finalValue ) {
- elem.className = finalValue;
+ // Only assign if different to avoid unneeded rendering.
+ finalValue = stripAndCollapse( cur );
+ if ( curValue !== finalValue ) {
+ elem.setAttribute( "class", finalValue );
}
}
}
@@ -8374,67 +7851,437 @@ jQuery.fn.extend({
}
if ( jQuery.isFunction( value ) ) {
- return this.each(function( i ) {
- jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
- });
+ return this.each( function( i ) {
+ jQuery( this ).toggleClass(
+ value.call( this, i, getClass( this ), stateVal ),
+ stateVal
+ );
+ } );
}
- return this.each(function() {
+ return this.each( function() {
+ var className, i, self, classNames;
+
if ( type === "string" ) {
- // toggle individual class names
- var className,
- i = 0,
- self = jQuery( this ),
- classNames = value.match( rnotwhite ) || [];
-
- while ( (className = classNames[ i++ ]) ) {
- // check each className given, space separated list
- if ( self.hasClass( className ) ) {
- self.removeClass( className );
- } else {
+
+ // Toggle individual class names
+ i = 0;
+ self = jQuery( this );
+ classNames = value.match( rnothtmlwhite ) || [];
+
+ while ( ( className = classNames[ i++ ] ) ) {
+
+ // Check each className given, space separated list
+ if ( self.hasClass( className ) ) {
+ self.removeClass( className );
+ } else {
self.addClass( className );
}
- }
+ }
+
+ // Toggle whole class name
+ } else if ( value === undefined || type === "boolean" ) {
+ className = getClass( this );
+ if ( className ) {
+
+ // Store className if set
+ dataPriv.set( this, "__className__", className );
+ }
+
+ // If the element has a class name or if we're passed `false`,
+ // then remove the whole classname (if there was one, the above saved it).
+ // Otherwise bring back whatever was previously saved (if anything),
+ // falling back to the empty string if nothing was stored.
+ if ( this.setAttribute ) {
+ this.setAttribute( "class",
+ className || value === false ?
+ "" :
+ dataPriv.get( this, "__className__" ) || ""
+ );
+ }
+ }
+ } );
+ },
+
+ hasClass: function( selector ) {
+ var className, elem,
+ i = 0;
+
+ className = " " + selector + " ";
+ while ( ( elem = this[ i++ ] ) ) {
+ if ( elem.nodeType === 1 &&
+ ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+} );
+
+
+
+
+var rreturn = /\r/g;
+
+jQuery.fn.extend( {
+ val: function( value ) {
+ var hooks, ret, isFunction,
+ elem = this[ 0 ];
+
+ if ( !arguments.length ) {
+ if ( elem ) {
+ hooks = jQuery.valHooks[ elem.type ] ||
+ jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+
+ if ( hooks &&
+ "get" in hooks &&
+ ( ret = hooks.get( elem, "value" ) ) !== undefined
+ ) {
+ return ret;
+ }
+
+ ret = elem.value;
+
+ // Handle most common string cases
+ if ( typeof ret === "string" ) {
+ return ret.replace( rreturn, "" );
+ }
+
+ // Handle cases where value is null/undef or number
+ return ret == null ? "" : ret;
+ }
+
+ return;
+ }
+
+ isFunction = jQuery.isFunction( value );
+
+ return this.each( function( i ) {
+ var val;
+
+ if ( this.nodeType !== 1 ) {
+ return;
+ }
+
+ if ( isFunction ) {
+ val = value.call( this, i, jQuery( this ).val() );
+ } else {
+ val = value;
+ }
+
+ // Treat null/undefined as ""; convert numbers to string
+ if ( val == null ) {
+ val = "";
+
+ } else if ( typeof val === "number" ) {
+ val += "";
+
+ } else if ( Array.isArray( val ) ) {
+ val = jQuery.map( val, function( value ) {
+ return value == null ? "" : value + "";
+ } );
+ }
+
+ hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
+
+ // If set returns undefined, fall back to normal setting
+ if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) {
+ this.value = val;
+ }
+ } );
+ }
+} );
+
+jQuery.extend( {
+ valHooks: {
+ option: {
+ get: function( elem ) {
+
+ var val = jQuery.find.attr( elem, "value" );
+ return val != null ?
+ val :
+
+ // Support: IE <=10 - 11 only
+ // option.text throws exceptions (#14686, #14858)
+ // Strip and collapse whitespace
+ // https://html.spec.whatwg.org/#strip-and-collapse-whitespace
+ stripAndCollapse( jQuery.text( elem ) );
+ }
+ },
+ select: {
+ get: function( elem ) {
+ var value, option, i,
+ options = elem.options,
+ index = elem.selectedIndex,
+ one = elem.type === "select-one",
+ values = one ? null : [],
+ max = one ? index + 1 : options.length;
+
+ if ( index < 0 ) {
+ i = max;
+
+ } else {
+ i = one ? index : 0;
+ }
+
+ // Loop through all the selected options
+ for ( ; i < max; i++ ) {
+ option = options[ i ];
+
+ // Support: IE <=9 only
+ // IE8-9 doesn't update selected after form reset (#2551)
+ if ( ( option.selected || i === index ) &&
+
+ // Don't return options that are disabled or in a disabled optgroup
+ !option.disabled &&
+ ( !option.parentNode.disabled ||
+ !nodeName( option.parentNode, "optgroup" ) ) ) {
+
+ // Get the specific value for the option
+ value = jQuery( option ).val();
+
+ // We don't need an array for one selects
+ if ( one ) {
+ return value;
+ }
+
+ // Multi-Selects return an array
+ values.push( value );
+ }
+ }
+
+ return values;
+ },
+
+ set: function( elem, value ) {
+ var optionSet, option,
+ options = elem.options,
+ values = jQuery.makeArray( value ),
+ i = options.length;
+
+ while ( i-- ) {
+ option = options[ i ];
+
+ /* eslint-disable no-cond-assign */
+
+ if ( option.selected =
+ jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1
+ ) {
+ optionSet = true;
+ }
+
+ /* eslint-enable no-cond-assign */
+ }
+
+ // Force browsers to behave consistently when non-matching value is set
+ if ( !optionSet ) {
+ elem.selectedIndex = -1;
+ }
+ return values;
+ }
+ }
+ }
+} );
+
+// Radios and checkboxes getter/setter
+jQuery.each( [ "radio", "checkbox" ], function() {
+ jQuery.valHooks[ this ] = {
+ set: function( elem, value ) {
+ if ( Array.isArray( value ) ) {
+ return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 );
+ }
+ }
+ };
+ if ( !support.checkOn ) {
+ jQuery.valHooks[ this ].get = function( elem ) {
+ return elem.getAttribute( "value" ) === null ? "on" : elem.value;
+ };
+ }
+} );
+
+
+
+
+// Return jQuery for attributes-only inclusion
+
+
+var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/;
+
+jQuery.extend( jQuery.event, {
+
+ trigger: function( event, data, elem, onlyHandlers ) {
+
+ var i, cur, tmp, bubbleType, ontype, handle, special,
+ eventPath = [ elem || document ],
+ type = hasOwn.call( event, "type" ) ? event.type : event,
+ namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : [];
+
+ cur = tmp = elem = elem || document;
+
+ // Don't do events on text and comment nodes
+ if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
+ return;
+ }
+
+ // focus/blur morphs to focusin/out; ensure we're not firing them right now
+ if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
+ return;
+ }
+
+ if ( type.indexOf( "." ) > -1 ) {
+
+ // Namespaced trigger; create a regexp to match event type in handle()
+ namespaces = type.split( "." );
+ type = namespaces.shift();
+ namespaces.sort();
+ }
+ ontype = type.indexOf( ":" ) < 0 && "on" + type;
+
+ // Caller can pass in a jQuery.Event object, Object, or just an event type string
+ event = event[ jQuery.expando ] ?
+ event :
+ new jQuery.Event( type, typeof event === "object" && event );
+
+ // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
+ event.isTrigger = onlyHandlers ? 2 : 3;
+ event.namespace = namespaces.join( "." );
+ event.rnamespace = event.namespace ?
+ new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) :
+ null;
+
+ // Clean up the event in case it is being reused
+ event.result = undefined;
+ if ( !event.target ) {
+ event.target = elem;
+ }
+
+ // Clone any incoming data and prepend the event, creating the handler arg list
+ data = data == null ?
+ [ event ] :
+ jQuery.makeArray( data, [ event ] );
+
+ // Allow special events to draw outside the lines
+ special = jQuery.event.special[ type ] || {};
+ if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
+ return;
+ }
+
+ // Determine event propagation path in advance, per W3C events spec (#9951)
+ // Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
+ if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
+
+ bubbleType = special.delegateType || type;
+ if ( !rfocusMorph.test( bubbleType + type ) ) {
+ cur = cur.parentNode;
+ }
+ for ( ; cur; cur = cur.parentNode ) {
+ eventPath.push( cur );
+ tmp = cur;
+ }
+
+ // Only add window if we got to document (e.g., not plain obj or detached DOM)
+ if ( tmp === ( elem.ownerDocument || document ) ) {
+ eventPath.push( tmp.defaultView || tmp.parentWindow || window );
+ }
+ }
+
+ // Fire handlers on the event path
+ i = 0;
+ while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) {
+
+ event.type = i > 1 ?
+ bubbleType :
+ special.bindType || type;
+
+ // jQuery handler
+ handle = ( dataPriv.get( cur, "events" ) || {} )[ event.type ] &&
+ dataPriv.get( cur, "handle" );
+ if ( handle ) {
+ handle.apply( cur, data );
+ }
+
+ // Native handler
+ handle = ontype && cur[ ontype ];
+ if ( handle && handle.apply && acceptData( cur ) ) {
+ event.result = handle.apply( cur, data );
+ if ( event.result === false ) {
+ event.preventDefault();
+ }
+ }
+ }
+ event.type = type;
+
+ // If nobody prevented the default action, do it now
+ if ( !onlyHandlers && !event.isDefaultPrevented() ) {
+
+ if ( ( !special._default ||
+ special._default.apply( eventPath.pop(), data ) === false ) &&
+ acceptData( elem ) ) {
+
+ // Call a native DOM method on the target with the same name as the event.
+ // Don't do default actions on window, that's where global variables be (#6170)
+ if ( ontype && jQuery.isFunction( elem[ type ] ) && !jQuery.isWindow( elem ) ) {
+
+ // Don't re-trigger an onFOO event when we call its FOO() method
+ tmp = elem[ ontype ];
+
+ if ( tmp ) {
+ elem[ ontype ] = null;
+ }
- // Toggle whole class name
- } else if ( type === strundefined || type === "boolean" ) {
- if ( this.className ) {
- // store className if set
- jQuery._data( this, "__className__", this.className );
- }
+ // Prevent re-triggering of the same event, since we already bubbled it above
+ jQuery.event.triggered = type;
+ elem[ type ]();
+ jQuery.event.triggered = undefined;
- // If the element has a class name or if we're passed "false",
- // then remove the whole classname (if there was one, the above saved it).
- // Otherwise bring back whatever was previously saved (if anything),
- // falling back to the empty string if nothing was stored.
- this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
+ if ( tmp ) {
+ elem[ ontype ] = tmp;
+ }
+ }
}
- });
+ }
+
+ return event.result;
},
- hasClass: function( selector ) {
- var className = " " + selector + " ",
- i = 0,
- l = this.length;
- for ( ; i < l; i++ ) {
- if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) {
- return true;
+ // Piggyback on a donor event to simulate a different one
+ // Used only for `focus(in | out)` events
+ simulate: function( type, elem, event ) {
+ var e = jQuery.extend(
+ new jQuery.Event(),
+ event,
+ {
+ type: type,
+ isSimulated: true
}
- }
+ );
- return false;
+ jQuery.event.trigger( e, null, elem );
}
-});
+} );
+jQuery.fn.extend( {
-
-// Return jQuery for attributes-only inclusion
+ trigger: function( type, data ) {
+ return this.each( function() {
+ jQuery.event.trigger( type, data, this );
+ } );
+ },
+ triggerHandler: function( type, data ) {
+ var elem = this[ 0 ];
+ if ( elem ) {
+ return jQuery.event.trigger( type, data, elem, true );
+ }
+ }
+} );
-jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
+jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " +
"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
- "change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
+ "change select submit keydown keypress keyup contextmenu" ).split( " " ),
+ function( i, name ) {
// Handle event binding
jQuery.fn[ name ] = function( data, fn ) {
@@ -8442,100 +8289,85 @@ jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblcl
this.on( name, null, data, fn ) :
this.trigger( name );
};
-});
+} );
-jQuery.fn.extend({
+jQuery.fn.extend( {
hover: function( fnOver, fnOut ) {
return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
- },
-
- bind: function( types, data, fn ) {
- return this.on( types, null, data, fn );
- },
- unbind: function( types, fn ) {
- return this.off( types, null, fn );
- },
-
- delegate: function( selector, types, data, fn ) {
- return this.on( types, selector, data, fn );
- },
- undelegate: function( selector, types, fn ) {
- // ( namespace ) or ( selector, types [, fn] )
- return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn );
}
-});
+} );
-var nonce = jQuery.now();
-var rquery = (/\?/);
+support.focusin = "onfocusin" in window;
-var rvalidtokens = /(,)|(\[|{)|(}|])|"(?:[^"\\\r\n]|\\["\\\/bfnrt]|\\u[\da-fA-F]{4})*"\s*:?|true|false|null|-?(?!0\d)\d+(?:\.\d+|)(?:[eE][+-]?\d+|)/g;
+// Support: Firefox <=44
+// Firefox doesn't have focus(in | out) events
+// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787
+//
+// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1
+// focus(in | out) events fire after focus & blur events,
+// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order
+// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857
+if ( !support.focusin ) {
+ jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) {
-jQuery.parseJSON = function( data ) {
- // Attempt to parse using the native JSON parser first
- if ( window.JSON && window.JSON.parse ) {
- // Support: Android 2.3
- // Workaround failure to string-cast null input
- return window.JSON.parse( data + "" );
- }
+ // Attach a single capturing handler on the document while someone wants focusin/focusout
+ var handler = function( event ) {
+ jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) );
+ };
- var requireNonComma,
- depth = null,
- str = jQuery.trim( data + "" );
+ jQuery.event.special[ fix ] = {
+ setup: function() {
+ var doc = this.ownerDocument || this,
+ attaches = dataPriv.access( doc, fix );
- // Guard against invalid (and possibly dangerous) input by ensuring that nothing remains
- // after removing valid tokens
- return str && !jQuery.trim( str.replace( rvalidtokens, function( token, comma, open, close ) {
+ if ( !attaches ) {
+ doc.addEventListener( orig, handler, true );
+ }
+ dataPriv.access( doc, fix, ( attaches || 0 ) + 1 );
+ },
+ teardown: function() {
+ var doc = this.ownerDocument || this,
+ attaches = dataPriv.access( doc, fix ) - 1;
- // Force termination if we see a misplaced comma
- if ( requireNonComma && comma ) {
- depth = 0;
- }
+ if ( !attaches ) {
+ doc.removeEventListener( orig, handler, true );
+ dataPriv.remove( doc, fix );
- // Perform no more replacements after returning to outermost depth
- if ( depth === 0 ) {
- return token;
- }
+ } else {
+ dataPriv.access( doc, fix, attaches );
+ }
+ }
+ };
+ } );
+}
+var location = window.location;
- // Commas must not follow "[", "{", or ","
- requireNonComma = open || comma;
+var nonce = jQuery.now();
- // Determine new depth
- // array/object open ("[" or "{"): depth += true - false (increment)
- // array/object close ("]" or "}"): depth += false - true (decrement)
- // other cases ("," or primitive): depth += true - true (numeric cast)
- depth += !close - !open;
+var rquery = ( /\?/ );
- // Remove this token
- return "";
- }) ) ?
- ( Function( "return " + str ) )() :
- jQuery.error( "Invalid JSON: " + data );
-};
// Cross-browser xml parsing
jQuery.parseXML = function( data ) {
- var xml, tmp;
+ var xml;
if ( !data || typeof data !== "string" ) {
return null;
}
+
+ // Support: IE 9 - 11 only
+ // IE throws on parseFromString with invalid input.
try {
- if ( window.DOMParser ) { // Standard
- tmp = new DOMParser();
- xml = tmp.parseFromString( data, "text/xml" );
- } else { // IE
- xml = new ActiveXObject( "Microsoft.XMLDOM" );
- xml.async = "false";
- xml.loadXML( data );
- }
- } catch( e ) {
+ xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" );
+ } catch ( e ) {
xml = undefined;
}
- if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
+
+ if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) {
jQuery.error( "Invalid XML: " + data );
}
return xml;
@@ -8543,18 +8375,134 @@ jQuery.parseXML = function( data ) {
var
- // Document location
- ajaxLocParts,
- ajaxLocation,
+ rbracket = /\[\]$/,
+ rCRLF = /\r?\n/g,
+ rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
+ rsubmittable = /^(?:input|select|textarea|keygen)/i;
+
+function buildParams( prefix, obj, traditional, add ) {
+ var name;
+
+ if ( Array.isArray( obj ) ) {
+
+ // Serialize array item.
+ jQuery.each( obj, function( i, v ) {
+ if ( traditional || rbracket.test( prefix ) ) {
+
+ // Treat each array item as a scalar.
+ add( prefix, v );
+
+ } else {
+
+ // Item is non-scalar (array or object), encode its numeric index.
+ buildParams(
+ prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]",
+ v,
+ traditional,
+ add
+ );
+ }
+ } );
+
+ } else if ( !traditional && jQuery.type( obj ) === "object" ) {
+
+ // Serialize object item.
+ for ( name in obj ) {
+ buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+ }
+
+ } else {
+
+ // Serialize scalar item.
+ add( prefix, obj );
+ }
+}
+
+// Serialize an array of form elements or a set of
+// key/values into a query string
+jQuery.param = function( a, traditional ) {
+ var prefix,
+ s = [],
+ add = function( key, valueOrFunction ) {
+ // If value is a function, invoke it and use its return value
+ var value = jQuery.isFunction( valueOrFunction ) ?
+ valueOrFunction() :
+ valueOrFunction;
+
+ s[ s.length ] = encodeURIComponent( key ) + "=" +
+ encodeURIComponent( value == null ? "" : value );
+ };
+
+ // If an array was passed in, assume that it is an array of form elements.
+ if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
+
+ // Serialize the form elements
+ jQuery.each( a, function() {
+ add( this.name, this.value );
+ } );
+
+ } else {
+
+ // If traditional, encode the "old" way (the way 1.3.2 or older
+ // did it), otherwise encode params recursively.
+ for ( prefix in a ) {
+ buildParams( prefix, a[ prefix ], traditional, add );
+ }
+ }
+
+ // Return the resulting serialization
+ return s.join( "&" );
+};
+
+jQuery.fn.extend( {
+ serialize: function() {
+ return jQuery.param( this.serializeArray() );
+ },
+ serializeArray: function() {
+ return this.map( function() {
+
+ // Can add propHook for "elements" to filter or add form elements
+ var elements = jQuery.prop( this, "elements" );
+ return elements ? jQuery.makeArray( elements ) : this;
+ } )
+ .filter( function() {
+ var type = this.type;
+
+ // Use .is( ":disabled" ) so that fieldset[disabled] works
+ return this.name && !jQuery( this ).is( ":disabled" ) &&
+ rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
+ ( this.checked || !rcheckableType.test( type ) );
+ } )
+ .map( function( i, elem ) {
+ var val = jQuery( this ).val();
+
+ if ( val == null ) {
+ return null;
+ }
+
+ if ( Array.isArray( val ) ) {
+ return jQuery.map( val, function( val ) {
+ return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+ } );
+ }
+
+ return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+ } ).get();
+ }
+} );
+
+
+var
+ r20 = /%20/g,
rhash = /#.*$/,
- rts = /([?&])_=[^&]*/,
- rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
+ rantiCache = /([?&])_=[^&]*/,
+ rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg,
+
// #7653, #8125, #8152: local protocol detection
rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
rnoContent = /^(?:GET|HEAD)$/,
rprotocol = /^\/\//,
- rurl = /^([\w.+-]+:)(?:\/\/(?:[^\/?#]*@|)([^\/?#:]*)(?::(\d+)|)|)/,
/* Prefilters
* 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
@@ -8575,22 +8523,11 @@ var
transports = {},
// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
- allTypes = "*/".concat("*");
-
-// #8138, IE may throw an exception when accessing
-// a field from window.location if document.domain has been set
-try {
- ajaxLocation = location.href;
-} catch( e ) {
- // Use the href attribute of an A element
- // since IE will modify it given document.location
- ajaxLocation = document.createElement( "a" );
- ajaxLocation.href = "";
- ajaxLocation = ajaxLocation.href;
-}
+ allTypes = "*/".concat( "*" ),
-// Segment location into parts
-ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
+ // Anchor tag for parsing the document origin
+ originAnchor = document.createElement( "a" );
+ originAnchor.href = location.href;
// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
function addToPrefiltersOrTransports( structure ) {
@@ -8605,19 +8542,21 @@ function addToPrefiltersOrTransports( structure ) {
var dataType,
i = 0,
- dataTypes = dataTypeExpression.toLowerCase().match( rnotwhite ) || [];
+ dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || [];
if ( jQuery.isFunction( func ) ) {
+
// For each dataType in the dataTypeExpression
- while ( (dataType = dataTypes[i++]) ) {
+ while ( ( dataType = dataTypes[ i++ ] ) ) {
+
// Prepend if requested
- if ( dataType.charAt( 0 ) === "+" ) {
+ if ( dataType[ 0 ] === "+" ) {
dataType = dataType.slice( 1 ) || "*";
- (structure[ dataType ] = structure[ dataType ] || []).unshift( func );
+ ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func );
// Otherwise append
} else {
- (structure[ dataType ] = structure[ dataType ] || []).push( func );
+ ( structure[ dataType ] = structure[ dataType ] || [] ).push( func );
}
}
}
@@ -8635,14 +8574,16 @@ function inspectPrefiltersOrTransports( structure, options, originalOptions, jqX
inspected[ dataType ] = true;
jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
- if ( typeof dataTypeOrTransport === "string" && !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
+ if ( typeof dataTypeOrTransport === "string" &&
+ !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
+
options.dataTypes.unshift( dataTypeOrTransport );
inspect( dataTypeOrTransport );
return false;
} else if ( seekingTransport ) {
return !( selected = dataTypeOrTransport );
}
- });
+ } );
return selected;
}
@@ -8653,12 +8594,12 @@ function inspectPrefiltersOrTransports( structure, options, originalOptions, jqX
// that takes "flat" options (not to be deep extended)
// Fixes #9887
function ajaxExtend( target, src ) {
- var deep, key,
+ var key, deep,
flatOptions = jQuery.ajaxSettings.flatOptions || {};
for ( key in src ) {
if ( src[ key ] !== undefined ) {
- ( flatOptions[ key ] ? target : ( deep || (deep = {}) ) )[ key ] = src[ key ];
+ ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
}
}
if ( deep ) {
@@ -8673,7 +8614,8 @@ function ajaxExtend( target, src ) {
* - returns the corresponding response
*/
function ajaxHandleResponses( s, jqXHR, responses ) {
- var firstDataType, ct, finalDataType, type,
+
+ var ct, type, finalDataType, firstDataType,
contents = s.contents,
dataTypes = s.dataTypes;
@@ -8681,7 +8623,7 @@ function ajaxHandleResponses( s, jqXHR, responses ) {
while ( dataTypes[ 0 ] === "*" ) {
dataTypes.shift();
if ( ct === undefined ) {
- ct = s.mimeType || jqXHR.getResponseHeader("Content-Type");
+ ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" );
}
}
@@ -8699,9 +8641,10 @@ function ajaxHandleResponses( s, jqXHR, responses ) {
if ( dataTypes[ 0 ] in responses ) {
finalDataType = dataTypes[ 0 ];
} else {
+
// Try convertible dataTypes
for ( type in responses ) {
- if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
+ if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) {
finalDataType = type;
break;
}
@@ -8709,6 +8652,7 @@ function ajaxHandleResponses( s, jqXHR, responses ) {
firstDataType = type;
}
}
+
// Or just use first one
finalDataType = finalDataType || firstDataType;
}
@@ -8730,6 +8674,7 @@ function ajaxHandleResponses( s, jqXHR, responses ) {
function ajaxConvert( s, response, jqXHR, isSuccess ) {
var conv2, current, conv, tmp, prev,
converters = {},
+
// Work with a copy of dataTypes in case we need to modify it for conversion
dataTypes = s.dataTypes.slice();
@@ -8782,6 +8727,7 @@ function ajaxConvert( s, response, jqXHR, isSuccess ) {
conv = converters[ prev + " " + tmp[ 0 ] ] ||
converters[ "* " + tmp[ 0 ] ];
if ( conv ) {
+
// Condense equivalence converters
if ( conv === true ) {
conv = converters[ conv2 ];
@@ -8801,13 +8747,16 @@ function ajaxConvert( s, response, jqXHR, isSuccess ) {
if ( conv !== true ) {
// Unless errors are allowed to bubble, catch and return them
- if ( conv && s[ "throws" ] ) {
+ if ( conv && s.throws ) {
response = conv( response );
} else {
try {
response = conv( response );
} catch ( e ) {
- return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current };
+ return {
+ state: "parsererror",
+ error: conv ? e : "No conversion from " + prev + " to " + current
+ };
}
}
}
@@ -8818,7 +8767,7 @@ function ajaxConvert( s, response, jqXHR, isSuccess ) {
return { state: "success", data: response };
}
-jQuery.extend({
+jQuery.extend( {
// Counter for holding the number of active queries
active: 0,
@@ -8828,13 +8777,14 @@ jQuery.extend({
etag: {},
ajaxSettings: {
- url: ajaxLocation,
+ url: location.href,
type: "GET",
- isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
+ isLocal: rlocalProtocol.test( location.protocol ),
global: true,
processData: true,
async: true,
contentType: "application/x-www-form-urlencoded; charset=UTF-8",
+
/*
timeout: 0,
data: null,
@@ -8856,9 +8806,9 @@ jQuery.extend({
},
contents: {
- xml: /xml/,
- html: /html/,
- json: /json/
+ xml: /\bxml\b/,
+ html: /\bhtml/,
+ json: /\bjson\b/
},
responseFields: {
@@ -8878,7 +8828,7 @@ jQuery.extend({
"text html": true,
// Evaluate text as a json expression
- "text json": jQuery.parseJSON,
+ "text json": JSON.parse,
// Parse text as xml
"text xml": jQuery.parseXML
@@ -8922,43 +8872,59 @@ jQuery.extend({
// Force options to be an object
options = options || {};
- var // Cross-domain detection vars
- parts,
- // Loop variable
- i,
+ var transport,
+
// URL without anti-cache param
cacheURL,
- // Response headers as string
+
+ // Response headers
responseHeadersString,
+ responseHeaders,
+
// timeout handle
timeoutTimer,
+ // Url cleanup var
+ urlAnchor,
+
+ // Request state (becomes false upon send and true upon completion)
+ completed,
+
// To know if global events are to be dispatched
fireGlobals,
- transport,
- // Response headers
- responseHeaders,
+ // Loop variable
+ i,
+
+ // uncached part of the url
+ uncached,
+
// Create the final options object
s = jQuery.ajaxSetup( {}, options ),
+
// Callbacks context
callbackContext = s.context || s,
+
// Context for global events is callbackContext if it is a DOM node or jQuery collection
- globalEventContext = s.context && ( callbackContext.nodeType || callbackContext.jquery ) ?
- jQuery( callbackContext ) :
- jQuery.event,
+ globalEventContext = s.context &&
+ ( callbackContext.nodeType || callbackContext.jquery ) ?
+ jQuery( callbackContext ) :
+ jQuery.event,
+
// Deferreds
deferred = jQuery.Deferred(),
- completeDeferred = jQuery.Callbacks("once memory"),
+ completeDeferred = jQuery.Callbacks( "once memory" ),
+
// Status-dependent callbacks
statusCode = s.statusCode || {},
+
// Headers (they are sent all at once)
requestHeaders = {},
requestHeadersNames = {},
- // The jqXHR state
- state = 0,
+
// Default abort message
strAbort = "canceled",
+
// Fake xhr
jqXHR = {
readyState: 0,
@@ -8966,11 +8932,11 @@ jQuery.extend({
// Builds headers hashtable if needed
getResponseHeader: function( key ) {
var match;
- if ( state === 2 ) {
+ if ( completed ) {
if ( !responseHeaders ) {
responseHeaders = {};
- while ( (match = rheaders.exec( responseHeadersString )) ) {
- responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
+ while ( ( match = rheaders.exec( responseHeadersString ) ) ) {
+ responseHeaders[ match[ 1 ].toLowerCase() ] = match[ 2 ];
}
}
match = responseHeaders[ key.toLowerCase() ];
@@ -8980,14 +8946,14 @@ jQuery.extend({
// Raw string
getAllResponseHeaders: function() {
- return state === 2 ? responseHeadersString : null;
+ return completed ? responseHeadersString : null;
},
// Caches the header
setRequestHeader: function( name, value ) {
- var lname = name.toLowerCase();
- if ( !state ) {
- name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
+ if ( completed == null ) {
+ name = requestHeadersNames[ name.toLowerCase() ] =
+ requestHeadersNames[ name.toLowerCase() ] || name;
requestHeaders[ name ] = value;
}
return this;
@@ -8995,7 +8961,7 @@ jQuery.extend({
// Overrides response content-type header
overrideMimeType: function( type ) {
- if ( !state ) {
+ if ( completed == null ) {
s.mimeType = type;
}
return this;
@@ -9005,14 +8971,16 @@ jQuery.extend({
statusCode: function( map ) {
var code;
if ( map ) {
- if ( state < 2 ) {
+ if ( completed ) {
+
+ // Execute the appropriate callbacks
+ jqXHR.always( map[ jqXHR.status ] );
+ } else {
+
+ // Lazy-add the new callbacks in a way that preserves old ones
for ( code in map ) {
- // Lazy-add the new callback in a way that preserves old ones
statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
}
- } else {
- // Execute the appropriate callbacks
- jqXHR.always( map[ jqXHR.status ] );
}
}
return this;
@@ -9030,30 +8998,41 @@ jQuery.extend({
};
// Attach deferreds
- deferred.promise( jqXHR ).complete = completeDeferred.add;
- jqXHR.success = jqXHR.done;
- jqXHR.error = jqXHR.fail;
+ deferred.promise( jqXHR );
- // Remove hash character (#7531: and string promotion)
- // Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
+ // Add protocol if not provided (prefilters might expect it)
// Handle falsy url in the settings object (#10093: consistency with old signature)
// We also use the url parameter if available
- s.url = ( ( url || s.url || ajaxLocation ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
+ s.url = ( ( url || s.url || location.href ) + "" )
+ .replace( rprotocol, location.protocol + "//" );
// Alias method option to type as per ticket #12004
s.type = options.method || options.type || s.method || s.type;
// Extract dataTypes list
- s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().match( rnotwhite ) || [ "" ];
+ s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ];
- // A cross-domain request is in order when we have a protocol:host:port mismatch
+ // A cross-domain request is in order when the origin doesn't match the current origin.
if ( s.crossDomain == null ) {
- parts = rurl.exec( s.url.toLowerCase() );
- s.crossDomain = !!( parts &&
- ( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] ||
- ( parts[ 3 ] || ( parts[ 1 ] === "http:" ? "80" : "443" ) ) !==
- ( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? "80" : "443" ) ) )
- );
+ urlAnchor = document.createElement( "a" );
+
+ // Support: IE <=8 - 11, Edge 12 - 13
+ // IE throws exception on accessing the href property if url is malformed,
+ // e.g. http://example.com:80x/
+ try {
+ urlAnchor.href = s.url;
+
+ // Support: IE <=8 - 11 only
+ // Anchor's host property isn't correctly set when s.url is relative
+ urlAnchor.href = urlAnchor.href;
+ s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !==
+ urlAnchor.protocol + "//" + urlAnchor.host;
+ } catch ( e ) {
+
+ // If there is an error parsing the URL, assume it is crossDomain,
+ // it can be rejected by the transport if it is invalid
+ s.crossDomain = true;
+ }
}
// Convert data if not already a string
@@ -9065,16 +9044,17 @@ jQuery.extend({
inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
// If request was aborted inside a prefilter, stop there
- if ( state === 2 ) {
+ if ( completed ) {
return jqXHR;
}
// We can fire global events as of now if asked to
- fireGlobals = s.global;
+ // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
+ fireGlobals = jQuery.event && s.global;
// Watch for a new set of requests
if ( fireGlobals && jQuery.active++ === 0 ) {
- jQuery.event.trigger("ajaxStart");
+ jQuery.event.trigger( "ajaxStart" );
}
// Uppercase the type
@@ -9085,28 +9065,36 @@ jQuery.extend({
// Save the URL in case we're toying with the If-Modified-Since
// and/or If-None-Match header later on
- cacheURL = s.url;
+ // Remove hash to simplify url manipulation
+ cacheURL = s.url.replace( rhash, "" );
// More options handling for requests with no content
if ( !s.hasContent ) {
+ // Remember the hash so we can put it back
+ uncached = s.url.slice( cacheURL.length );
+
// If data is available, append data to url
if ( s.data ) {
- cacheURL = ( s.url += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data );
+ cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data;
+
// #9682: remove data so that it's not used in an eventual retry
delete s.data;
}
- // Add anti-cache in url if needed
+ // Add or update anti-cache param if needed
if ( s.cache === false ) {
- s.url = rts.test( cacheURL ) ?
+ cacheURL = cacheURL.replace( rantiCache, "$1" );
+ uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce++ ) + uncached;
+ }
- // If there is already a '_' parameter, set its value
- cacheURL.replace( rts, "$1_=" + nonce++ ) :
+ // Put hash and anti-cache on the URL that will be requested (gh-1732)
+ s.url = cacheURL + uncached;
- // Otherwise add one to the end
- cacheURL + ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + nonce++;
- }
+ // Change '%20' to '+' if this is encoded form body content (gh-2658)
+ } else if ( s.data && s.processData &&
+ ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) {
+ s.data = s.data.replace( r20, "+" );
}
// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
@@ -9127,8 +9115,9 @@ jQuery.extend({
// Set the Accepts header for the server, depending on the dataType
jqXHR.setRequestHeader(
"Accept",
- s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
- s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
+ s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ?
+ s.accepts[ s.dataTypes[ 0 ] ] +
+ ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
s.accepts[ "*" ]
);
@@ -9138,18 +9127,20 @@ jQuery.extend({
}
// Allow custom headers/mimetypes and early abort
- if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
+ if ( s.beforeSend &&
+ ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) {
+
// Abort if not done already and return
return jqXHR.abort();
}
- // aborting is no longer a cancellation
+ // Aborting is no longer a cancellation
strAbort = "abort";
// Install callbacks on deferreds
- for ( i in { success: 1, error: 1, complete: 1 } ) {
- jqXHR[ i ]( s[ i ] );
- }
+ completeDeferred.add( s.complete );
+ jqXHR.done( s.success );
+ jqXHR.fail( s.error );
// Get transport
transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
@@ -9164,24 +9155,31 @@ jQuery.extend({
if ( fireGlobals ) {
globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
}
+
+ // If request was aborted inside ajaxSend, stop there
+ if ( completed ) {
+ return jqXHR;
+ }
+
// Timeout
if ( s.async && s.timeout > 0 ) {
- timeoutTimer = setTimeout(function() {
- jqXHR.abort("timeout");
+ timeoutTimer = window.setTimeout( function() {
+ jqXHR.abort( "timeout" );
}, s.timeout );
}
try {
- state = 1;
+ completed = false;
transport.send( requestHeaders, done );
} catch ( e ) {
- // Propagate exception as error if not done
- if ( state < 2 ) {
- done( -1, e );
- // Simply rethrow otherwise
- } else {
+
+ // Rethrow post-completion exceptions
+ if ( completed ) {
throw e;
}
+
+ // Propagate others as results
+ done( -1, e );
}
}
@@ -9190,17 +9188,16 @@ jQuery.extend({
var isSuccess, success, error, response, modified,
statusText = nativeStatusText;
- // Called once
- if ( state === 2 ) {
+ // Ignore repeat invocations
+ if ( completed ) {
return;
}
- // State is "done" now
- state = 2;
+ completed = true;
// Clear timeout if it exists
if ( timeoutTimer ) {
- clearTimeout( timeoutTimer );
+ window.clearTimeout( timeoutTimer );
}
// Dereference transport for early garbage collection
@@ -9229,11 +9226,11 @@ jQuery.extend({
// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
if ( s.ifModified ) {
- modified = jqXHR.getResponseHeader("Last-Modified");
+ modified = jqXHR.getResponseHeader( "Last-Modified" );
if ( modified ) {
jQuery.lastModified[ cacheURL ] = modified;
}
- modified = jqXHR.getResponseHeader("etag");
+ modified = jqXHR.getResponseHeader( "etag" );
if ( modified ) {
jQuery.etag[ cacheURL ] = modified;
}
@@ -9255,8 +9252,8 @@ jQuery.extend({
isSuccess = !error;
}
} else {
- // We extract error from statusText
- // then normalize statusText and status for non-aborts
+
+ // Extract error from statusText and normalize for non-aborts
error = statusText;
if ( status || !statusText ) {
statusText = "error";
@@ -9291,9 +9288,10 @@ jQuery.extend({
if ( fireGlobals ) {
globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
+
// Handle the global AJAX counter
if ( !( --jQuery.active ) ) {
- jQuery.event.trigger("ajaxStop");
+ jQuery.event.trigger( "ajaxStop" );
}
}
}
@@ -9308,72 +9306,70 @@ jQuery.extend({
getScript: function( url, callback ) {
return jQuery.get( url, undefined, callback, "script" );
}
-});
+} );
jQuery.each( [ "get", "post" ], function( i, method ) {
jQuery[ method ] = function( url, data, callback, type ) {
- // shift arguments if data argument was omitted
+
+ // Shift arguments if data argument was omitted
if ( jQuery.isFunction( data ) ) {
type = type || callback;
callback = data;
data = undefined;
}
- return jQuery.ajax({
+ // The url can be an options object (which then must have .url)
+ return jQuery.ajax( jQuery.extend( {
url: url,
type: method,
dataType: type,
data: data,
success: callback
- });
- };
-});
-
-// Attach a bunch of functions for handling common AJAX events
-jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) {
- jQuery.fn[ type ] = function( fn ) {
- return this.on( type, fn );
+ }, jQuery.isPlainObject( url ) && url ) );
};
-});
+} );
jQuery._evalUrl = function( url ) {
- return jQuery.ajax({
+ return jQuery.ajax( {
url: url,
+
+ // Make this explicit, since user can override this through ajaxSetup (#11264)
type: "GET",
dataType: "script",
+ cache: true,
async: false,
global: false,
"throws": true
- });
+ } );
};
-jQuery.fn.extend({
+jQuery.fn.extend( {
wrapAll: function( html ) {
- if ( jQuery.isFunction( html ) ) {
- return this.each(function(i) {
- jQuery(this).wrapAll( html.call(this, i) );
- });
- }
+ var wrap;
+
+ if ( this[ 0 ] ) {
+ if ( jQuery.isFunction( html ) ) {
+ html = html.call( this[ 0 ] );
+ }
- if ( this[0] ) {
// The elements to wrap the target around
- var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
+ wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true );
- if ( this[0].parentNode ) {
- wrap.insertBefore( this[0] );
+ if ( this[ 0 ].parentNode ) {
+ wrap.insertBefore( this[ 0 ] );
}
- wrap.map(function() {
+ wrap.map( function() {
var elem = this;
- while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
- elem = elem.firstChild;
+ while ( elem.firstElementChild ) {
+ elem = elem.firstElementChild;
}
return elem;
- }).append( this );
+ } ).append( this );
}
return this;
@@ -9381,12 +9377,12 @@ jQuery.fn.extend({
wrapInner: function( html ) {
if ( jQuery.isFunction( html ) ) {
- return this.each(function(i) {
- jQuery(this).wrapInner( html.call(this, i) );
- });
+ return this.each( function( i ) {
+ jQuery( this ).wrapInner( html.call( this, i ) );
+ } );
}
- return this.each(function() {
+ return this.each( function() {
var self = jQuery( this ),
contents = self.contents();
@@ -9396,342 +9392,214 @@ jQuery.fn.extend({
} else {
self.append( html );
}
- });
+ } );
},
wrap: function( html ) {
var isFunction = jQuery.isFunction( html );
- return this.each(function(i) {
- jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
- });
+ return this.each( function( i ) {
+ jQuery( this ).wrapAll( isFunction ? html.call( this, i ) : html );
+ } );
},
- unwrap: function() {
- return this.parent().each(function() {
- if ( !jQuery.nodeName( this, "body" ) ) {
- jQuery( this ).replaceWith( this.childNodes );
- }
- }).end();
+ unwrap: function( selector ) {
+ this.parent( selector ).not( "body" ).each( function() {
+ jQuery( this ).replaceWith( this.childNodes );
+ } );
+ return this;
}
-});
+} );
-jQuery.expr.filters.hidden = function( elem ) {
- // Support: Opera <= 12.12
- // Opera reports offsetWidths and offsetHeights less than zero on some elements
- return elem.offsetWidth <= 0 && elem.offsetHeight <= 0 ||
- (!support.reliableHiddenOffsets() &&
- ((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none");
+jQuery.expr.pseudos.hidden = function( elem ) {
+ return !jQuery.expr.pseudos.visible( elem );
};
-
-jQuery.expr.filters.visible = function( elem ) {
- return !jQuery.expr.filters.hidden( elem );
+jQuery.expr.pseudos.visible = function( elem ) {
+ return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length );
};
-var r20 = /%20/g,
- rbracket = /\[\]$/,
- rCRLF = /\r?\n/g,
- rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
- rsubmittable = /^(?:input|select|textarea|keygen)/i;
-
-function buildParams( prefix, obj, traditional, add ) {
- var name;
-
- if ( jQuery.isArray( obj ) ) {
- // Serialize array item.
- jQuery.each( obj, function( i, v ) {
- if ( traditional || rbracket.test( prefix ) ) {
- // Treat each array item as a scalar.
- add( prefix, v );
-
- } else {
- // Item is non-scalar (array or object), encode its numeric index.
- buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
- }
- });
-
- } else if ( !traditional && jQuery.type( obj ) === "object" ) {
- // Serialize object item.
- for ( name in obj ) {
- buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
- }
-
- } else {
- // Serialize scalar item.
- add( prefix, obj );
- }
-}
-
-// Serialize an array of form elements or a set of
-// key/values into a query string
-jQuery.param = function( a, traditional ) {
- var prefix,
- s = [],
- add = function( key, value ) {
- // If value is a function, invoke it and return its value
- value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value );
- s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
- };
-
- // Set traditional to true for jQuery <= 1.3.2 behavior.
- if ( traditional === undefined ) {
- traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional;
- }
-
- // If an array was passed in, assume that it is an array of form elements.
- if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
- // Serialize the form elements
- jQuery.each( a, function() {
- add( this.name, this.value );
- });
-
- } else {
- // If traditional, encode the "old" way (the way 1.3.2 or older
- // did it), otherwise encode params recursively.
- for ( prefix in a ) {
- buildParams( prefix, a[ prefix ], traditional, add );
- }
- }
-
- // Return the resulting serialization
- return s.join( "&" ).replace( r20, "+" );
+jQuery.ajaxSettings.xhr = function() {
+ try {
+ return new window.XMLHttpRequest();
+ } catch ( e ) {}
};
-jQuery.fn.extend({
- serialize: function() {
- return jQuery.param( this.serializeArray() );
- },
- serializeArray: function() {
- return this.map(function() {
- // Can add propHook for "elements" to filter or add form elements
- var elements = jQuery.prop( this, "elements" );
- return elements ? jQuery.makeArray( elements ) : this;
- })
- .filter(function() {
- var type = this.type;
- // Use .is(":disabled") so that fieldset[disabled] works
- return this.name && !jQuery( this ).is( ":disabled" ) &&
- rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
- ( this.checked || !rcheckableType.test( type ) );
- })
- .map(function( i, elem ) {
- var val = jQuery( this ).val();
-
- return val == null ?
- null :
- jQuery.isArray( val ) ?
- jQuery.map( val, function( val ) {
- return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- }) :
- { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- }).get();
- }
-});
-
+var xhrSuccessStatus = {
-// Create the request object
-// (This is still attached to ajaxSettings for backward compatibility)
-jQuery.ajaxSettings.xhr = window.ActiveXObject !== undefined ?
- // Support: IE6+
- function() {
-
- // XHR cannot access local files, always use ActiveX for that case
- return !this.isLocal &&
-
- // Support: IE7-8
- // oldIE XHR does not support non-RFC2616 methods (#13240)
- // See http://msdn.microsoft.com/en-us/library/ie/ms536648(v=vs.85).aspx
- // and http://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html#sec9
- // Although this check for six methods instead of eight
- // since IE also does not support "trace" and "connect"
- /^(get|post|head|put|delete|options)$/i.test( this.type ) &&
-
- createStandardXHR() || createActiveXHR();
- } :
- // For all other browsers, use the standard XMLHttpRequest object
- createStandardXHR;
+ // File protocol always yields status code 0, assume 200
+ 0: 200,
-var xhrId = 0,
- xhrCallbacks = {},
+ // Support: IE <=9 only
+ // #1450: sometimes IE returns 1223 when it should be 204
+ 1223: 204
+ },
xhrSupported = jQuery.ajaxSettings.xhr();
-// Support: IE<10
-// Open requests must be manually aborted on unload (#5280)
-if ( window.ActiveXObject ) {
- jQuery( window ).on( "unload", function() {
- for ( var key in xhrCallbacks ) {
- xhrCallbacks[ key ]( undefined, true );
- }
- });
-}
-
-// Determine support properties
support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
-xhrSupported = support.ajax = !!xhrSupported;
-
-// Create transport if the browser can provide an xhr
-if ( xhrSupported ) {
-
- jQuery.ajaxTransport(function( options ) {
- // Cross domain only allowed if supported through XMLHttpRequest
- if ( !options.crossDomain || support.cors ) {
-
- var callback;
+support.ajax = xhrSupported = !!xhrSupported;
- return {
- send: function( headers, complete ) {
- var i,
- xhr = options.xhr(),
- id = ++xhrId;
+jQuery.ajaxTransport( function( options ) {
+ var callback, errorCallback;
- // Open the socket
- xhr.open( options.type, options.url, options.async, options.username, options.password );
-
- // Apply custom fields if provided
- if ( options.xhrFields ) {
- for ( i in options.xhrFields ) {
- xhr[ i ] = options.xhrFields[ i ];
- }
- }
-
- // Override mime type if needed
- if ( options.mimeType && xhr.overrideMimeType ) {
- xhr.overrideMimeType( options.mimeType );
- }
+ // Cross domain only allowed if supported through XMLHttpRequest
+ if ( support.cors || xhrSupported && !options.crossDomain ) {
+ return {
+ send: function( headers, complete ) {
+ var i,
+ xhr = options.xhr();
+
+ xhr.open(
+ options.type,
+ options.url,
+ options.async,
+ options.username,
+ options.password
+ );
- // X-Requested-With header
- // For cross-domain requests, seeing as conditions for a preflight are
- // akin to a jigsaw puzzle, we simply never set it to be sure.
- // (it can always be set on a per-request basis or even using ajaxSetup)
- // For same-domain requests, won't change header if already provided.
- if ( !options.crossDomain && !headers["X-Requested-With"] ) {
- headers["X-Requested-With"] = "XMLHttpRequest";
+ // Apply custom fields if provided
+ if ( options.xhrFields ) {
+ for ( i in options.xhrFields ) {
+ xhr[ i ] = options.xhrFields[ i ];
}
+ }
- // Set headers
- for ( i in headers ) {
- // Support: IE<9
- // IE's ActiveXObject throws a 'Type Mismatch' exception when setting
- // request header to a null-value.
- //
- // To keep consistent with other XHR implementations, cast the value
- // to string and ignore `undefined`.
- if ( headers[ i ] !== undefined ) {
- xhr.setRequestHeader( i, headers[ i ] + "" );
- }
- }
+ // Override mime type if needed
+ if ( options.mimeType && xhr.overrideMimeType ) {
+ xhr.overrideMimeType( options.mimeType );
+ }
- // Do send the request
- // This may raise an exception which is actually
- // handled in jQuery.ajax (so no try/catch here)
- xhr.send( ( options.hasContent && options.data ) || null );
-
- // Listener
- callback = function( _, isAbort ) {
- var status, statusText, responses;
-
- // Was never called and is aborted or complete
- if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
- // Clean up
- delete xhrCallbacks[ id ];
- callback = undefined;
- xhr.onreadystatechange = jQuery.noop;
-
- // Abort manually if needed
- if ( isAbort ) {
- if ( xhr.readyState !== 4 ) {
- xhr.abort();
- }
- } else {
- responses = {};
- status = xhr.status;
-
- // Support: IE<10
- // Accessing binary-data responseText throws an exception
- // (#11426)
- if ( typeof xhr.responseText === "string" ) {
- responses.text = xhr.responseText;
- }
+ // X-Requested-With header
+ // For cross-domain requests, seeing as conditions for a preflight are
+ // akin to a jigsaw puzzle, we simply never set it to be sure.
+ // (it can always be set on a per-request basis or even using ajaxSetup)
+ // For same-domain requests, won't change header if already provided.
+ if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) {
+ headers[ "X-Requested-With" ] = "XMLHttpRequest";
+ }
- // Firefox throws an exception when accessing
- // statusText for faulty cross-domain requests
- try {
- statusText = xhr.statusText;
- } catch( e ) {
- // We normalize with Webkit giving an empty statusText
- statusText = "";
- }
+ // Set headers
+ for ( i in headers ) {
+ xhr.setRequestHeader( i, headers[ i ] );
+ }
- // Filter status for non standard behaviors
+ // Callback
+ callback = function( type ) {
+ return function() {
+ if ( callback ) {
+ callback = errorCallback = xhr.onload =
+ xhr.onerror = xhr.onabort = xhr.onreadystatechange = null;
+
+ if ( type === "abort" ) {
+ xhr.abort();
+ } else if ( type === "error" ) {
+
+ // Support: IE <=9 only
+ // On a manual native abort, IE9 throws
+ // errors on any property access that is not readyState
+ if ( typeof xhr.status !== "number" ) {
+ complete( 0, "error" );
+ } else {
+ complete(
- // If the request is local and we have data: assume a success
- // (success with no data won't get notified, that's the best we
- // can do given current implementations)
- if ( !status && options.isLocal && !options.crossDomain ) {
- status = responses.text ? 200 : 404;
- // IE - #1450: sometimes returns 1223 when it should be 204
- } else if ( status === 1223 ) {
- status = 204;
+ // File: protocol always yields status 0; see #8605, #14207
+ xhr.status,
+ xhr.statusText
+ );
}
+ } else {
+ complete(
+ xhrSuccessStatus[ xhr.status ] || xhr.status,
+ xhr.statusText,
+
+ // Support: IE <=9 only
+ // IE9 has no XHR2 but throws on binary (trac-11426)
+ // For XHR2 non-text, let the caller handle it (gh-2498)
+ ( xhr.responseType || "text" ) !== "text" ||
+ typeof xhr.responseText !== "string" ?
+ { binary: xhr.response } :
+ { text: xhr.responseText },
+ xhr.getAllResponseHeaders()
+ );
}
}
+ };
+ };
+
+ // Listen to events
+ xhr.onload = callback();
+ errorCallback = xhr.onerror = callback( "error" );
- // Call complete if needed
- if ( responses ) {
- complete( status, statusText, responses, xhr.getAllResponseHeaders() );
+ // Support: IE 9 only
+ // Use onreadystatechange to replace onabort
+ // to handle uncaught aborts
+ if ( xhr.onabort !== undefined ) {
+ xhr.onabort = errorCallback;
+ } else {
+ xhr.onreadystatechange = function() {
+
+ // Check readyState before timeout as it changes
+ if ( xhr.readyState === 4 ) {
+
+ // Allow onerror to be called first,
+ // but that will not handle a native abort
+ // Also, save errorCallback to a variable
+ // as xhr.onerror cannot be accessed
+ window.setTimeout( function() {
+ if ( callback ) {
+ errorCallback();
+ }
+ } );
}
};
+ }
- if ( !options.async ) {
- // if we're in sync mode we fire the callback
- callback();
- } else if ( xhr.readyState === 4 ) {
- // (IE6 & IE7) if it's in cache and has been
- // retrieved directly we need to fire the callback
- setTimeout( callback );
- } else {
- // Add to the list of active xhr callbacks
- xhr.onreadystatechange = xhrCallbacks[ id ] = callback;
- }
- },
+ // Create the abort callback
+ callback = callback( "abort" );
- abort: function() {
+ try {
+
+ // Do send the request (this may raise an exception)
+ xhr.send( options.hasContent && options.data || null );
+ } catch ( e ) {
+
+ // #14683: Only rethrow if this hasn't been notified as an error yet
if ( callback ) {
- callback( undefined, true );
+ throw e;
}
}
- };
- }
- });
-}
+ },
-// Functions to create xhrs
-function createStandardXHR() {
- try {
- return new window.XMLHttpRequest();
- } catch( e ) {}
-}
+ abort: function() {
+ if ( callback ) {
+ callback();
+ }
+ }
+ };
+ }
+} );
-function createActiveXHR() {
- try {
- return new window.ActiveXObject( "Microsoft.XMLHTTP" );
- } catch( e ) {}
-}
+// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432)
+jQuery.ajaxPrefilter( function( s ) {
+ if ( s.crossDomain ) {
+ s.contents.script = false;
+ }
+} );
// Install script dataType
-jQuery.ajaxSetup({
+jQuery.ajaxSetup( {
accepts: {
- script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
+ script: "text/javascript, application/javascript, " +
+ "application/ecmascript, application/x-ecmascript"
},
contents: {
- script: /(?:java|ecma)script/
+ script: /\b(?:java|ecma)script\b/
},
converters: {
"text script": function( text ) {
@@ -9739,78 +9607,51 @@ jQuery.ajaxSetup({
return text;
}
}
-});
+} );
-// Handle cache's special case and global
+// Handle cache's special case and crossDomain
jQuery.ajaxPrefilter( "script", function( s ) {
if ( s.cache === undefined ) {
s.cache = false;
}
if ( s.crossDomain ) {
s.type = "GET";
- s.global = false;
}
-});
+} );
// Bind script tag hack transport
-jQuery.ajaxTransport( "script", function(s) {
+jQuery.ajaxTransport( "script", function( s ) {
// This transport only deals with cross domain requests
if ( s.crossDomain ) {
-
- var script,
- head = document.head || jQuery("head")[0] || document.documentElement;
-
+ var script, callback;
return {
-
- send: function( _, callback ) {
-
- script = document.createElement("script");
-
- script.async = true;
-
- if ( s.scriptCharset ) {
- script.charset = s.scriptCharset;
- }
-
- script.src = s.url;
-
- // Attach handlers for all browsers
- script.onload = script.onreadystatechange = function( _, isAbort ) {
-
- if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
-
- // Handle memory leak in IE
- script.onload = script.onreadystatechange = null;
-
- // Remove the script
- if ( script.parentNode ) {
- script.parentNode.removeChild( script );
- }
-
- // Dereference the script
- script = null;
-
- // Callback if not abort
- if ( !isAbort ) {
- callback( 200, "success" );
+ send: function( _, complete ) {
+ script = jQuery( "<script>" ).prop( {
+ charset: s.scriptCharset,
+ src: s.url
+ } ).on(
+ "load error",
+ callback = function( evt ) {
+ script.remove();
+ callback = null;
+ if ( evt ) {
+ complete( evt.type === "error" ? 404 : 200, evt.type );
}
}
- };
+ );
- // Circumvent IE6 bugs with base elements (#2709 and #4378) by prepending
// Use native DOM manipulation to avoid our domManip AJAX trickery
- head.insertBefore( script, head.firstChild );
+ document.head.appendChild( script[ 0 ] );
},
-
abort: function() {
- if ( script ) {
- script.onload( undefined, true );
+ if ( callback ) {
+ callback();
}
}
};
}
-});
+} );
@@ -9819,14 +9660,14 @@ var oldCallbacks = [],
rjsonp = /(=)\?(?=&|$)|\?\?/;
// Default jsonp settings
-jQuery.ajaxSetup({
+jQuery.ajaxSetup( {
jsonp: "callback",
jsonpCallback: function() {
var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
this[ callback ] = true;
return callback;
}
-});
+} );
// Detect, normalize options and install callbacks for jsonp requests
jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
@@ -9834,7 +9675,10 @@ jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
var callbackName, overwritten, responseContainer,
jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
"url" :
- typeof s.data === "string" && !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") && rjsonp.test( s.data ) && "data"
+ typeof s.data === "string" &&
+ ( s.contentType || "" )
+ .indexOf( "application/x-www-form-urlencoded" ) === 0 &&
+ rjsonp.test( s.data ) && "data"
);
// Handle iff the expected data type is "jsonp" or we have a parameter to set
@@ -9853,14 +9697,14 @@ jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
}
// Use data converter to retrieve json after script execution
- s.converters["script json"] = function() {
+ s.converters[ "script json" ] = function() {
if ( !responseContainer ) {
jQuery.error( callbackName + " was not called" );
}
return responseContainer[ 0 ];
};
- // force json dataType
+ // Force json dataType
s.dataTypes[ 0 ] = "json";
// Install callback
@@ -9870,16 +9714,24 @@ jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
};
// Clean-up function (fires after converters)
- jqXHR.always(function() {
- // Restore preexisting value
- window[ callbackName ] = overwritten;
+ jqXHR.always( function() {
+
+ // If previous value didn't exist - remove it
+ if ( overwritten === undefined ) {
+ jQuery( window ).removeProp( callbackName );
+
+ // Otherwise restore preexisting value
+ } else {
+ window[ callbackName ] = overwritten;
+ }
// Save back as free
if ( s[ callbackName ] ) {
- // make sure that re-using the options doesn't screw things around
+
+ // Make sure that re-using the options doesn't screw things around
s.jsonpCallback = originalSettings.jsonpCallback;
- // save the callback name for future use
+ // Save the callback name for future use
oldCallbacks.push( callbackName );
}
@@ -9889,38 +9741,70 @@ jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
}
responseContainer = overwritten = undefined;
- });
+ } );
// Delegate to script
return "script";
}
-});
+} );
+
+// Support: Safari 8 only
+// In Safari 8 documents created via document.implementation.createHTMLDocument
+// collapse sibling forms: the second one becomes a child of the first one.
+// Because of that, this security measure has to be disabled in Safari 8.
+// https://bugs.webkit.org/show_bug.cgi?id=137337
+support.createHTMLDocument = ( function() {
+ var body = document.implementation.createHTMLDocument( "" ).body;
+ body.innerHTML = "<form></form><form></form>";
+ return body.childNodes.length === 2;
+} )();
-// data: string of html
-// context (optional): If specified, the fragment will be created in this context, defaults to document
+
+// Argument "data" should be string of html
+// context (optional): If specified, the fragment will be created in this context,
+// defaults to document
// keepScripts (optional): If true, will include scripts passed in the html string
jQuery.parseHTML = function( data, context, keepScripts ) {
- if ( !data || typeof data !== "string" ) {
- return null;
+ if ( typeof data !== "string" ) {
+ return [];
}
if ( typeof context === "boolean" ) {
keepScripts = context;
context = false;
}
- context = context || document;
- var parsed = rsingleTag.exec( data ),
- scripts = !keepScripts && [];
+ var base, parsed, scripts;
+
+ if ( !context ) {
+
+ // Stop scripts or inline event handlers from being executed immediately
+ // by using document.implementation
+ if ( support.createHTMLDocument ) {
+ context = document.implementation.createHTMLDocument( "" );
+
+ // Set the base href for the created document
+ // so any parsed elements with URLs
+ // are based on the document's URL (gh-2965)
+ base = context.createElement( "base" );
+ base.href = document.location.href;
+ context.head.appendChild( base );
+ } else {
+ context = document;
+ }
+ }
+
+ parsed = rsingleTag.exec( data );
+ scripts = !keepScripts && [];
// Single tag
if ( parsed ) {
- return [ context.createElement( parsed[1] ) ];
+ return [ context.createElement( parsed[ 1 ] ) ];
}
- parsed = jQuery.buildFragment( [ data ], context, scripts );
+ parsed = buildFragment( [ data ], context, scripts );
if ( scripts && scripts.length ) {
jQuery( scripts ).remove();
@@ -9930,23 +9814,16 @@ jQuery.parseHTML = function( data, context, keepScripts ) {
};
-// Keep a copy of the old load method
-var _load = jQuery.fn.load;
-
/**
* Load a url into a page
*/
jQuery.fn.load = function( url, params, callback ) {
- if ( typeof url !== "string" && _load ) {
- return _load.apply( this, arguments );
- }
-
- var selector, response, type,
+ var selector, type, response,
self = this,
- off = url.indexOf(" ");
+ off = url.indexOf( " " );
- if ( off >= 0 ) {
- selector = jQuery.trim( url.slice( off, url.length ) );
+ if ( off > -1 ) {
+ selector = stripAndCollapse( url.slice( off ) );
url = url.slice( 0, off );
}
@@ -9964,14 +9841,16 @@ jQuery.fn.load = function( url, params, callback ) {
// If we have elements to modify, make the request
if ( self.length > 0 ) {
- jQuery.ajax({
+ jQuery.ajax( {
url: url,
- // if "type" variable is undefined, then "GET" method will be used
- type: type,
+ // If "type" variable is undefined, then "GET" method will be used.
+ // Make value of this field explicit since
+ // user can override it through ajaxSetup method
+ type: type || "GET",
dataType: "html",
data: params
- }).done(function( responseText ) {
+ } ).done( function( responseText ) {
// Save response for use in complete callback
response = arguments;
@@ -9980,14 +9859,19 @@ jQuery.fn.load = function( url, params, callback ) {
// If a selector was specified, locate the right elements in a dummy div
// Exclude scripts to avoid IE 'Permission Denied' errors
- jQuery("<div>").append( jQuery.parseHTML( responseText ) ).find( selector ) :
+ jQuery( "<div>" ).append( jQuery.parseHTML( responseText ) ).find( selector ) :
// Otherwise use the full result
responseText );
- }).complete( callback && function( jqXHR, status ) {
- self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] );
- });
+ // If the request succeeds, this function gets "data", "status", "jqXHR"
+ // but they are ignored because response was set above.
+ // If it fails, this function gets "jqXHR", "status", "error"
+ } ).always( callback && function( jqXHR, status ) {
+ self.each( function() {
+ callback.apply( this, response || [ jqXHR.responseText, status, jqXHR ] );
+ } );
+ } );
}
return this;
@@ -9996,28 +9880,31 @@ jQuery.fn.load = function( url, params, callback ) {
-jQuery.expr.filters.animated = function( elem ) {
- return jQuery.grep(jQuery.timers, function( fn ) {
- return elem === fn.elem;
- }).length;
-};
+// Attach a bunch of functions for handling common AJAX events
+jQuery.each( [
+ "ajaxStart",
+ "ajaxStop",
+ "ajaxComplete",
+ "ajaxError",
+ "ajaxSuccess",
+ "ajaxSend"
+], function( i, type ) {
+ jQuery.fn[ type ] = function( fn ) {
+ return this.on( type, fn );
+ };
+} );
+jQuery.expr.pseudos.animated = function( elem ) {
+ return jQuery.grep( jQuery.timers, function( fn ) {
+ return elem === fn.elem;
+ } ).length;
+};
+
-var docElem = window.document.documentElement;
-/**
- * Gets a window from an element
- */
-function getWindow( elem ) {
- return jQuery.isWindow( elem ) ?
- elem :
- elem.nodeType === 9 ?
- elem.defaultView || elem.parentWindow :
- false;
-}
jQuery.offset = {
setOffset: function( elem, options, i ) {
@@ -10026,7 +9913,7 @@ jQuery.offset = {
curElem = jQuery( elem ),
props = {};
- // set position first, in-case top/left are set even on static elem
+ // Set position first, in-case top/left are set even on static elem
if ( position === "static" ) {
elem.style.position = "relative";
}
@@ -10035,20 +9922,24 @@ jQuery.offset = {
curCSSTop = jQuery.css( elem, "top" );
curCSSLeft = jQuery.css( elem, "left" );
calculatePosition = ( position === "absolute" || position === "fixed" ) &&
- jQuery.inArray("auto", [ curCSSTop, curCSSLeft ] ) > -1;
+ ( curCSSTop + curCSSLeft ).indexOf( "auto" ) > -1;
- // need to be able to calculate position if either top or left is auto and position is either absolute or fixed
+ // Need to be able to calculate position if either
+ // top or left is auto and position is either absolute or fixed
if ( calculatePosition ) {
curPosition = curElem.position();
curTop = curPosition.top;
curLeft = curPosition.left;
+
} else {
curTop = parseFloat( curCSSTop ) || 0;
curLeft = parseFloat( curCSSLeft ) || 0;
}
if ( jQuery.isFunction( options ) ) {
- options = options.call( elem, i, curOffset );
+
+ // Use jQuery.extend here to allow modification of coordinates argument (gh-1848)
+ options = options.call( elem, i, jQuery.extend( {}, curOffset ) );
}
if ( options.top != null ) {
@@ -10060,47 +9951,49 @@ jQuery.offset = {
if ( "using" in options ) {
options.using.call( elem, props );
+
} else {
curElem.css( props );
}
}
};
-jQuery.fn.extend({
+jQuery.fn.extend( {
offset: function( options ) {
+
+ // Preserve chaining for setter
if ( arguments.length ) {
return options === undefined ?
this :
- this.each(function( i ) {
+ this.each( function( i ) {
jQuery.offset.setOffset( this, options, i );
- });
+ } );
}
- var docElem, win,
- box = { top: 0, left: 0 },
- elem = this[ 0 ],
- doc = elem && elem.ownerDocument;
+ var doc, docElem, rect, win,
+ elem = this[ 0 ];
- if ( !doc ) {
+ if ( !elem ) {
return;
}
- docElem = doc.documentElement;
-
- // Make sure it's not a disconnected DOM node
- if ( !jQuery.contains( docElem, elem ) ) {
- return box;
+ // Return zeros for disconnected and hidden (display: none) elements (gh-2310)
+ // Support: IE <=11 only
+ // Running getBoundingClientRect on a
+ // disconnected node in IE throws an error
+ if ( !elem.getClientRects().length ) {
+ return { top: 0, left: 0 };
}
- // If we don't have gBCR, just use 0,0 rather than error
- // BlackBerry 5, iOS 3 (original iPhone)
- if ( typeof elem.getBoundingClientRect !== strundefined ) {
- box = elem.getBoundingClientRect();
- }
- win = getWindow( doc );
+ rect = elem.getBoundingClientRect();
+
+ doc = elem.ownerDocument;
+ docElem = doc.documentElement;
+ win = doc.defaultView;
+
return {
- top: box.top + ( win.pageYOffset || docElem.scrollTop ) - ( docElem.clientTop || 0 ),
- left: box.left + ( win.pageXOffset || docElem.scrollLeft ) - ( docElem.clientLeft || 0 )
+ top: rect.top + win.pageYOffset - docElem.clientTop,
+ left: rect.left + win.pageXOffset - docElem.clientLeft
};
},
@@ -10110,99 +10003,124 @@ jQuery.fn.extend({
}
var offsetParent, offset,
- parentOffset = { top: 0, left: 0 },
- elem = this[ 0 ];
+ elem = this[ 0 ],
+ parentOffset = { top: 0, left: 0 };
- // fixed elements are offset from window (parentOffset = {top:0, left: 0}, because it is its only offset parent
+ // Fixed elements are offset from window (parentOffset = {top:0, left: 0},
+ // because it is its only offset parent
if ( jQuery.css( elem, "position" ) === "fixed" ) {
- // we assume that getBoundingClientRect is available when computed position is fixed
+
+ // Assume getBoundingClientRect is there when computed position is fixed
offset = elem.getBoundingClientRect();
+
} else {
+
// Get *real* offsetParent
offsetParent = this.offsetParent();
// Get correct offsets
offset = this.offset();
- if ( !jQuery.nodeName( offsetParent[ 0 ], "html" ) ) {
+ if ( !nodeName( offsetParent[ 0 ], "html" ) ) {
parentOffset = offsetParent.offset();
}
// Add offsetParent borders
- parentOffset.top += jQuery.css( offsetParent[ 0 ], "borderTopWidth", true );
- parentOffset.left += jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true );
+ parentOffset = {
+ top: parentOffset.top + jQuery.css( offsetParent[ 0 ], "borderTopWidth", true ),
+ left: parentOffset.left + jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true )
+ };
}
// Subtract parent offsets and element margins
- // note: when an element has margin: auto the offsetLeft and marginLeft
- // are the same in Safari causing offset.left to incorrectly be 0
return {
- top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ),
- left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true)
+ top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ),
+ left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true )
};
},
+ // This method will return documentElement in the following cases:
+ // 1) For the element inside the iframe without offsetParent, this method will return
+ // documentElement of the parent window
+ // 2) For the hidden or detached element
+ // 3) For body or html element, i.e. in case of the html node - it will return itself
+ //
+ // but those exceptions were never presented as a real life use-cases
+ // and might be considered as more preferable results.
+ //
+ // This logic, however, is not guaranteed and can change at any point in the future
offsetParent: function() {
- return this.map(function() {
- var offsetParent = this.offsetParent || docElem;
+ return this.map( function() {
+ var offsetParent = this.offsetParent;
- while ( offsetParent && ( !jQuery.nodeName( offsetParent, "html" ) && jQuery.css( offsetParent, "position" ) === "static" ) ) {
+ while ( offsetParent && jQuery.css( offsetParent, "position" ) === "static" ) {
offsetParent = offsetParent.offsetParent;
}
- return offsetParent || docElem;
- });
+
+ return offsetParent || documentElement;
+ } );
}
-});
+} );
// Create scrollLeft and scrollTop methods
jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
- var top = /Y/.test( prop );
+ var top = "pageYOffset" === prop;
jQuery.fn[ method ] = function( val ) {
return access( this, function( elem, method, val ) {
- var win = getWindow( elem );
+
+ // Coalesce documents and windows
+ var win;
+ if ( jQuery.isWindow( elem ) ) {
+ win = elem;
+ } else if ( elem.nodeType === 9 ) {
+ win = elem.defaultView;
+ }
if ( val === undefined ) {
- return win ? (prop in win) ? win[ prop ] :
- win.document.documentElement[ method ] :
- elem[ method ];
+ return win ? win[ prop ] : elem[ method ];
}
if ( win ) {
win.scrollTo(
- !top ? val : jQuery( win ).scrollLeft(),
- top ? val : jQuery( win ).scrollTop()
+ !top ? val : win.pageXOffset,
+ top ? val : win.pageYOffset
);
} else {
elem[ method ] = val;
}
- }, method, val, arguments.length, null );
+ }, method, val, arguments.length );
};
-});
+} );
+// Support: Safari <=7 - 9.1, Chrome <=37 - 49
// Add the top/left cssHooks using jQuery.fn.position
// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
-// getComputedStyle returns percent when specified for top/left/bottom/right
-// rather than make the css module depend on the offset module, we just check for it here
+// Blink bug: https://bugs.chromium.org/p/chromium/issues/detail?id=589347
+// getComputedStyle returns percent when specified for top/left/bottom/right;
+// rather than make the css module depend on the offset module, just check for it here
jQuery.each( [ "top", "left" ], function( i, prop ) {
jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
function( elem, computed ) {
if ( computed ) {
computed = curCSS( elem, prop );
- // if curCSS returns percentage, fallback to offset
+
+ // If curCSS returns percentage, fallback to offset
return rnumnonpx.test( computed ) ?
jQuery( elem ).position()[ prop ] + "px" :
computed;
}
}
);
-});
+} );
// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
- jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {
- // margin is only for outerHeight, outerWidth
+ jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name },
+ function( defaultExtra, funcName ) {
+
+ // Margin is only for outerHeight, outerWidth
jQuery.fn[ funcName ] = function( margin, value ) {
var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
@@ -10211,18 +10129,19 @@ jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
var doc;
if ( jQuery.isWindow( elem ) ) {
- // As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there
- // isn't a whole lot we can do. See pull request at this URL for discussion:
- // https://github.com/jquery/jquery/pull/764
- return elem.document.documentElement[ "client" + name ];
+
+ // $( window ).outerWidth/Height return w/h including scrollbars (gh-1729)
+ return funcName.indexOf( "outer" ) === 0 ?
+ elem[ "inner" + name ] :
+ elem.document.documentElement[ "client" + name ];
}
// Get document width or height
if ( elem.nodeType === 9 ) {
doc = elem.documentElement;
- // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest
- // unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it.
+ // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height],
+ // whichever is greatest
return Math.max(
elem.body[ "scroll" + name ], doc[ "scroll" + name ],
elem.body[ "offset" + name ], doc[ "offset" + name ],
@@ -10231,23 +10150,49 @@ jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
}
return value === undefined ?
+
// Get width or height on the element, requesting but not forcing parseFloat
jQuery.css( elem, type, extra ) :
// Set width or height on the element
jQuery.style( elem, type, value, extra );
- }, type, chainable ? margin : undefined, chainable, null );
+ }, type, chainable ? margin : undefined, chainable );
};
- });
-});
+ } );
+} );
-// The number of elements contained in the matched element set
-jQuery.fn.size = function() {
- return this.length;
-};
+jQuery.fn.extend( {
+
+ bind: function( types, data, fn ) {
+ return this.on( types, null, data, fn );
+ },
+ unbind: function( types, fn ) {
+ return this.off( types, null, fn );
+ },
+
+ delegate: function( selector, types, data, fn ) {
+ return this.on( types, selector, data, fn );
+ },
+ undelegate: function( selector, types, fn ) {
+
+ // ( namespace ) or ( selector, types [, fn] )
+ return arguments.length === 1 ?
+ this.off( selector, "**" ) :
+ this.off( types, selector || "**", fn );
+ }
+} );
-jQuery.fn.andSelf = jQuery.fn.addBack;
+jQuery.holdReady = function( hold ) {
+ if ( hold ) {
+ jQuery.readyWait++;
+ } else {
+ jQuery.ready( true );
+ }
+};
+jQuery.isArray = Array.isArray;
+jQuery.parseJSON = JSON.parse;
+jQuery.nodeName = nodeName;
@@ -10268,13 +10213,14 @@ jQuery.fn.andSelf = jQuery.fn.addBack;
if ( typeof define === "function" && define.amd ) {
define( "jquery", [], function() {
return jQuery;
- });
+ } );
}
var
+
// Map over jQuery in case of overwrite
_jQuery = window.jQuery,
@@ -10293,10 +10239,10 @@ jQuery.noConflict = function( deep ) {
return jQuery;
};
-// Expose jQuery and $ identifiers, even in
-// AMD (#7102#comment:10, https://github.com/jquery/jquery/pull/557)
+// Expose jQuery and $ identifiers, even in AMD
+// (#7102#comment:10, https://github.com/jquery/jquery/pull/557)
// and CommonJS for browser emulators (#13566)
-if ( typeof noGlobal === strundefined ) {
+if ( !noGlobal ) {
window.jQuery = window.$ = jQuery;
}
@@ -10304,5 +10250,4 @@ if ( typeof noGlobal === strundefined ) {
return jQuery;
-
-}));
+} );
diff --git a/doc/html/_static/jquery.js b/doc/html/_static/jquery.js
index ab28a24729b320bffd3d2f60302af949db39ab85..644d35e274fd64ddaf6d12af813e820c424176a9 100644
--- a/doc/html/_static/jquery.js
+++ b/doc/html/_static/jquery.js
@@ -1,4 +1,4 @@
-/*! jQuery v1.11.1 | (c) 2005, 2014 jQuery Foundation, Inc. | jquery.org/license */
-!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){var c=[],d=c.slice,e=c.concat,f=c.push,g=c.indexOf,h={},i=h.toString,j=h.hasOwnProperty,k={},l="1.11.1",m=function(a,b){return new m.fn.init(a,b)},n=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,o=/^-ms-/,p=/-([\da-z])/gi,q=function(a,b){return b.toUpperCase()};m.fn=m.prototype={jquery:l,constructor:m,selector:"",length:0,toArray:function(){return d.call(this)},get:function(a){return null!=a?0>a?this[a+this.length]:this[a]:d.call(this)},pushStack:function(a){var b=m.merge(this.constructor(),a);return b.prevObject=this,b.context=this.context,b},each:function(a,b){return m.each(this,a,b)},map:function(a){return this.pushStack(m.map(this,function(b,c){return a.call(b,c,b)}))},slice:function(){return this.pushStack(d.apply(this,arguments))},first:function(){return this.eq(0)},last:function(){return this.eq(-1)},eq:function(a){var b=this.length,c=+a+(0>a?b:0);return this.pushStack(c>=0&&b>c?[this[c]]:[])},end:function(){return this.prevObject||this.constructor(null)},push:f,sort:c.sort,splice:c.splice},m.extend=m.fn.extend=function(){var a,b,c,d,e,f,g=arguments[0]||{},h=1,i=arguments.length,j=!1;for("boolean"==typeof g&&(j=g,g=arguments[h]||{},h++),"object"==typeof g||m.isFunction(g)||(g={}),h===i&&(g=this,h--);i>h;h++)if(null!=(e=arguments[h]))for(d in e)a=g[d],c=e[d],g!==c&&(j&&c&&(m.isPlainObject(c)||(b=m.isArray(c)))?(b?(b=!1,f=a&&m.isArray(a)?a:[]):f=a&&m.isPlainObject(a)?a:{},g[d]=m.extend(j,f,c)):void 0!==c&&(g[d]=c));return g},m.extend({expando:"jQuery"+(l+Math.random()).replace(/\D/g,""),isReady:!0,error:function(a){throw new Error(a)},noop:function(){},isFunction:function(a){return"function"===m.type(a)},isArray:Array.isArray||function(a){return"array"===m.type(a)},isWindow:function(a){return null!=a&&a==a.window},isNumeric:function(a){return!m.isArray(a)&&a-parseFloat(a)>=0},isEmptyObject:function(a){var b;for(b in a)return!1;return!0},isPlainObject:function(a){var b;if(!a||"object"!==m.type(a)||a.nodeType||m.isWindow(a))return!1;try{if(a.constructor&&!j.call(a,"constructor")&&!j.call(a.constructor.prototype,"isPrototypeOf"))return!1}catch(c){return!1}if(k.ownLast)for(b in a)return j.call(a,b);for(b in a);return void 0===b||j.call(a,b)},type:function(a){return null==a?a+"":"object"==typeof a||"function"==typeof a?h[i.call(a)]||"object":typeof a},globalEval:function(b){b&&m.trim(b)&&(a.execScript||function(b){a.eval.call(a,b)})(b)},camelCase:function(a){return a.replace(o,"ms-").replace(p,q)},nodeName:function(a,b){return a.nodeName&&a.nodeName.toLowerCase()===b.toLowerCase()},each:function(a,b,c){var d,e=0,f=a.length,g=r(a);if(c){if(g){for(;f>e;e++)if(d=b.apply(a[e],c),d===!1)break}else for(e in a)if(d=b.apply(a[e],c),d===!1)break}else if(g){for(;f>e;e++)if(d=b.call(a[e],e,a[e]),d===!1)break}else for(e in a)if(d=b.call(a[e],e,a[e]),d===!1)break;return a},trim:function(a){return null==a?"":(a+"").replace(n,"")},makeArray:function(a,b){var c=b||[];return null!=a&&(r(Object(a))?m.merge(c,"string"==typeof a?[a]:a):f.call(c,a)),c},inArray:function(a,b,c){var d;if(b){if(g)return g.call(b,a,c);for(d=b.length,c=c?0>c?Math.max(0,d+c):c:0;d>c;c++)if(c in b&&b[c]===a)return c}return-1},merge:function(a,b){var c=+b.length,d=0,e=a.length;while(c>d)a[e++]=b[d++];if(c!==c)while(void 0!==b[d])a[e++]=b[d++];return a.length=e,a},grep:function(a,b,c){for(var d,e=[],f=0,g=a.length,h=!c;g>f;f++)d=!b(a[f],f),d!==h&&e.push(a[f]);return e},map:function(a,b,c){var d,f=0,g=a.length,h=r(a),i=[];if(h)for(;g>f;f++)d=b(a[f],f,c),null!=d&&i.push(d);else for(f in a)d=b(a[f],f,c),null!=d&&i.push(d);return e.apply([],i)},guid:1,proxy:function(a,b){var c,e,f;return"string"==typeof b&&(f=a[b],b=a,a=f),m.isFunction(a)?(c=d.call(arguments,2),e=function(){return a.apply(b||this,c.concat(d.call(arguments)))},e.guid=a.guid=a.guid||m.guid++,e):void 0},now:function(){return+new Date},support:k}),m.each("Boolean Number String Function Array Date RegExp Object Error".split(" "),function(a,b){h["[object "+b+"]"]=b.toLowerCase()});function r(a){var b=a.length,c=m.type(a);return"function"===c||m.isWindow(a)?!1:1===a.nodeType&&b?!0:"array"===c||0===b||"number"==typeof b&&b>0&&b-1 in a}var s=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u="sizzle"+-new Date,v=a.document,w=0,x=0,y=gb(),z=gb(),A=gb(),B=function(a,b){return a===b&&(l=!0),0},C="undefined",D=1<<31,E={}.hasOwnProperty,F=[],G=F.pop,H=F.push,I=F.push,J=F.slice,K=F.indexOf||function(a){for(var b=0,c=this.length;c>b;b++)if(this[b]===a)return b;return-1},L="checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",M="[\\x20\\t\\r\\n\\f]",N="(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+",O=N.replace("w","w#"),P="\\["+M+"*("+N+")(?:"+M+"*([*^$|!~]?=)"+M+"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|("+O+"))|)"+M+"*\\]",Q=":("+N+")(?:\\((('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|((?:\\\\.|[^\\\\()[\\]]|"+P+")*)|.*)\\)|)",R=new RegExp("^"+M+"+|((?:^|[^\\\\])(?:\\\\.)*)"+M+"+$","g"),S=new RegExp("^"+M+"*,"+M+"*"),T=new RegExp("^"+M+"*([>+~]|"+M+")"+M+"*"),U=new RegExp("="+M+"*([^\\]'\"]*?)"+M+"*\\]","g"),V=new RegExp(Q),W=new RegExp("^"+O+"$"),X={ID:new RegExp("^#("+N+")"),CLASS:new RegExp("^\\.("+N+")"),TAG:new RegExp("^("+N.replace("w","w*")+")"),ATTR:new RegExp("^"+P),PSEUDO:new RegExp("^"+Q),CHILD:new RegExp("^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\("+M+"*(even|odd|(([+-]|)(\\d*)n|)"+M+"*(?:([+-]|)"+M+"*(\\d+)|))"+M+"*\\)|)","i"),bool:new RegExp("^(?:"+L+")$","i"),needsContext:new RegExp("^"+M+"*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\("+M+"*((?:-\\d)?\\d*)"+M+"*\\)|)(?=[^-]|$)","i")},Y=/^(?:input|select|textarea|button)$/i,Z=/^h\d$/i,$=/^[^{]+\{\s*\[native \w/,_=/^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,ab=/[+~]/,bb=/'|\\/g,cb=new RegExp("\\\\([\\da-f]{1,6}"+M+"?|("+M+")|.)","ig"),db=function(a,b,c){var d="0x"+b-65536;return d!==d||c?b:0>d?String.fromCharCode(d+65536):String.fromCharCode(d>>10|55296,1023&d|56320)};try{I.apply(F=J.call(v.childNodes),v.childNodes),F[v.childNodes.length].nodeType}catch(eb){I={apply:F.length?function(a,b){H.apply(a,J.call(b))}:function(a,b){var c=a.length,d=0;while(a[c++]=b[d++]);a.length=c-1}}}function fb(a,b,d,e){var f,h,j,k,l,o,r,s,w,x;if((b?b.ownerDocument||b:v)!==n&&m(b),b=b||n,d=d||[],!a||"string"!=typeof a)return d;if(1!==(k=b.nodeType)&&9!==k)return[];if(p&&!e){if(f=_.exec(a))if(j=f[1]){if(9===k){if(h=b.getElementById(j),!h||!h.parentNode)return d;if(h.id===j)return d.push(h),d}else if(b.ownerDocument&&(h=b.ownerDocument.getElementById(j))&&t(b,h)&&h.id===j)return d.push(h),d}else{if(f[2])return I.apply(d,b.getElementsByTagName(a)),d;if((j=f[3])&&c.getElementsByClassName&&b.getElementsByClassName)return I.apply(d,b.getElementsByClassName(j)),d}if(c.qsa&&(!q||!q.test(a))){if(s=r=u,w=b,x=9===k&&a,1===k&&"object"!==b.nodeName.toLowerCase()){o=g(a),(r=b.getAttribute("id"))?s=r.replace(bb,"\\$&"):b.setAttribute("id",s),s="[id='"+s+"'] ",l=o.length;while(l--)o[l]=s+qb(o[l]);w=ab.test(a)&&ob(b.parentNode)||b,x=o.join(",")}if(x)try{return I.apply(d,w.querySelectorAll(x)),d}catch(y){}finally{r||b.removeAttribute("id")}}}return i(a.replace(R,"$1"),b,d,e)}function gb(){var a=[];function b(c,e){return a.push(c+" ")>d.cacheLength&&delete b[a.shift()],b[c+" "]=e}return b}function hb(a){return a[u]=!0,a}function ib(a){var b=n.createElement("div");try{return!!a(b)}catch(c){return!1}finally{b.parentNode&&b.parentNode.removeChild(b),b=null}}function jb(a,b){var c=a.split("|"),e=a.length;while(e--)d.attrHandle[c[e]]=b}function kb(a,b){var c=b&&a,d=c&&1===a.nodeType&&1===b.nodeType&&(~b.sourceIndex||D)-(~a.sourceIndex||D);if(d)return d;if(c)while(c=c.nextSibling)if(c===b)return-1;return a?1:-1}function lb(a){return function(b){var c=b.nodeName.toLowerCase();return"input"===c&&b.type===a}}function mb(a){return function(b){var c=b.nodeName.toLowerCase();return("input"===c||"button"===c)&&b.type===a}}function nb(a){return hb(function(b){return b=+b,hb(function(c,d){var e,f=a([],c.length,b),g=f.length;while(g--)c[e=f[g]]&&(c[e]=!(d[e]=c[e]))})})}function ob(a){return a&&typeof a.getElementsByTagName!==C&&a}c=fb.support={},f=fb.isXML=function(a){var b=a&&(a.ownerDocument||a).documentElement;return b?"HTML"!==b.nodeName:!1},m=fb.setDocument=function(a){var b,e=a?a.ownerDocument||a:v,g=e.defaultView;return e!==n&&9===e.nodeType&&e.documentElement?(n=e,o=e.documentElement,p=!f(e),g&&g!==g.top&&(g.addEventListener?g.addEventListener("unload",function(){m()},!1):g.attachEvent&&g.attachEvent("onunload",function(){m()})),c.attributes=ib(function(a){return a.className="i",!a.getAttribute("className")}),c.getElementsByTagName=ib(function(a){return a.appendChild(e.createComment("")),!a.getElementsByTagName("*").length}),c.getElementsByClassName=$.test(e.getElementsByClassName)&&ib(function(a){return a.innerHTML="<div class='a'></div><div class='a i'></div>",a.firstChild.className="i",2===a.getElementsByClassName("i").length}),c.getById=ib(function(a){return o.appendChild(a).id=u,!e.getElementsByName||!e.getElementsByName(u).length}),c.getById?(d.find.ID=function(a,b){if(typeof b.getElementById!==C&&p){var c=b.getElementById(a);return c&&c.parentNode?[c]:[]}},d.filter.ID=function(a){var b=a.replace(cb,db);return function(a){return a.getAttribute("id")===b}}):(delete d.find.ID,d.filter.ID=function(a){var b=a.replace(cb,db);return function(a){var c=typeof a.getAttributeNode!==C&&a.getAttributeNode("id");return c&&c.value===b}}),d.find.TAG=c.getElementsByTagName?function(a,b){return typeof b.getElementsByTagName!==C?b.getElementsByTagName(a):void 0}:function(a,b){var c,d=[],e=0,f=b.getElementsByTagName(a);if("*"===a){while(c=f[e++])1===c.nodeType&&d.push(c);return d}return f},d.find.CLASS=c.getElementsByClassName&&function(a,b){return typeof b.getElementsByClassName!==C&&p?b.getElementsByClassName(a):void 0},r=[],q=[],(c.qsa=$.test(e.querySelectorAll))&&(ib(function(a){a.innerHTML="<select msallowclip=''><option selected=''></option></select>",a.querySelectorAll("[msallowclip^='']").length&&q.push("[*^$]="+M+"*(?:''|\"\")"),a.querySelectorAll("[selected]").length||q.push("\\["+M+"*(?:value|"+L+")"),a.querySelectorAll(":checked").length||q.push(":checked")}),ib(function(a){var b=e.createElement("input");b.setAttribute("type","hidden"),a.appendChild(b).setAttribute("name","D"),a.querySelectorAll("[name=d]").length&&q.push("name"+M+"*[*^$|!~]?="),a.querySelectorAll(":enabled").length||q.push(":enabled",":disabled"),a.querySelectorAll("*,:x"),q.push(",.*:")})),(c.matchesSelector=$.test(s=o.matches||o.webkitMatchesSelector||o.mozMatchesSelector||o.oMatchesSelector||o.msMatchesSelector))&&ib(function(a){c.disconnectedMatch=s.call(a,"div"),s.call(a,"[s!='']:x"),r.push("!=",Q)}),q=q.length&&new RegExp(q.join("|")),r=r.length&&new RegExp(r.join("|")),b=$.test(o.compareDocumentPosition),t=b||$.test(o.contains)?function(a,b){var c=9===a.nodeType?a.documentElement:a,d=b&&b.parentNode;return a===d||!(!d||1!==d.nodeType||!(c.contains?c.contains(d):a.compareDocumentPosition&&16&a.compareDocumentPosition(d)))}:function(a,b){if(b)while(b=b.parentNode)if(b===a)return!0;return!1},B=b?function(a,b){if(a===b)return l=!0,0;var d=!a.compareDocumentPosition-!b.compareDocumentPosition;return d?d:(d=(a.ownerDocument||a)===(b.ownerDocument||b)?a.compareDocumentPosition(b):1,1&d||!c.sortDetached&&b.compareDocumentPosition(a)===d?a===e||a.ownerDocument===v&&t(v,a)?-1:b===e||b.ownerDocument===v&&t(v,b)?1:k?K.call(k,a)-K.call(k,b):0:4&d?-1:1)}:function(a,b){if(a===b)return l=!0,0;var c,d=0,f=a.parentNode,g=b.parentNode,h=[a],i=[b];if(!f||!g)return a===e?-1:b===e?1:f?-1:g?1:k?K.call(k,a)-K.call(k,b):0;if(f===g)return kb(a,b);c=a;while(c=c.parentNode)h.unshift(c);c=b;while(c=c.parentNode)i.unshift(c);while(h[d]===i[d])d++;return d?kb(h[d],i[d]):h[d]===v?-1:i[d]===v?1:0},e):n},fb.matches=function(a,b){return fb(a,null,null,b)},fb.matchesSelector=function(a,b){if((a.ownerDocument||a)!==n&&m(a),b=b.replace(U,"='$1']"),!(!c.matchesSelector||!p||r&&r.test(b)||q&&q.test(b)))try{var d=s.call(a,b);if(d||c.disconnectedMatch||a.document&&11!==a.document.nodeType)return d}catch(e){}return fb(b,n,null,[a]).length>0},fb.contains=function(a,b){return(a.ownerDocument||a)!==n&&m(a),t(a,b)},fb.attr=function(a,b){(a.ownerDocument||a)!==n&&m(a);var e=d.attrHandle[b.toLowerCase()],f=e&&E.call(d.attrHandle,b.toLowerCase())?e(a,b,!p):void 0;return void 0!==f?f:c.attributes||!p?a.getAttribute(b):(f=a.getAttributeNode(b))&&f.specified?f.value:null},fb.error=function(a){throw new Error("Syntax error, unrecognized expression: "+a)},fb.uniqueSort=function(a){var b,d=[],e=0,f=0;if(l=!c.detectDuplicates,k=!c.sortStable&&a.slice(0),a.sort(B),l){while(b=a[f++])b===a[f]&&(e=d.push(f));while(e--)a.splice(d[e],1)}return k=null,a},e=fb.getText=function(a){var b,c="",d=0,f=a.nodeType;if(f){if(1===f||9===f||11===f){if("string"==typeof a.textContent)return a.textContent;for(a=a.firstChild;a;a=a.nextSibling)c+=e(a)}else if(3===f||4===f)return a.nodeValue}else while(b=a[d++])c+=e(b);return c},d=fb.selectors={cacheLength:50,createPseudo:hb,match:X,attrHandle:{},find:{},relative:{">":{dir:"parentNode",first:!0}," ":{dir:"parentNode"},"+":{dir:"previousSibling",first:!0},"~":{dir:"previousSibling"}},preFilter:{ATTR:function(a){return a[1]=a[1].replace(cb,db),a[3]=(a[3]||a[4]||a[5]||"").replace(cb,db),"~="===a[2]&&(a[3]=" "+a[3]+" "),a.slice(0,4)},CHILD:function(a){return a[1]=a[1].toLowerCase(),"nth"===a[1].slice(0,3)?(a[3]||fb.error(a[0]),a[4]=+(a[4]?a[5]+(a[6]||1):2*("even"===a[3]||"odd"===a[3])),a[5]=+(a[7]+a[8]||"odd"===a[3])):a[3]&&fb.error(a[0]),a},PSEUDO:function(a){var b,c=!a[6]&&a[2];return X.CHILD.test(a[0])?null:(a[3]?a[2]=a[4]||a[5]||"":c&&V.test(c)&&(b=g(c,!0))&&(b=c.indexOf(")",c.length-b)-c.length)&&(a[0]=a[0].slice(0,b),a[2]=c.slice(0,b)),a.slice(0,3))}},filter:{TAG:function(a){var b=a.replace(cb,db).toLowerCase();return"*"===a?function(){return!0}:function(a){return a.nodeName&&a.nodeName.toLowerCase()===b}},CLASS:function(a){var b=y[a+" "];return b||(b=new RegExp("(^|"+M+")"+a+"("+M+"|$)"))&&y(a,function(a){return b.test("string"==typeof a.className&&a.className||typeof a.getAttribute!==C&&a.getAttribute("class")||"")})},ATTR:function(a,b,c){return function(d){var e=fb.attr(d,a);return null==e?"!="===b:b?(e+="","="===b?e===c:"!="===b?e!==c:"^="===b?c&&0===e.indexOf(c):"*="===b?c&&e.indexOf(c)>-1:"$="===b?c&&e.slice(-c.length)===c:"~="===b?(" "+e+" ").indexOf(c)>-1:"|="===b?e===c||e.slice(0,c.length+1)===c+"-":!1):!0}},CHILD:function(a,b,c,d,e){var f="nth"!==a.slice(0,3),g="last"!==a.slice(-4),h="of-type"===b;return 1===d&&0===e?function(a){return!!a.parentNode}:function(b,c,i){var j,k,l,m,n,o,p=f!==g?"nextSibling":"previousSibling",q=b.parentNode,r=h&&b.nodeName.toLowerCase(),s=!i&&!h;if(q){if(f){while(p){l=b;while(l=l[p])if(h?l.nodeName.toLowerCase()===r:1===l.nodeType)return!1;o=p="only"===a&&!o&&"nextSibling"}return!0}if(o=[g?q.firstChild:q.lastChild],g&&s){k=q[u]||(q[u]={}),j=k[a]||[],n=j[0]===w&&j[1],m=j[0]===w&&j[2],l=n&&q.childNodes[n];while(l=++n&&l&&l[p]||(m=n=0)||o.pop())if(1===l.nodeType&&++m&&l===b){k[a]=[w,n,m];break}}else if(s&&(j=(b[u]||(b[u]={}))[a])&&j[0]===w)m=j[1];else while(l=++n&&l&&l[p]||(m=n=0)||o.pop())if((h?l.nodeName.toLowerCase()===r:1===l.nodeType)&&++m&&(s&&((l[u]||(l[u]={}))[a]=[w,m]),l===b))break;return m-=e,m===d||m%d===0&&m/d>=0}}},PSEUDO:function(a,b){var c,e=d.pseudos[a]||d.setFilters[a.toLowerCase()]||fb.error("unsupported pseudo: "+a);return e[u]?e(b):e.length>1?(c=[a,a,"",b],d.setFilters.hasOwnProperty(a.toLowerCase())?hb(function(a,c){var d,f=e(a,b),g=f.length;while(g--)d=K.call(a,f[g]),a[d]=!(c[d]=f[g])}):function(a){return e(a,0,c)}):e}},pseudos:{not:hb(function(a){var b=[],c=[],d=h(a.replace(R,"$1"));return d[u]?hb(function(a,b,c,e){var f,g=d(a,null,e,[]),h=a.length;while(h--)(f=g[h])&&(a[h]=!(b[h]=f))}):function(a,e,f){return b[0]=a,d(b,null,f,c),!c.pop()}}),has:hb(function(a){return function(b){return fb(a,b).length>0}}),contains:hb(function(a){return function(b){return(b.textContent||b.innerText||e(b)).indexOf(a)>-1}}),lang:hb(function(a){return W.test(a||"")||fb.error("unsupported lang: "+a),a=a.replace(cb,db).toLowerCase(),function(b){var c;do if(c=p?b.lang:b.getAttribute("xml:lang")||b.getAttribute("lang"))return c=c.toLowerCase(),c===a||0===c.indexOf(a+"-");while((b=b.parentNode)&&1===b.nodeType);return!1}}),target:function(b){var c=a.location&&a.location.hash;return c&&c.slice(1)===b.id},root:function(a){return a===o},focus:function(a){return a===n.activeElement&&(!n.hasFocus||n.hasFocus())&&!!(a.type||a.href||~a.tabIndex)},enabled:function(a){return a.disabled===!1},disabled:function(a){return a.disabled===!0},checked:function(a){var b=a.nodeName.toLowerCase();return"input"===b&&!!a.checked||"option"===b&&!!a.selected},selected:function(a){return a.parentNode&&a.parentNode.selectedIndex,a.selected===!0},empty:function(a){for(a=a.firstChild;a;a=a.nextSibling)if(a.nodeType<6)return!1;return!0},parent:function(a){return!d.pseudos.empty(a)},header:function(a){return Z.test(a.nodeName)},input:function(a){return Y.test(a.nodeName)},button:function(a){var b=a.nodeName.toLowerCase();return"input"===b&&"button"===a.type||"button"===b},text:function(a){var b;return"input"===a.nodeName.toLowerCase()&&"text"===a.type&&(null==(b=a.getAttribute("type"))||"text"===b.toLowerCase())},first:nb(function(){return[0]}),last:nb(function(a,b){return[b-1]}),eq:nb(function(a,b,c){return[0>c?c+b:c]}),even:nb(function(a,b){for(var c=0;b>c;c+=2)a.push(c);return a}),odd:nb(function(a,b){for(var c=1;b>c;c+=2)a.push(c);return a}),lt:nb(function(a,b,c){for(var d=0>c?c+b:c;--d>=0;)a.push(d);return a}),gt:nb(function(a,b,c){for(var d=0>c?c+b:c;++d<b;)a.push(d);return a})}},d.pseudos.nth=d.pseudos.eq;for(b in{radio:!0,checkbox:!0,file:!0,password:!0,image:!0})d.pseudos[b]=lb(b);for(b in{submit:!0,reset:!0})d.pseudos[b]=mb(b);function pb(){}pb.prototype=d.filters=d.pseudos,d.setFilters=new pb,g=fb.tokenize=function(a,b){var c,e,f,g,h,i,j,k=z[a+" "];if(k)return b?0:k.slice(0);h=a,i=[],j=d.preFilter;while(h){(!c||(e=S.exec(h)))&&(e&&(h=h.slice(e[0].length)||h),i.push(f=[])),c=!1,(e=T.exec(h))&&(c=e.shift(),f.push({value:c,type:e[0].replace(R," ")}),h=h.slice(c.length));for(g in d.filter)!(e=X[g].exec(h))||j[g]&&!(e=j[g](e))||(c=e.shift(),f.push({value:c,type:g,matches:e}),h=h.slice(c.length));if(!c)break}return b?h.length:h?fb.error(a):z(a,i).slice(0)};function qb(a){for(var b=0,c=a.length,d="";c>b;b++)d+=a[b].value;return d}function rb(a,b,c){var d=b.dir,e=c&&"parentNode"===d,f=x++;return b.first?function(b,c,f){while(b=b[d])if(1===b.nodeType||e)return a(b,c,f)}:function(b,c,g){var h,i,j=[w,f];if(g){while(b=b[d])if((1===b.nodeType||e)&&a(b,c,g))return!0}else while(b=b[d])if(1===b.nodeType||e){if(i=b[u]||(b[u]={}),(h=i[d])&&h[0]===w&&h[1]===f)return j[2]=h[2];if(i[d]=j,j[2]=a(b,c,g))return!0}}}function sb(a){return a.length>1?function(b,c,d){var e=a.length;while(e--)if(!a[e](b,c,d))return!1;return!0}:a[0]}function tb(a,b,c){for(var d=0,e=b.length;e>d;d++)fb(a,b[d],c);return c}function ub(a,b,c,d,e){for(var f,g=[],h=0,i=a.length,j=null!=b;i>h;h++)(f=a[h])&&(!c||c(f,d,e))&&(g.push(f),j&&b.push(h));return g}function vb(a,b,c,d,e,f){return d&&!d[u]&&(d=vb(d)),e&&!e[u]&&(e=vb(e,f)),hb(function(f,g,h,i){var j,k,l,m=[],n=[],o=g.length,p=f||tb(b||"*",h.nodeType?[h]:h,[]),q=!a||!f&&b?p:ub(p,m,a,h,i),r=c?e||(f?a:o||d)?[]:g:q;if(c&&c(q,r,h,i),d){j=ub(r,n),d(j,[],h,i),k=j.length;while(k--)(l=j[k])&&(r[n[k]]=!(q[n[k]]=l))}if(f){if(e||a){if(e){j=[],k=r.length;while(k--)(l=r[k])&&j.push(q[k]=l);e(null,r=[],j,i)}k=r.length;while(k--)(l=r[k])&&(j=e?K.call(f,l):m[k])>-1&&(f[j]=!(g[j]=l))}}else r=ub(r===g?r.splice(o,r.length):r),e?e(null,g,r,i):I.apply(g,r)})}function wb(a){for(var b,c,e,f=a.length,g=d.relative[a[0].type],h=g||d.relative[" "],i=g?1:0,k=rb(function(a){return a===b},h,!0),l=rb(function(a){return K.call(b,a)>-1},h,!0),m=[function(a,c,d){return!g&&(d||c!==j)||((b=c).nodeType?k(a,c,d):l(a,c,d))}];f>i;i++)if(c=d.relative[a[i].type])m=[rb(sb(m),c)];else{if(c=d.filter[a[i].type].apply(null,a[i].matches),c[u]){for(e=++i;f>e;e++)if(d.relative[a[e].type])break;return vb(i>1&&sb(m),i>1&&qb(a.slice(0,i-1).concat({value:" "===a[i-2].type?"*":""})).replace(R,"$1"),c,e>i&&wb(a.slice(i,e)),f>e&&wb(a=a.slice(e)),f>e&&qb(a))}m.push(c)}return sb(m)}function xb(a,b){var c=b.length>0,e=a.length>0,f=function(f,g,h,i,k){var l,m,o,p=0,q="0",r=f&&[],s=[],t=j,u=f||e&&d.find.TAG("*",k),v=w+=null==t?1:Math.random()||.1,x=u.length;for(k&&(j=g!==n&&g);q!==x&&null!=(l=u[q]);q++){if(e&&l){m=0;while(o=a[m++])if(o(l,g,h)){i.push(l);break}k&&(w=v)}c&&((l=!o&&l)&&p--,f&&r.push(l))}if(p+=q,c&&q!==p){m=0;while(o=b[m++])o(r,s,g,h);if(f){if(p>0)while(q--)r[q]||s[q]||(s[q]=G.call(i));s=ub(s)}I.apply(i,s),k&&!f&&s.length>0&&p+b.length>1&&fb.uniqueSort(i)}return k&&(w=v,j=t),r};return c?hb(f):f}return h=fb.compile=function(a,b){var c,d=[],e=[],f=A[a+" "];if(!f){b||(b=g(a)),c=b.length;while(c--)f=wb(b[c]),f[u]?d.push(f):e.push(f);f=A(a,xb(e,d)),f.selector=a}return f},i=fb.select=function(a,b,e,f){var i,j,k,l,m,n="function"==typeof a&&a,o=!f&&g(a=n.selector||a);if(e=e||[],1===o.length){if(j=o[0]=o[0].slice(0),j.length>2&&"ID"===(k=j[0]).type&&c.getById&&9===b.nodeType&&p&&d.relative[j[1].type]){if(b=(d.find.ID(k.matches[0].replace(cb,db),b)||[])[0],!b)return e;n&&(b=b.parentNode),a=a.slice(j.shift().value.length)}i=X.needsContext.test(a)?0:j.length;while(i--){if(k=j[i],d.relative[l=k.type])break;if((m=d.find[l])&&(f=m(k.matches[0].replace(cb,db),ab.test(j[0].type)&&ob(b.parentNode)||b))){if(j.splice(i,1),a=f.length&&qb(j),!a)return I.apply(e,f),e;break}}}return(n||h(a,o))(f,b,!p,e,ab.test(a)&&ob(b.parentNode)||b),e},c.sortStable=u.split("").sort(B).join("")===u,c.detectDuplicates=!!l,m(),c.sortDetached=ib(function(a){return 1&a.compareDocumentPosition(n.createElement("div"))}),ib(function(a){return a.innerHTML="<a href='#'></a>","#"===a.firstChild.getAttribute("href")})||jb("type|href|height|width",function(a,b,c){return c?void 0:a.getAttribute(b,"type"===b.toLowerCase()?1:2)}),c.attributes&&ib(function(a){return a.innerHTML="<input/>",a.firstChild.setAttribute("value",""),""===a.firstChild.getAttribute("value")})||jb("value",function(a,b,c){return c||"input"!==a.nodeName.toLowerCase()?void 0:a.defaultValue}),ib(function(a){return null==a.getAttribute("disabled")})||jb(L,function(a,b,c){var d;return c?void 0:a[b]===!0?b.toLowerCase():(d=a.getAttributeNode(b))&&d.specified?d.value:null}),fb}(a);m.find=s,m.expr=s.selectors,m.expr[":"]=m.expr.pseudos,m.unique=s.uniqueSort,m.text=s.getText,m.isXMLDoc=s.isXML,m.contains=s.contains;var t=m.expr.match.needsContext,u=/^<(\w+)\s*\/?>(?:<\/\1>|)$/,v=/^.[^:#\[\.,]*$/;function w(a,b,c){if(m.isFunction(b))return m.grep(a,function(a,d){return!!b.call(a,d,a)!==c});if(b.nodeType)return m.grep(a,function(a){return a===b!==c});if("string"==typeof b){if(v.test(b))return m.filter(b,a,c);b=m.filter(b,a)}return m.grep(a,function(a){return m.inArray(a,b)>=0!==c})}m.filter=function(a,b,c){var d=b[0];return c&&(a=":not("+a+")"),1===b.length&&1===d.nodeType?m.find.matchesSelector(d,a)?[d]:[]:m.find.matches(a,m.grep(b,function(a){return 1===a.nodeType}))},m.fn.extend({find:function(a){var b,c=[],d=this,e=d.length;if("string"!=typeof a)return this.pushStack(m(a).filter(function(){for(b=0;e>b;b++)if(m.contains(d[b],this))return!0}));for(b=0;e>b;b++)m.find(a,d[b],c);return c=this.pushStack(e>1?m.unique(c):c),c.selector=this.selector?this.selector+" "+a:a,c},filter:function(a){return this.pushStack(w(this,a||[],!1))},not:function(a){return this.pushStack(w(this,a||[],!0))},is:function(a){return!!w(this,"string"==typeof a&&t.test(a)?m(a):a||[],!1).length}});var x,y=a.document,z=/^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,A=m.fn.init=function(a,b){var c,d;if(!a)return this;if("string"==typeof a){if(c="<"===a.charAt(0)&&">"===a.charAt(a.length-1)&&a.length>=3?[null,a,null]:z.exec(a),!c||!c[1]&&b)return!b||b.jquery?(b||x).find(a):this.constructor(b).find(a);if(c[1]){if(b=b instanceof m?b[0]:b,m.merge(this,m.parseHTML(c[1],b&&b.nodeType?b.ownerDocument||b:y,!0)),u.test(c[1])&&m.isPlainObject(b))for(c in b)m.isFunction(this[c])?this[c](b[c]):this.attr(c,b[c]);return this}if(d=y.getElementById(c[2]),d&&d.parentNode){if(d.id!==c[2])return x.find(a);this.length=1,this[0]=d}return this.context=y,this.selector=a,this}return a.nodeType?(this.context=this[0]=a,this.length=1,this):m.isFunction(a)?"undefined"!=typeof x.ready?x.ready(a):a(m):(void 0!==a.selector&&(this.selector=a.selector,this.context=a.context),m.makeArray(a,this))};A.prototype=m.fn,x=m(y);var B=/^(?:parents|prev(?:Until|All))/,C={children:!0,contents:!0,next:!0,prev:!0};m.extend({dir:function(a,b,c){var d=[],e=a[b];while(e&&9!==e.nodeType&&(void 0===c||1!==e.nodeType||!m(e).is(c)))1===e.nodeType&&d.push(e),e=e[b];return d},sibling:function(a,b){for(var c=[];a;a=a.nextSibling)1===a.nodeType&&a!==b&&c.push(a);return c}}),m.fn.extend({has:function(a){var b,c=m(a,this),d=c.length;return this.filter(function(){for(b=0;d>b;b++)if(m.contains(this,c[b]))return!0})},closest:function(a,b){for(var c,d=0,e=this.length,f=[],g=t.test(a)||"string"!=typeof a?m(a,b||this.context):0;e>d;d++)for(c=this[d];c&&c!==b;c=c.parentNode)if(c.nodeType<11&&(g?g.index(c)>-1:1===c.nodeType&&m.find.matchesSelector(c,a))){f.push(c);break}return this.pushStack(f.length>1?m.unique(f):f)},index:function(a){return a?"string"==typeof a?m.inArray(this[0],m(a)):m.inArray(a.jquery?a[0]:a,this):this[0]&&this[0].parentNode?this.first().prevAll().length:-1},add:function(a,b){return this.pushStack(m.unique(m.merge(this.get(),m(a,b))))},addBack:function(a){return this.add(null==a?this.prevObject:this.prevObject.filter(a))}});function D(a,b){do a=a[b];while(a&&1!==a.nodeType);return a}m.each({parent:function(a){var b=a.parentNode;return b&&11!==b.nodeType?b:null},parents:function(a){return m.dir(a,"parentNode")},parentsUntil:function(a,b,c){return m.dir(a,"parentNode",c)},next:function(a){return D(a,"nextSibling")},prev:function(a){return D(a,"previousSibling")},nextAll:function(a){return m.dir(a,"nextSibling")},prevAll:function(a){return m.dir(a,"previousSibling")},nextUntil:function(a,b,c){return m.dir(a,"nextSibling",c)},prevUntil:function(a,b,c){return m.dir(a,"previousSibling",c)},siblings:function(a){return m.sibling((a.parentNode||{}).firstChild,a)},children:function(a){return m.sibling(a.firstChild)},contents:function(a){return m.nodeName(a,"iframe")?a.contentDocument||a.contentWindow.document:m.merge([],a.childNodes)}},function(a,b){m.fn[a]=function(c,d){var e=m.map(this,b,c);return"Until"!==a.slice(-5)&&(d=c),d&&"string"==typeof d&&(e=m.filter(d,e)),this.length>1&&(C[a]||(e=m.unique(e)),B.test(a)&&(e=e.reverse())),this.pushStack(e)}});var E=/\S+/g,F={};function G(a){var b=F[a]={};return m.each(a.match(E)||[],function(a,c){b[c]=!0}),b}m.Callbacks=function(a){a="string"==typeof a?F[a]||G(a):m.extend({},a);var b,c,d,e,f,g,h=[],i=!a.once&&[],j=function(l){for(c=a.memory&&l,d=!0,f=g||0,g=0,e=h.length,b=!0;h&&e>f;f++)if(h[f].apply(l[0],l[1])===!1&&a.stopOnFalse){c=!1;break}b=!1,h&&(i?i.length&&j(i.shift()):c?h=[]:k.disable())},k={add:function(){if(h){var d=h.length;!function f(b){m.each(b,function(b,c){var d=m.type(c);"function"===d?a.unique&&k.has(c)||h.push(c):c&&c.length&&"string"!==d&&f(c)})}(arguments),b?e=h.length:c&&(g=d,j(c))}return this},remove:function(){return h&&m.each(arguments,function(a,c){var d;while((d=m.inArray(c,h,d))>-1)h.splice(d,1),b&&(e>=d&&e--,f>=d&&f--)}),this},has:function(a){return a?m.inArray(a,h)>-1:!(!h||!h.length)},empty:function(){return h=[],e=0,this},disable:function(){return h=i=c=void 0,this},disabled:function(){return!h},lock:function(){return i=void 0,c||k.disable(),this},locked:function(){return!i},fireWith:function(a,c){return!h||d&&!i||(c=c||[],c=[a,c.slice?c.slice():c],b?i.push(c):j(c)),this},fire:function(){return k.fireWith(this,arguments),this},fired:function(){return!!d}};return k},m.extend({Deferred:function(a){var b=[["resolve","done",m.Callbacks("once memory"),"resolved"],["reject","fail",m.Callbacks("once memory"),"rejected"],["notify","progress",m.Callbacks("memory")]],c="pending",d={state:function(){return c},always:function(){return e.done(arguments).fail(arguments),this},then:function(){var a=arguments;return m.Deferred(function(c){m.each(b,function(b,f){var g=m.isFunction(a[b])&&a[b];e[f[1]](function(){var a=g&&g.apply(this,arguments);a&&m.isFunction(a.promise)?a.promise().done(c.resolve).fail(c.reject).progress(c.notify):c[f[0]+"With"](this===d?c.promise():this,g?[a]:arguments)})}),a=null}).promise()},promise:function(a){return null!=a?m.extend(a,d):d}},e={};return d.pipe=d.then,m.each(b,function(a,f){var g=f[2],h=f[3];d[f[1]]=g.add,h&&g.add(function(){c=h},b[1^a][2].disable,b[2][2].lock),e[f[0]]=function(){return e[f[0]+"With"](this===e?d:this,arguments),this},e[f[0]+"With"]=g.fireWith}),d.promise(e),a&&a.call(e,e),e},when:function(a){var b=0,c=d.call(arguments),e=c.length,f=1!==e||a&&m.isFunction(a.promise)?e:0,g=1===f?a:m.Deferred(),h=function(a,b,c){return function(e){b[a]=this,c[a]=arguments.length>1?d.call(arguments):e,c===i?g.notifyWith(b,c):--f||g.resolveWith(b,c)}},i,j,k;if(e>1)for(i=new Array(e),j=new Array(e),k=new Array(e);e>b;b++)c[b]&&m.isFunction(c[b].promise)?c[b].promise().done(h(b,k,c)).fail(g.reject).progress(h(b,j,i)):--f;return f||g.resolveWith(k,c),g.promise()}});var H;m.fn.ready=function(a){return m.ready.promise().done(a),this},m.extend({isReady:!1,readyWait:1,holdReady:function(a){a?m.readyWait++:m.ready(!0)},ready:function(a){if(a===!0?!--m.readyWait:!m.isReady){if(!y.body)return setTimeout(m.ready);m.isReady=!0,a!==!0&&--m.readyWait>0||(H.resolveWith(y,[m]),m.fn.triggerHandler&&(m(y).triggerHandler("ready"),m(y).off("ready")))}}});function I(){y.addEventListener?(y.removeEventListener("DOMContentLoaded",J,!1),a.removeEventListener("load",J,!1)):(y.detachEvent("onreadystatechange",J),a.detachEvent("onload",J))}function J(){(y.addEventListener||"load"===event.type||"complete"===y.readyState)&&(I(),m.ready())}m.ready.promise=function(b){if(!H)if(H=m.Deferred(),"complete"===y.readyState)setTimeout(m.ready);else if(y.addEventListener)y.addEventListener("DOMContentLoaded",J,!1),a.addEventListener("load",J,!1);else{y.attachEvent("onreadystatechange",J),a.attachEvent("onload",J);var c=!1;try{c=null==a.frameElement&&y.documentElement}catch(d){}c&&c.doScroll&&!function e(){if(!m.isReady){try{c.doScroll("left")}catch(a){return setTimeout(e,50)}I(),m.ready()}}()}return H.promise(b)};var K="undefined",L;for(L in m(k))break;k.ownLast="0"!==L,k.inlineBlockNeedsLayout=!1,m(function(){var a,b,c,d;c=y.getElementsByTagName("body")[0],c&&c.style&&(b=y.createElement("div"),d=y.createElement("div"),d.style.cssText="position:absolute;border:0;width:0;height:0;top:0;left:-9999px",c.appendChild(d).appendChild(b),typeof b.style.zoom!==K&&(b.style.cssText="display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1",k.inlineBlockNeedsLayout=a=3===b.offsetWidth,a&&(c.style.zoom=1)),c.removeChild(d))}),function(){var a=y.createElement("div");if(null==k.deleteExpando){k.deleteExpando=!0;try{delete a.test}catch(b){k.deleteExpando=!1}}a=null}(),m.acceptData=function(a){var b=m.noData[(a.nodeName+" ").toLowerCase()],c=+a.nodeType||1;return 1!==c&&9!==c?!1:!b||b!==!0&&a.getAttribute("classid")===b};var M=/^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,N=/([A-Z])/g;function O(a,b,c){if(void 0===c&&1===a.nodeType){var d="data-"+b.replace(N,"-$1").toLowerCase();if(c=a.getAttribute(d),"string"==typeof c){try{c="true"===c?!0:"false"===c?!1:"null"===c?null:+c+""===c?+c:M.test(c)?m.parseJSON(c):c}catch(e){}m.data(a,b,c)}else c=void 0}return c}function P(a){var b;for(b in a)if(("data"!==b||!m.isEmptyObject(a[b]))&&"toJSON"!==b)return!1;return!0}function Q(a,b,d,e){if(m.acceptData(a)){var f,g,h=m.expando,i=a.nodeType,j=i?m.cache:a,k=i?a[h]:a[h]&&h;
-if(k&&j[k]&&(e||j[k].data)||void 0!==d||"string"!=typeof b)return k||(k=i?a[h]=c.pop()||m.guid++:h),j[k]||(j[k]=i?{}:{toJSON:m.noop}),("object"==typeof b||"function"==typeof b)&&(e?j[k]=m.extend(j[k],b):j[k].data=m.extend(j[k].data,b)),g=j[k],e||(g.data||(g.data={}),g=g.data),void 0!==d&&(g[m.camelCase(b)]=d),"string"==typeof b?(f=g[b],null==f&&(f=g[m.camelCase(b)])):f=g,f}}function R(a,b,c){if(m.acceptData(a)){var d,e,f=a.nodeType,g=f?m.cache:a,h=f?a[m.expando]:m.expando;if(g[h]){if(b&&(d=c?g[h]:g[h].data)){m.isArray(b)?b=b.concat(m.map(b,m.camelCase)):b in d?b=[b]:(b=m.camelCase(b),b=b in d?[b]:b.split(" ")),e=b.length;while(e--)delete d[b[e]];if(c?!P(d):!m.isEmptyObject(d))return}(c||(delete g[h].data,P(g[h])))&&(f?m.cleanData([a],!0):k.deleteExpando||g!=g.window?delete g[h]:g[h]=null)}}}m.extend({cache:{},noData:{"applet ":!0,"embed ":!0,"object ":"clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"},hasData:function(a){return a=a.nodeType?m.cache[a[m.expando]]:a[m.expando],!!a&&!P(a)},data:function(a,b,c){return Q(a,b,c)},removeData:function(a,b){return R(a,b)},_data:function(a,b,c){return Q(a,b,c,!0)},_removeData:function(a,b){return R(a,b,!0)}}),m.fn.extend({data:function(a,b){var c,d,e,f=this[0],g=f&&f.attributes;if(void 0===a){if(this.length&&(e=m.data(f),1===f.nodeType&&!m._data(f,"parsedAttrs"))){c=g.length;while(c--)g[c]&&(d=g[c].name,0===d.indexOf("data-")&&(d=m.camelCase(d.slice(5)),O(f,d,e[d])));m._data(f,"parsedAttrs",!0)}return e}return"object"==typeof a?this.each(function(){m.data(this,a)}):arguments.length>1?this.each(function(){m.data(this,a,b)}):f?O(f,a,m.data(f,a)):void 0},removeData:function(a){return this.each(function(){m.removeData(this,a)})}}),m.extend({queue:function(a,b,c){var d;return a?(b=(b||"fx")+"queue",d=m._data(a,b),c&&(!d||m.isArray(c)?d=m._data(a,b,m.makeArray(c)):d.push(c)),d||[]):void 0},dequeue:function(a,b){b=b||"fx";var c=m.queue(a,b),d=c.length,e=c.shift(),f=m._queueHooks(a,b),g=function(){m.dequeue(a,b)};"inprogress"===e&&(e=c.shift(),d--),e&&("fx"===b&&c.unshift("inprogress"),delete f.stop,e.call(a,g,f)),!d&&f&&f.empty.fire()},_queueHooks:function(a,b){var c=b+"queueHooks";return m._data(a,c)||m._data(a,c,{empty:m.Callbacks("once memory").add(function(){m._removeData(a,b+"queue"),m._removeData(a,c)})})}}),m.fn.extend({queue:function(a,b){var c=2;return"string"!=typeof a&&(b=a,a="fx",c--),arguments.length<c?m.queue(this[0],a):void 0===b?this:this.each(function(){var c=m.queue(this,a,b);m._queueHooks(this,a),"fx"===a&&"inprogress"!==c[0]&&m.dequeue(this,a)})},dequeue:function(a){return this.each(function(){m.dequeue(this,a)})},clearQueue:function(a){return this.queue(a||"fx",[])},promise:function(a,b){var c,d=1,e=m.Deferred(),f=this,g=this.length,h=function(){--d||e.resolveWith(f,[f])};"string"!=typeof a&&(b=a,a=void 0),a=a||"fx";while(g--)c=m._data(f[g],a+"queueHooks"),c&&c.empty&&(d++,c.empty.add(h));return h(),e.promise(b)}});var S=/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/.source,T=["Top","Right","Bottom","Left"],U=function(a,b){return a=b||a,"none"===m.css(a,"display")||!m.contains(a.ownerDocument,a)},V=m.access=function(a,b,c,d,e,f,g){var h=0,i=a.length,j=null==c;if("object"===m.type(c)){e=!0;for(h in c)m.access(a,b,h,c[h],!0,f,g)}else if(void 0!==d&&(e=!0,m.isFunction(d)||(g=!0),j&&(g?(b.call(a,d),b=null):(j=b,b=function(a,b,c){return j.call(m(a),c)})),b))for(;i>h;h++)b(a[h],c,g?d:d.call(a[h],h,b(a[h],c)));return e?a:j?b.call(a):i?b(a[0],c):f},W=/^(?:checkbox|radio)$/i;!function(){var a=y.createElement("input"),b=y.createElement("div"),c=y.createDocumentFragment();if(b.innerHTML=" <link/><table></table><a href='/a'>a</a><input type='checkbox'/>",k.leadingWhitespace=3===b.firstChild.nodeType,k.tbody=!b.getElementsByTagName("tbody").length,k.htmlSerialize=!!b.getElementsByTagName("link").length,k.html5Clone="<:nav></:nav>"!==y.createElement("nav").cloneNode(!0).outerHTML,a.type="checkbox",a.checked=!0,c.appendChild(a),k.appendChecked=a.checked,b.innerHTML="<textarea>x</textarea>",k.noCloneChecked=!!b.cloneNode(!0).lastChild.defaultValue,c.appendChild(b),b.innerHTML="<input type='radio' checked='checked' name='t'/>",k.checkClone=b.cloneNode(!0).cloneNode(!0).lastChild.checked,k.noCloneEvent=!0,b.attachEvent&&(b.attachEvent("onclick",function(){k.noCloneEvent=!1}),b.cloneNode(!0).click()),null==k.deleteExpando){k.deleteExpando=!0;try{delete b.test}catch(d){k.deleteExpando=!1}}}(),function(){var b,c,d=y.createElement("div");for(b in{submit:!0,change:!0,focusin:!0})c="on"+b,(k[b+"Bubbles"]=c in a)||(d.setAttribute(c,"t"),k[b+"Bubbles"]=d.attributes[c].expando===!1);d=null}();var X=/^(?:input|select|textarea)$/i,Y=/^key/,Z=/^(?:mouse|pointer|contextmenu)|click/,$=/^(?:focusinfocus|focusoutblur)$/,_=/^([^.]*)(?:\.(.+)|)$/;function ab(){return!0}function bb(){return!1}function cb(){try{return y.activeElement}catch(a){}}m.event={global:{},add:function(a,b,c,d,e){var f,g,h,i,j,k,l,n,o,p,q,r=m._data(a);if(r){c.handler&&(i=c,c=i.handler,e=i.selector),c.guid||(c.guid=m.guid++),(g=r.events)||(g=r.events={}),(k=r.handle)||(k=r.handle=function(a){return typeof m===K||a&&m.event.triggered===a.type?void 0:m.event.dispatch.apply(k.elem,arguments)},k.elem=a),b=(b||"").match(E)||[""],h=b.length;while(h--)f=_.exec(b[h])||[],o=q=f[1],p=(f[2]||"").split(".").sort(),o&&(j=m.event.special[o]||{},o=(e?j.delegateType:j.bindType)||o,j=m.event.special[o]||{},l=m.extend({type:o,origType:q,data:d,handler:c,guid:c.guid,selector:e,needsContext:e&&m.expr.match.needsContext.test(e),namespace:p.join(".")},i),(n=g[o])||(n=g[o]=[],n.delegateCount=0,j.setup&&j.setup.call(a,d,p,k)!==!1||(a.addEventListener?a.addEventListener(o,k,!1):a.attachEvent&&a.attachEvent("on"+o,k))),j.add&&(j.add.call(a,l),l.handler.guid||(l.handler.guid=c.guid)),e?n.splice(n.delegateCount++,0,l):n.push(l),m.event.global[o]=!0);a=null}},remove:function(a,b,c,d,e){var f,g,h,i,j,k,l,n,o,p,q,r=m.hasData(a)&&m._data(a);if(r&&(k=r.events)){b=(b||"").match(E)||[""],j=b.length;while(j--)if(h=_.exec(b[j])||[],o=q=h[1],p=(h[2]||"").split(".").sort(),o){l=m.event.special[o]||{},o=(d?l.delegateType:l.bindType)||o,n=k[o]||[],h=h[2]&&new RegExp("(^|\\.)"+p.join("\\.(?:.*\\.|)")+"(\\.|$)"),i=f=n.length;while(f--)g=n[f],!e&&q!==g.origType||c&&c.guid!==g.guid||h&&!h.test(g.namespace)||d&&d!==g.selector&&("**"!==d||!g.selector)||(n.splice(f,1),g.selector&&n.delegateCount--,l.remove&&l.remove.call(a,g));i&&!n.length&&(l.teardown&&l.teardown.call(a,p,r.handle)!==!1||m.removeEvent(a,o,r.handle),delete k[o])}else for(o in k)m.event.remove(a,o+b[j],c,d,!0);m.isEmptyObject(k)&&(delete r.handle,m._removeData(a,"events"))}},trigger:function(b,c,d,e){var f,g,h,i,k,l,n,o=[d||y],p=j.call(b,"type")?b.type:b,q=j.call(b,"namespace")?b.namespace.split("."):[];if(h=l=d=d||y,3!==d.nodeType&&8!==d.nodeType&&!$.test(p+m.event.triggered)&&(p.indexOf(".")>=0&&(q=p.split("."),p=q.shift(),q.sort()),g=p.indexOf(":")<0&&"on"+p,b=b[m.expando]?b:new m.Event(p,"object"==typeof b&&b),b.isTrigger=e?2:3,b.namespace=q.join("."),b.namespace_re=b.namespace?new RegExp("(^|\\.)"+q.join("\\.(?:.*\\.|)")+"(\\.|$)"):null,b.result=void 0,b.target||(b.target=d),c=null==c?[b]:m.makeArray(c,[b]),k=m.event.special[p]||{},e||!k.trigger||k.trigger.apply(d,c)!==!1)){if(!e&&!k.noBubble&&!m.isWindow(d)){for(i=k.delegateType||p,$.test(i+p)||(h=h.parentNode);h;h=h.parentNode)o.push(h),l=h;l===(d.ownerDocument||y)&&o.push(l.defaultView||l.parentWindow||a)}n=0;while((h=o[n++])&&!b.isPropagationStopped())b.type=n>1?i:k.bindType||p,f=(m._data(h,"events")||{})[b.type]&&m._data(h,"handle"),f&&f.apply(h,c),f=g&&h[g],f&&f.apply&&m.acceptData(h)&&(b.result=f.apply(h,c),b.result===!1&&b.preventDefault());if(b.type=p,!e&&!b.isDefaultPrevented()&&(!k._default||k._default.apply(o.pop(),c)===!1)&&m.acceptData(d)&&g&&d[p]&&!m.isWindow(d)){l=d[g],l&&(d[g]=null),m.event.triggered=p;try{d[p]()}catch(r){}m.event.triggered=void 0,l&&(d[g]=l)}return b.result}},dispatch:function(a){a=m.event.fix(a);var b,c,e,f,g,h=[],i=d.call(arguments),j=(m._data(this,"events")||{})[a.type]||[],k=m.event.special[a.type]||{};if(i[0]=a,a.delegateTarget=this,!k.preDispatch||k.preDispatch.call(this,a)!==!1){h=m.event.handlers.call(this,a,j),b=0;while((f=h[b++])&&!a.isPropagationStopped()){a.currentTarget=f.elem,g=0;while((e=f.handlers[g++])&&!a.isImmediatePropagationStopped())(!a.namespace_re||a.namespace_re.test(e.namespace))&&(a.handleObj=e,a.data=e.data,c=((m.event.special[e.origType]||{}).handle||e.handler).apply(f.elem,i),void 0!==c&&(a.result=c)===!1&&(a.preventDefault(),a.stopPropagation()))}return k.postDispatch&&k.postDispatch.call(this,a),a.result}},handlers:function(a,b){var c,d,e,f,g=[],h=b.delegateCount,i=a.target;if(h&&i.nodeType&&(!a.button||"click"!==a.type))for(;i!=this;i=i.parentNode||this)if(1===i.nodeType&&(i.disabled!==!0||"click"!==a.type)){for(e=[],f=0;h>f;f++)d=b[f],c=d.selector+" ",void 0===e[c]&&(e[c]=d.needsContext?m(c,this).index(i)>=0:m.find(c,this,null,[i]).length),e[c]&&e.push(d);e.length&&g.push({elem:i,handlers:e})}return h<b.length&&g.push({elem:this,handlers:b.slice(h)}),g},fix:function(a){if(a[m.expando])return a;var b,c,d,e=a.type,f=a,g=this.fixHooks[e];g||(this.fixHooks[e]=g=Z.test(e)?this.mouseHooks:Y.test(e)?this.keyHooks:{}),d=g.props?this.props.concat(g.props):this.props,a=new m.Event(f),b=d.length;while(b--)c=d[b],a[c]=f[c];return a.target||(a.target=f.srcElement||y),3===a.target.nodeType&&(a.target=a.target.parentNode),a.metaKey=!!a.metaKey,g.filter?g.filter(a,f):a},props:"altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),fixHooks:{},keyHooks:{props:"char charCode key keyCode".split(" "),filter:function(a,b){return null==a.which&&(a.which=null!=b.charCode?b.charCode:b.keyCode),a}},mouseHooks:{props:"button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),filter:function(a,b){var c,d,e,f=b.button,g=b.fromElement;return null==a.pageX&&null!=b.clientX&&(d=a.target.ownerDocument||y,e=d.documentElement,c=d.body,a.pageX=b.clientX+(e&&e.scrollLeft||c&&c.scrollLeft||0)-(e&&e.clientLeft||c&&c.clientLeft||0),a.pageY=b.clientY+(e&&e.scrollTop||c&&c.scrollTop||0)-(e&&e.clientTop||c&&c.clientTop||0)),!a.relatedTarget&&g&&(a.relatedTarget=g===a.target?b.toElement:g),a.which||void 0===f||(a.which=1&f?1:2&f?3:4&f?2:0),a}},special:{load:{noBubble:!0},focus:{trigger:function(){if(this!==cb()&&this.focus)try{return this.focus(),!1}catch(a){}},delegateType:"focusin"},blur:{trigger:function(){return this===cb()&&this.blur?(this.blur(),!1):void 0},delegateType:"focusout"},click:{trigger:function(){return m.nodeName(this,"input")&&"checkbox"===this.type&&this.click?(this.click(),!1):void 0},_default:function(a){return m.nodeName(a.target,"a")}},beforeunload:{postDispatch:function(a){void 0!==a.result&&a.originalEvent&&(a.originalEvent.returnValue=a.result)}}},simulate:function(a,b,c,d){var e=m.extend(new m.Event,c,{type:a,isSimulated:!0,originalEvent:{}});d?m.event.trigger(e,null,b):m.event.dispatch.call(b,e),e.isDefaultPrevented()&&c.preventDefault()}},m.removeEvent=y.removeEventListener?function(a,b,c){a.removeEventListener&&a.removeEventListener(b,c,!1)}:function(a,b,c){var d="on"+b;a.detachEvent&&(typeof a[d]===K&&(a[d]=null),a.detachEvent(d,c))},m.Event=function(a,b){return this instanceof m.Event?(a&&a.type?(this.originalEvent=a,this.type=a.type,this.isDefaultPrevented=a.defaultPrevented||void 0===a.defaultPrevented&&a.returnValue===!1?ab:bb):this.type=a,b&&m.extend(this,b),this.timeStamp=a&&a.timeStamp||m.now(),void(this[m.expando]=!0)):new m.Event(a,b)},m.Event.prototype={isDefaultPrevented:bb,isPropagationStopped:bb,isImmediatePropagationStopped:bb,preventDefault:function(){var a=this.originalEvent;this.isDefaultPrevented=ab,a&&(a.preventDefault?a.preventDefault():a.returnValue=!1)},stopPropagation:function(){var a=this.originalEvent;this.isPropagationStopped=ab,a&&(a.stopPropagation&&a.stopPropagation(),a.cancelBubble=!0)},stopImmediatePropagation:function(){var a=this.originalEvent;this.isImmediatePropagationStopped=ab,a&&a.stopImmediatePropagation&&a.stopImmediatePropagation(),this.stopPropagation()}},m.each({mouseenter:"mouseover",mouseleave:"mouseout",pointerenter:"pointerover",pointerleave:"pointerout"},function(a,b){m.event.special[a]={delegateType:b,bindType:b,handle:function(a){var c,d=this,e=a.relatedTarget,f=a.handleObj;return(!e||e!==d&&!m.contains(d,e))&&(a.type=f.origType,c=f.handler.apply(this,arguments),a.type=b),c}}}),k.submitBubbles||(m.event.special.submit={setup:function(){return m.nodeName(this,"form")?!1:void m.event.add(this,"click._submit keypress._submit",function(a){var b=a.target,c=m.nodeName(b,"input")||m.nodeName(b,"button")?b.form:void 0;c&&!m._data(c,"submitBubbles")&&(m.event.add(c,"submit._submit",function(a){a._submit_bubble=!0}),m._data(c,"submitBubbles",!0))})},postDispatch:function(a){a._submit_bubble&&(delete a._submit_bubble,this.parentNode&&!a.isTrigger&&m.event.simulate("submit",this.parentNode,a,!0))},teardown:function(){return m.nodeName(this,"form")?!1:void m.event.remove(this,"._submit")}}),k.changeBubbles||(m.event.special.change={setup:function(){return X.test(this.nodeName)?(("checkbox"===this.type||"radio"===this.type)&&(m.event.add(this,"propertychange._change",function(a){"checked"===a.originalEvent.propertyName&&(this._just_changed=!0)}),m.event.add(this,"click._change",function(a){this._just_changed&&!a.isTrigger&&(this._just_changed=!1),m.event.simulate("change",this,a,!0)})),!1):void m.event.add(this,"beforeactivate._change",function(a){var b=a.target;X.test(b.nodeName)&&!m._data(b,"changeBubbles")&&(m.event.add(b,"change._change",function(a){!this.parentNode||a.isSimulated||a.isTrigger||m.event.simulate("change",this.parentNode,a,!0)}),m._data(b,"changeBubbles",!0))})},handle:function(a){var b=a.target;return this!==b||a.isSimulated||a.isTrigger||"radio"!==b.type&&"checkbox"!==b.type?a.handleObj.handler.apply(this,arguments):void 0},teardown:function(){return m.event.remove(this,"._change"),!X.test(this.nodeName)}}),k.focusinBubbles||m.each({focus:"focusin",blur:"focusout"},function(a,b){var c=function(a){m.event.simulate(b,a.target,m.event.fix(a),!0)};m.event.special[b]={setup:function(){var d=this.ownerDocument||this,e=m._data(d,b);e||d.addEventListener(a,c,!0),m._data(d,b,(e||0)+1)},teardown:function(){var d=this.ownerDocument||this,e=m._data(d,b)-1;e?m._data(d,b,e):(d.removeEventListener(a,c,!0),m._removeData(d,b))}}}),m.fn.extend({on:function(a,b,c,d,e){var f,g;if("object"==typeof a){"string"!=typeof b&&(c=c||b,b=void 0);for(f in a)this.on(f,b,c,a[f],e);return this}if(null==c&&null==d?(d=b,c=b=void 0):null==d&&("string"==typeof b?(d=c,c=void 0):(d=c,c=b,b=void 0)),d===!1)d=bb;else if(!d)return this;return 1===e&&(g=d,d=function(a){return m().off(a),g.apply(this,arguments)},d.guid=g.guid||(g.guid=m.guid++)),this.each(function(){m.event.add(this,a,d,c,b)})},one:function(a,b,c,d){return this.on(a,b,c,d,1)},off:function(a,b,c){var d,e;if(a&&a.preventDefault&&a.handleObj)return d=a.handleObj,m(a.delegateTarget).off(d.namespace?d.origType+"."+d.namespace:d.origType,d.selector,d.handler),this;if("object"==typeof a){for(e in a)this.off(e,b,a[e]);return this}return(b===!1||"function"==typeof b)&&(c=b,b=void 0),c===!1&&(c=bb),this.each(function(){m.event.remove(this,a,c,b)})},trigger:function(a,b){return this.each(function(){m.event.trigger(a,b,this)})},triggerHandler:function(a,b){var c=this[0];return c?m.event.trigger(a,b,c,!0):void 0}});function db(a){var b=eb.split("|"),c=a.createDocumentFragment();if(c.createElement)while(b.length)c.createElement(b.pop());return c}var eb="abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",fb=/ jQuery\d+="(?:null|\d+)"/g,gb=new RegExp("<(?:"+eb+")[\\s/>]","i"),hb=/^\s+/,ib=/<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,jb=/<([\w:]+)/,kb=/<tbody/i,lb=/<|&#?\w+;/,mb=/<(?:script|style|link)/i,nb=/checked\s*(?:[^=]|=\s*.checked.)/i,ob=/^$|\/(?:java|ecma)script/i,pb=/^true\/(.*)/,qb=/^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g,rb={option:[1,"<select multiple='multiple'>","</select>"],legend:[1,"<fieldset>","</fieldset>"],area:[1,"<map>","</map>"],param:[1,"<object>","</object>"],thead:[1,"<table>","</table>"],tr:[2,"<table><tbody>","</tbody></table>"],col:[2,"<table><tbody></tbody><colgroup>","</colgroup></table>"],td:[3,"<table><tbody><tr>","</tr></tbody></table>"],_default:k.htmlSerialize?[0,"",""]:[1,"X<div>","</div>"]},sb=db(y),tb=sb.appendChild(y.createElement("div"));rb.optgroup=rb.option,rb.tbody=rb.tfoot=rb.colgroup=rb.caption=rb.thead,rb.th=rb.td;function ub(a,b){var c,d,e=0,f=typeof a.getElementsByTagName!==K?a.getElementsByTagName(b||"*"):typeof a.querySelectorAll!==K?a.querySelectorAll(b||"*"):void 0;if(!f)for(f=[],c=a.childNodes||a;null!=(d=c[e]);e++)!b||m.nodeName(d,b)?f.push(d):m.merge(f,ub(d,b));return void 0===b||b&&m.nodeName(a,b)?m.merge([a],f):f}function vb(a){W.test(a.type)&&(a.defaultChecked=a.checked)}function wb(a,b){return m.nodeName(a,"table")&&m.nodeName(11!==b.nodeType?b:b.firstChild,"tr")?a.getElementsByTagName("tbody")[0]||a.appendChild(a.ownerDocument.createElement("tbody")):a}function xb(a){return a.type=(null!==m.find.attr(a,"type"))+"/"+a.type,a}function yb(a){var b=pb.exec(a.type);return b?a.type=b[1]:a.removeAttribute("type"),a}function zb(a,b){for(var c,d=0;null!=(c=a[d]);d++)m._data(c,"globalEval",!b||m._data(b[d],"globalEval"))}function Ab(a,b){if(1===b.nodeType&&m.hasData(a)){var c,d,e,f=m._data(a),g=m._data(b,f),h=f.events;if(h){delete g.handle,g.events={};for(c in h)for(d=0,e=h[c].length;e>d;d++)m.event.add(b,c,h[c][d])}g.data&&(g.data=m.extend({},g.data))}}function Bb(a,b){var c,d,e;if(1===b.nodeType){if(c=b.nodeName.toLowerCase(),!k.noCloneEvent&&b[m.expando]){e=m._data(b);for(d in e.events)m.removeEvent(b,d,e.handle);b.removeAttribute(m.expando)}"script"===c&&b.text!==a.text?(xb(b).text=a.text,yb(b)):"object"===c?(b.parentNode&&(b.outerHTML=a.outerHTML),k.html5Clone&&a.innerHTML&&!m.trim(b.innerHTML)&&(b.innerHTML=a.innerHTML)):"input"===c&&W.test(a.type)?(b.defaultChecked=b.checked=a.checked,b.value!==a.value&&(b.value=a.value)):"option"===c?b.defaultSelected=b.selected=a.defaultSelected:("input"===c||"textarea"===c)&&(b.defaultValue=a.defaultValue)}}m.extend({clone:function(a,b,c){var d,e,f,g,h,i=m.contains(a.ownerDocument,a);if(k.html5Clone||m.isXMLDoc(a)||!gb.test("<"+a.nodeName+">")?f=a.cloneNode(!0):(tb.innerHTML=a.outerHTML,tb.removeChild(f=tb.firstChild)),!(k.noCloneEvent&&k.noCloneChecked||1!==a.nodeType&&11!==a.nodeType||m.isXMLDoc(a)))for(d=ub(f),h=ub(a),g=0;null!=(e=h[g]);++g)d[g]&&Bb(e,d[g]);if(b)if(c)for(h=h||ub(a),d=d||ub(f),g=0;null!=(e=h[g]);g++)Ab(e,d[g]);else Ab(a,f);return d=ub(f,"script"),d.length>0&&zb(d,!i&&ub(a,"script")),d=h=e=null,f},buildFragment:function(a,b,c,d){for(var e,f,g,h,i,j,l,n=a.length,o=db(b),p=[],q=0;n>q;q++)if(f=a[q],f||0===f)if("object"===m.type(f))m.merge(p,f.nodeType?[f]:f);else if(lb.test(f)){h=h||o.appendChild(b.createElement("div")),i=(jb.exec(f)||["",""])[1].toLowerCase(),l=rb[i]||rb._default,h.innerHTML=l[1]+f.replace(ib,"<$1></$2>")+l[2],e=l[0];while(e--)h=h.lastChild;if(!k.leadingWhitespace&&hb.test(f)&&p.push(b.createTextNode(hb.exec(f)[0])),!k.tbody){f="table"!==i||kb.test(f)?"<table>"!==l[1]||kb.test(f)?0:h:h.firstChild,e=f&&f.childNodes.length;while(e--)m.nodeName(j=f.childNodes[e],"tbody")&&!j.childNodes.length&&f.removeChild(j)}m.merge(p,h.childNodes),h.textContent="";while(h.firstChild)h.removeChild(h.firstChild);h=o.lastChild}else p.push(b.createTextNode(f));h&&o.removeChild(h),k.appendChecked||m.grep(ub(p,"input"),vb),q=0;while(f=p[q++])if((!d||-1===m.inArray(f,d))&&(g=m.contains(f.ownerDocument,f),h=ub(o.appendChild(f),"script"),g&&zb(h),c)){e=0;while(f=h[e++])ob.test(f.type||"")&&c.push(f)}return h=null,o},cleanData:function(a,b){for(var d,e,f,g,h=0,i=m.expando,j=m.cache,l=k.deleteExpando,n=m.event.special;null!=(d=a[h]);h++)if((b||m.acceptData(d))&&(f=d[i],g=f&&j[f])){if(g.events)for(e in g.events)n[e]?m.event.remove(d,e):m.removeEvent(d,e,g.handle);j[f]&&(delete j[f],l?delete d[i]:typeof d.removeAttribute!==K?d.removeAttribute(i):d[i]=null,c.push(f))}}}),m.fn.extend({text:function(a){return V(this,function(a){return void 0===a?m.text(this):this.empty().append((this[0]&&this[0].ownerDocument||y).createTextNode(a))},null,a,arguments.length)},append:function(){return this.domManip(arguments,function(a){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var b=wb(this,a);b.appendChild(a)}})},prepend:function(){return this.domManip(arguments,function(a){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var b=wb(this,a);b.insertBefore(a,b.firstChild)}})},before:function(){return this.domManip(arguments,function(a){this.parentNode&&this.parentNode.insertBefore(a,this)})},after:function(){return this.domManip(arguments,function(a){this.parentNode&&this.parentNode.insertBefore(a,this.nextSibling)})},remove:function(a,b){for(var c,d=a?m.filter(a,this):this,e=0;null!=(c=d[e]);e++)b||1!==c.nodeType||m.cleanData(ub(c)),c.parentNode&&(b&&m.contains(c.ownerDocument,c)&&zb(ub(c,"script")),c.parentNode.removeChild(c));return this},empty:function(){for(var a,b=0;null!=(a=this[b]);b++){1===a.nodeType&&m.cleanData(ub(a,!1));while(a.firstChild)a.removeChild(a.firstChild);a.options&&m.nodeName(a,"select")&&(a.options.length=0)}return this},clone:function(a,b){return a=null==a?!1:a,b=null==b?a:b,this.map(function(){return m.clone(this,a,b)})},html:function(a){return V(this,function(a){var b=this[0]||{},c=0,d=this.length;if(void 0===a)return 1===b.nodeType?b.innerHTML.replace(fb,""):void 0;if(!("string"!=typeof a||mb.test(a)||!k.htmlSerialize&&gb.test(a)||!k.leadingWhitespace&&hb.test(a)||rb[(jb.exec(a)||["",""])[1].toLowerCase()])){a=a.replace(ib,"<$1></$2>");try{for(;d>c;c++)b=this[c]||{},1===b.nodeType&&(m.cleanData(ub(b,!1)),b.innerHTML=a);b=0}catch(e){}}b&&this.empty().append(a)},null,a,arguments.length)},replaceWith:function(){var a=arguments[0];return this.domManip(arguments,function(b){a=this.parentNode,m.cleanData(ub(this)),a&&a.replaceChild(b,this)}),a&&(a.length||a.nodeType)?this:this.remove()},detach:function(a){return this.remove(a,!0)},domManip:function(a,b){a=e.apply([],a);var c,d,f,g,h,i,j=0,l=this.length,n=this,o=l-1,p=a[0],q=m.isFunction(p);if(q||l>1&&"string"==typeof p&&!k.checkClone&&nb.test(p))return this.each(function(c){var d=n.eq(c);q&&(a[0]=p.call(this,c,d.html())),d.domManip(a,b)});if(l&&(i=m.buildFragment(a,this[0].ownerDocument,!1,this),c=i.firstChild,1===i.childNodes.length&&(i=c),c)){for(g=m.map(ub(i,"script"),xb),f=g.length;l>j;j++)d=i,j!==o&&(d=m.clone(d,!0,!0),f&&m.merge(g,ub(d,"script"))),b.call(this[j],d,j);if(f)for(h=g[g.length-1].ownerDocument,m.map(g,yb),j=0;f>j;j++)d=g[j],ob.test(d.type||"")&&!m._data(d,"globalEval")&&m.contains(h,d)&&(d.src?m._evalUrl&&m._evalUrl(d.src):m.globalEval((d.text||d.textContent||d.innerHTML||"").replace(qb,"")));i=c=null}return this}}),m.each({appendTo:"append",prependTo:"prepend",insertBefore:"before",insertAfter:"after",replaceAll:"replaceWith"},function(a,b){m.fn[a]=function(a){for(var c,d=0,e=[],g=m(a),h=g.length-1;h>=d;d++)c=d===h?this:this.clone(!0),m(g[d])[b](c),f.apply(e,c.get());return this.pushStack(e)}});var Cb,Db={};function Eb(b,c){var d,e=m(c.createElement(b)).appendTo(c.body),f=a.getDefaultComputedStyle&&(d=a.getDefaultComputedStyle(e[0]))?d.display:m.css(e[0],"display");return e.detach(),f}function Fb(a){var b=y,c=Db[a];return c||(c=Eb(a,b),"none"!==c&&c||(Cb=(Cb||m("<iframe frameborder='0' width='0' height='0'/>")).appendTo(b.documentElement),b=(Cb[0].contentWindow||Cb[0].contentDocument).document,b.write(),b.close(),c=Eb(a,b),Cb.detach()),Db[a]=c),c}!function(){var a;k.shrinkWrapBlocks=function(){if(null!=a)return a;a=!1;var b,c,d;return c=y.getElementsByTagName("body")[0],c&&c.style?(b=y.createElement("div"),d=y.createElement("div"),d.style.cssText="position:absolute;border:0;width:0;height:0;top:0;left:-9999px",c.appendChild(d).appendChild(b),typeof b.style.zoom!==K&&(b.style.cssText="-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;display:block;margin:0;border:0;padding:1px;width:1px;zoom:1",b.appendChild(y.createElement("div")).style.width="5px",a=3!==b.offsetWidth),c.removeChild(d),a):void 0}}();var Gb=/^margin/,Hb=new RegExp("^("+S+")(?!px)[a-z%]+$","i"),Ib,Jb,Kb=/^(top|right|bottom|left)$/;a.getComputedStyle?(Ib=function(a){return a.ownerDocument.defaultView.getComputedStyle(a,null)},Jb=function(a,b,c){var d,e,f,g,h=a.style;return c=c||Ib(a),g=c?c.getPropertyValue(b)||c[b]:void 0,c&&(""!==g||m.contains(a.ownerDocument,a)||(g=m.style(a,b)),Hb.test(g)&&Gb.test(b)&&(d=h.width,e=h.minWidth,f=h.maxWidth,h.minWidth=h.maxWidth=h.width=g,g=c.width,h.width=d,h.minWidth=e,h.maxWidth=f)),void 0===g?g:g+""}):y.documentElement.currentStyle&&(Ib=function(a){return a.currentStyle},Jb=function(a,b,c){var d,e,f,g,h=a.style;return c=c||Ib(a),g=c?c[b]:void 0,null==g&&h&&h[b]&&(g=h[b]),Hb.test(g)&&!Kb.test(b)&&(d=h.left,e=a.runtimeStyle,f=e&&e.left,f&&(e.left=a.currentStyle.left),h.left="fontSize"===b?"1em":g,g=h.pixelLeft+"px",h.left=d,f&&(e.left=f)),void 0===g?g:g+""||"auto"});function Lb(a,b){return{get:function(){var c=a();if(null!=c)return c?void delete this.get:(this.get=b).apply(this,arguments)}}}!function(){var b,c,d,e,f,g,h;if(b=y.createElement("div"),b.innerHTML=" <link/><table></table><a href='/a'>a</a><input type='checkbox'/>",d=b.getElementsByTagName("a")[0],c=d&&d.style){c.cssText="float:left;opacity:.5",k.opacity="0.5"===c.opacity,k.cssFloat=!!c.cssFloat,b.style.backgroundClip="content-box",b.cloneNode(!0).style.backgroundClip="",k.clearCloneStyle="content-box"===b.style.backgroundClip,k.boxSizing=""===c.boxSizing||""===c.MozBoxSizing||""===c.WebkitBoxSizing,m.extend(k,{reliableHiddenOffsets:function(){return null==g&&i(),g},boxSizingReliable:function(){return null==f&&i(),f},pixelPosition:function(){return null==e&&i(),e},reliableMarginRight:function(){return null==h&&i(),h}});function i(){var b,c,d,i;c=y.getElementsByTagName("body")[0],c&&c.style&&(b=y.createElement("div"),d=y.createElement("div"),d.style.cssText="position:absolute;border:0;width:0;height:0;top:0;left:-9999px",c.appendChild(d).appendChild(b),b.style.cssText="-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;display:block;margin-top:1%;top:1%;border:1px;padding:1px;width:4px;position:absolute",e=f=!1,h=!0,a.getComputedStyle&&(e="1%"!==(a.getComputedStyle(b,null)||{}).top,f="4px"===(a.getComputedStyle(b,null)||{width:"4px"}).width,i=b.appendChild(y.createElement("div")),i.style.cssText=b.style.cssText="-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;display:block;margin:0;border:0;padding:0",i.style.marginRight=i.style.width="0",b.style.width="1px",h=!parseFloat((a.getComputedStyle(i,null)||{}).marginRight)),b.innerHTML="<table><tr><td></td><td>t</td></tr></table>",i=b.getElementsByTagName("td"),i[0].style.cssText="margin:0;border:0;padding:0;display:none",g=0===i[0].offsetHeight,g&&(i[0].style.display="",i[1].style.display="none",g=0===i[0].offsetHeight),c.removeChild(d))}}}(),m.swap=function(a,b,c,d){var e,f,g={};for(f in b)g[f]=a.style[f],a.style[f]=b[f];e=c.apply(a,d||[]);for(f in b)a.style[f]=g[f];return e};var Mb=/alpha\([^)]*\)/i,Nb=/opacity\s*=\s*([^)]*)/,Ob=/^(none|table(?!-c[ea]).+)/,Pb=new RegExp("^("+S+")(.*)$","i"),Qb=new RegExp("^([+-])=("+S+")","i"),Rb={position:"absolute",visibility:"hidden",display:"block"},Sb={letterSpacing:"0",fontWeight:"400"},Tb=["Webkit","O","Moz","ms"];function Ub(a,b){if(b in a)return b;var c=b.charAt(0).toUpperCase()+b.slice(1),d=b,e=Tb.length;while(e--)if(b=Tb[e]+c,b in a)return b;return d}function Vb(a,b){for(var c,d,e,f=[],g=0,h=a.length;h>g;g++)d=a[g],d.style&&(f[g]=m._data(d,"olddisplay"),c=d.style.display,b?(f[g]||"none"!==c||(d.style.display=""),""===d.style.display&&U(d)&&(f[g]=m._data(d,"olddisplay",Fb(d.nodeName)))):(e=U(d),(c&&"none"!==c||!e)&&m._data(d,"olddisplay",e?c:m.css(d,"display"))));for(g=0;h>g;g++)d=a[g],d.style&&(b&&"none"!==d.style.display&&""!==d.style.display||(d.style.display=b?f[g]||"":"none"));return a}function Wb(a,b,c){var d=Pb.exec(b);return d?Math.max(0,d[1]-(c||0))+(d[2]||"px"):b}function Xb(a,b,c,d,e){for(var f=c===(d?"border":"content")?4:"width"===b?1:0,g=0;4>f;f+=2)"margin"===c&&(g+=m.css(a,c+T[f],!0,e)),d?("content"===c&&(g-=m.css(a,"padding"+T[f],!0,e)),"margin"!==c&&(g-=m.css(a,"border"+T[f]+"Width",!0,e))):(g+=m.css(a,"padding"+T[f],!0,e),"padding"!==c&&(g+=m.css(a,"border"+T[f]+"Width",!0,e)));return g}function Yb(a,b,c){var d=!0,e="width"===b?a.offsetWidth:a.offsetHeight,f=Ib(a),g=k.boxSizing&&"border-box"===m.css(a,"boxSizing",!1,f);if(0>=e||null==e){if(e=Jb(a,b,f),(0>e||null==e)&&(e=a.style[b]),Hb.test(e))return e;d=g&&(k.boxSizingReliable()||e===a.style[b]),e=parseFloat(e)||0}return e+Xb(a,b,c||(g?"border":"content"),d,f)+"px"}m.extend({cssHooks:{opacity:{get:function(a,b){if(b){var c=Jb(a,"opacity");return""===c?"1":c}}}},cssNumber:{columnCount:!0,fillOpacity:!0,flexGrow:!0,flexShrink:!0,fontWeight:!0,lineHeight:!0,opacity:!0,order:!0,orphans:!0,widows:!0,zIndex:!0,zoom:!0},cssProps:{"float":k.cssFloat?"cssFloat":"styleFloat"},style:function(a,b,c,d){if(a&&3!==a.nodeType&&8!==a.nodeType&&a.style){var e,f,g,h=m.camelCase(b),i=a.style;if(b=m.cssProps[h]||(m.cssProps[h]=Ub(i,h)),g=m.cssHooks[b]||m.cssHooks[h],void 0===c)return g&&"get"in g&&void 0!==(e=g.get(a,!1,d))?e:i[b];if(f=typeof c,"string"===f&&(e=Qb.exec(c))&&(c=(e[1]+1)*e[2]+parseFloat(m.css(a,b)),f="number"),null!=c&&c===c&&("number"!==f||m.cssNumber[h]||(c+="px"),k.clearCloneStyle||""!==c||0!==b.indexOf("background")||(i[b]="inherit"),!(g&&"set"in g&&void 0===(c=g.set(a,c,d)))))try{i[b]=c}catch(j){}}},css:function(a,b,c,d){var e,f,g,h=m.camelCase(b);return b=m.cssProps[h]||(m.cssProps[h]=Ub(a.style,h)),g=m.cssHooks[b]||m.cssHooks[h],g&&"get"in g&&(f=g.get(a,!0,c)),void 0===f&&(f=Jb(a,b,d)),"normal"===f&&b in Sb&&(f=Sb[b]),""===c||c?(e=parseFloat(f),c===!0||m.isNumeric(e)?e||0:f):f}}),m.each(["height","width"],function(a,b){m.cssHooks[b]={get:function(a,c,d){return c?Ob.test(m.css(a,"display"))&&0===a.offsetWidth?m.swap(a,Rb,function(){return Yb(a,b,d)}):Yb(a,b,d):void 0},set:function(a,c,d){var e=d&&Ib(a);return Wb(a,c,d?Xb(a,b,d,k.boxSizing&&"border-box"===m.css(a,"boxSizing",!1,e),e):0)}}}),k.opacity||(m.cssHooks.opacity={get:function(a,b){return Nb.test((b&&a.currentStyle?a.currentStyle.filter:a.style.filter)||"")?.01*parseFloat(RegExp.$1)+"":b?"1":""},set:function(a,b){var c=a.style,d=a.currentStyle,e=m.isNumeric(b)?"alpha(opacity="+100*b+")":"",f=d&&d.filter||c.filter||"";c.zoom=1,(b>=1||""===b)&&""===m.trim(f.replace(Mb,""))&&c.removeAttribute&&(c.removeAttribute("filter"),""===b||d&&!d.filter)||(c.filter=Mb.test(f)?f.replace(Mb,e):f+" "+e)}}),m.cssHooks.marginRight=Lb(k.reliableMarginRight,function(a,b){return b?m.swap(a,{display:"inline-block"},Jb,[a,"marginRight"]):void 0}),m.each({margin:"",padding:"",border:"Width"},function(a,b){m.cssHooks[a+b]={expand:function(c){for(var d=0,e={},f="string"==typeof c?c.split(" "):[c];4>d;d++)e[a+T[d]+b]=f[d]||f[d-2]||f[0];return e}},Gb.test(a)||(m.cssHooks[a+b].set=Wb)}),m.fn.extend({css:function(a,b){return V(this,function(a,b,c){var d,e,f={},g=0;if(m.isArray(b)){for(d=Ib(a),e=b.length;e>g;g++)f[b[g]]=m.css(a,b[g],!1,d);return f}return void 0!==c?m.style(a,b,c):m.css(a,b)},a,b,arguments.length>1)},show:function(){return Vb(this,!0)},hide:function(){return Vb(this)},toggle:function(a){return"boolean"==typeof a?a?this.show():this.hide():this.each(function(){U(this)?m(this).show():m(this).hide()})}});function Zb(a,b,c,d,e){return new Zb.prototype.init(a,b,c,d,e)}m.Tween=Zb,Zb.prototype={constructor:Zb,init:function(a,b,c,d,e,f){this.elem=a,this.prop=c,this.easing=e||"swing",this.options=b,this.start=this.now=this.cur(),this.end=d,this.unit=f||(m.cssNumber[c]?"":"px")
-},cur:function(){var a=Zb.propHooks[this.prop];return a&&a.get?a.get(this):Zb.propHooks._default.get(this)},run:function(a){var b,c=Zb.propHooks[this.prop];return this.pos=b=this.options.duration?m.easing[this.easing](a,this.options.duration*a,0,1,this.options.duration):a,this.now=(this.end-this.start)*b+this.start,this.options.step&&this.options.step.call(this.elem,this.now,this),c&&c.set?c.set(this):Zb.propHooks._default.set(this),this}},Zb.prototype.init.prototype=Zb.prototype,Zb.propHooks={_default:{get:function(a){var b;return null==a.elem[a.prop]||a.elem.style&&null!=a.elem.style[a.prop]?(b=m.css(a.elem,a.prop,""),b&&"auto"!==b?b:0):a.elem[a.prop]},set:function(a){m.fx.step[a.prop]?m.fx.step[a.prop](a):a.elem.style&&(null!=a.elem.style[m.cssProps[a.prop]]||m.cssHooks[a.prop])?m.style(a.elem,a.prop,a.now+a.unit):a.elem[a.prop]=a.now}}},Zb.propHooks.scrollTop=Zb.propHooks.scrollLeft={set:function(a){a.elem.nodeType&&a.elem.parentNode&&(a.elem[a.prop]=a.now)}},m.easing={linear:function(a){return a},swing:function(a){return.5-Math.cos(a*Math.PI)/2}},m.fx=Zb.prototype.init,m.fx.step={};var $b,_b,ac=/^(?:toggle|show|hide)$/,bc=new RegExp("^(?:([+-])=|)("+S+")([a-z%]*)$","i"),cc=/queueHooks$/,dc=[ic],ec={"*":[function(a,b){var c=this.createTween(a,b),d=c.cur(),e=bc.exec(b),f=e&&e[3]||(m.cssNumber[a]?"":"px"),g=(m.cssNumber[a]||"px"!==f&&+d)&&bc.exec(m.css(c.elem,a)),h=1,i=20;if(g&&g[3]!==f){f=f||g[3],e=e||[],g=+d||1;do h=h||".5",g/=h,m.style(c.elem,a,g+f);while(h!==(h=c.cur()/d)&&1!==h&&--i)}return e&&(g=c.start=+g||+d||0,c.unit=f,c.end=e[1]?g+(e[1]+1)*e[2]:+e[2]),c}]};function fc(){return setTimeout(function(){$b=void 0}),$b=m.now()}function gc(a,b){var c,d={height:a},e=0;for(b=b?1:0;4>e;e+=2-b)c=T[e],d["margin"+c]=d["padding"+c]=a;return b&&(d.opacity=d.width=a),d}function hc(a,b,c){for(var d,e=(ec[b]||[]).concat(ec["*"]),f=0,g=e.length;g>f;f++)if(d=e[f].call(c,b,a))return d}function ic(a,b,c){var d,e,f,g,h,i,j,l,n=this,o={},p=a.style,q=a.nodeType&&U(a),r=m._data(a,"fxshow");c.queue||(h=m._queueHooks(a,"fx"),null==h.unqueued&&(h.unqueued=0,i=h.empty.fire,h.empty.fire=function(){h.unqueued||i()}),h.unqueued++,n.always(function(){n.always(function(){h.unqueued--,m.queue(a,"fx").length||h.empty.fire()})})),1===a.nodeType&&("height"in b||"width"in b)&&(c.overflow=[p.overflow,p.overflowX,p.overflowY],j=m.css(a,"display"),l="none"===j?m._data(a,"olddisplay")||Fb(a.nodeName):j,"inline"===l&&"none"===m.css(a,"float")&&(k.inlineBlockNeedsLayout&&"inline"!==Fb(a.nodeName)?p.zoom=1:p.display="inline-block")),c.overflow&&(p.overflow="hidden",k.shrinkWrapBlocks()||n.always(function(){p.overflow=c.overflow[0],p.overflowX=c.overflow[1],p.overflowY=c.overflow[2]}));for(d in b)if(e=b[d],ac.exec(e)){if(delete b[d],f=f||"toggle"===e,e===(q?"hide":"show")){if("show"!==e||!r||void 0===r[d])continue;q=!0}o[d]=r&&r[d]||m.style(a,d)}else j=void 0;if(m.isEmptyObject(o))"inline"===("none"===j?Fb(a.nodeName):j)&&(p.display=j);else{r?"hidden"in r&&(q=r.hidden):r=m._data(a,"fxshow",{}),f&&(r.hidden=!q),q?m(a).show():n.done(function(){m(a).hide()}),n.done(function(){var b;m._removeData(a,"fxshow");for(b in o)m.style(a,b,o[b])});for(d in o)g=hc(q?r[d]:0,d,n),d in r||(r[d]=g.start,q&&(g.end=g.start,g.start="width"===d||"height"===d?1:0))}}function jc(a,b){var c,d,e,f,g;for(c in a)if(d=m.camelCase(c),e=b[d],f=a[c],m.isArray(f)&&(e=f[1],f=a[c]=f[0]),c!==d&&(a[d]=f,delete a[c]),g=m.cssHooks[d],g&&"expand"in g){f=g.expand(f),delete a[d];for(c in f)c in a||(a[c]=f[c],b[c]=e)}else b[d]=e}function kc(a,b,c){var d,e,f=0,g=dc.length,h=m.Deferred().always(function(){delete i.elem}),i=function(){if(e)return!1;for(var b=$b||fc(),c=Math.max(0,j.startTime+j.duration-b),d=c/j.duration||0,f=1-d,g=0,i=j.tweens.length;i>g;g++)j.tweens[g].run(f);return h.notifyWith(a,[j,f,c]),1>f&&i?c:(h.resolveWith(a,[j]),!1)},j=h.promise({elem:a,props:m.extend({},b),opts:m.extend(!0,{specialEasing:{}},c),originalProperties:b,originalOptions:c,startTime:$b||fc(),duration:c.duration,tweens:[],createTween:function(b,c){var d=m.Tween(a,j.opts,b,c,j.opts.specialEasing[b]||j.opts.easing);return j.tweens.push(d),d},stop:function(b){var c=0,d=b?j.tweens.length:0;if(e)return this;for(e=!0;d>c;c++)j.tweens[c].run(1);return b?h.resolveWith(a,[j,b]):h.rejectWith(a,[j,b]),this}}),k=j.props;for(jc(k,j.opts.specialEasing);g>f;f++)if(d=dc[f].call(j,a,k,j.opts))return d;return m.map(k,hc,j),m.isFunction(j.opts.start)&&j.opts.start.call(a,j),m.fx.timer(m.extend(i,{elem:a,anim:j,queue:j.opts.queue})),j.progress(j.opts.progress).done(j.opts.done,j.opts.complete).fail(j.opts.fail).always(j.opts.always)}m.Animation=m.extend(kc,{tweener:function(a,b){m.isFunction(a)?(b=a,a=["*"]):a=a.split(" ");for(var c,d=0,e=a.length;e>d;d++)c=a[d],ec[c]=ec[c]||[],ec[c].unshift(b)},prefilter:function(a,b){b?dc.unshift(a):dc.push(a)}}),m.speed=function(a,b,c){var d=a&&"object"==typeof a?m.extend({},a):{complete:c||!c&&b||m.isFunction(a)&&a,duration:a,easing:c&&b||b&&!m.isFunction(b)&&b};return d.duration=m.fx.off?0:"number"==typeof d.duration?d.duration:d.duration in m.fx.speeds?m.fx.speeds[d.duration]:m.fx.speeds._default,(null==d.queue||d.queue===!0)&&(d.queue="fx"),d.old=d.complete,d.complete=function(){m.isFunction(d.old)&&d.old.call(this),d.queue&&m.dequeue(this,d.queue)},d},m.fn.extend({fadeTo:function(a,b,c,d){return this.filter(U).css("opacity",0).show().end().animate({opacity:b},a,c,d)},animate:function(a,b,c,d){var e=m.isEmptyObject(a),f=m.speed(b,c,d),g=function(){var b=kc(this,m.extend({},a),f);(e||m._data(this,"finish"))&&b.stop(!0)};return g.finish=g,e||f.queue===!1?this.each(g):this.queue(f.queue,g)},stop:function(a,b,c){var d=function(a){var b=a.stop;delete a.stop,b(c)};return"string"!=typeof a&&(c=b,b=a,a=void 0),b&&a!==!1&&this.queue(a||"fx",[]),this.each(function(){var b=!0,e=null!=a&&a+"queueHooks",f=m.timers,g=m._data(this);if(e)g[e]&&g[e].stop&&d(g[e]);else for(e in g)g[e]&&g[e].stop&&cc.test(e)&&d(g[e]);for(e=f.length;e--;)f[e].elem!==this||null!=a&&f[e].queue!==a||(f[e].anim.stop(c),b=!1,f.splice(e,1));(b||!c)&&m.dequeue(this,a)})},finish:function(a){return a!==!1&&(a=a||"fx"),this.each(function(){var b,c=m._data(this),d=c[a+"queue"],e=c[a+"queueHooks"],f=m.timers,g=d?d.length:0;for(c.finish=!0,m.queue(this,a,[]),e&&e.stop&&e.stop.call(this,!0),b=f.length;b--;)f[b].elem===this&&f[b].queue===a&&(f[b].anim.stop(!0),f.splice(b,1));for(b=0;g>b;b++)d[b]&&d[b].finish&&d[b].finish.call(this);delete c.finish})}}),m.each(["toggle","show","hide"],function(a,b){var c=m.fn[b];m.fn[b]=function(a,d,e){return null==a||"boolean"==typeof a?c.apply(this,arguments):this.animate(gc(b,!0),a,d,e)}}),m.each({slideDown:gc("show"),slideUp:gc("hide"),slideToggle:gc("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(a,b){m.fn[a]=function(a,c,d){return this.animate(b,a,c,d)}}),m.timers=[],m.fx.tick=function(){var a,b=m.timers,c=0;for($b=m.now();c<b.length;c++)a=b[c],a()||b[c]!==a||b.splice(c--,1);b.length||m.fx.stop(),$b=void 0},m.fx.timer=function(a){m.timers.push(a),a()?m.fx.start():m.timers.pop()},m.fx.interval=13,m.fx.start=function(){_b||(_b=setInterval(m.fx.tick,m.fx.interval))},m.fx.stop=function(){clearInterval(_b),_b=null},m.fx.speeds={slow:600,fast:200,_default:400},m.fn.delay=function(a,b){return a=m.fx?m.fx.speeds[a]||a:a,b=b||"fx",this.queue(b,function(b,c){var d=setTimeout(b,a);c.stop=function(){clearTimeout(d)}})},function(){var a,b,c,d,e;b=y.createElement("div"),b.setAttribute("className","t"),b.innerHTML=" <link/><table></table><a href='/a'>a</a><input type='checkbox'/>",d=b.getElementsByTagName("a")[0],c=y.createElement("select"),e=c.appendChild(y.createElement("option")),a=b.getElementsByTagName("input")[0],d.style.cssText="top:1px",k.getSetAttribute="t"!==b.className,k.style=/top/.test(d.getAttribute("style")),k.hrefNormalized="/a"===d.getAttribute("href"),k.checkOn=!!a.value,k.optSelected=e.selected,k.enctype=!!y.createElement("form").enctype,c.disabled=!0,k.optDisabled=!e.disabled,a=y.createElement("input"),a.setAttribute("value",""),k.input=""===a.getAttribute("value"),a.value="t",a.setAttribute("type","radio"),k.radioValue="t"===a.value}();var lc=/\r/g;m.fn.extend({val:function(a){var b,c,d,e=this[0];{if(arguments.length)return d=m.isFunction(a),this.each(function(c){var e;1===this.nodeType&&(e=d?a.call(this,c,m(this).val()):a,null==e?e="":"number"==typeof e?e+="":m.isArray(e)&&(e=m.map(e,function(a){return null==a?"":a+""})),b=m.valHooks[this.type]||m.valHooks[this.nodeName.toLowerCase()],b&&"set"in b&&void 0!==b.set(this,e,"value")||(this.value=e))});if(e)return b=m.valHooks[e.type]||m.valHooks[e.nodeName.toLowerCase()],b&&"get"in b&&void 0!==(c=b.get(e,"value"))?c:(c=e.value,"string"==typeof c?c.replace(lc,""):null==c?"":c)}}}),m.extend({valHooks:{option:{get:function(a){var b=m.find.attr(a,"value");return null!=b?b:m.trim(m.text(a))}},select:{get:function(a){for(var b,c,d=a.options,e=a.selectedIndex,f="select-one"===a.type||0>e,g=f?null:[],h=f?e+1:d.length,i=0>e?h:f?e:0;h>i;i++)if(c=d[i],!(!c.selected&&i!==e||(k.optDisabled?c.disabled:null!==c.getAttribute("disabled"))||c.parentNode.disabled&&m.nodeName(c.parentNode,"optgroup"))){if(b=m(c).val(),f)return b;g.push(b)}return g},set:function(a,b){var c,d,e=a.options,f=m.makeArray(b),g=e.length;while(g--)if(d=e[g],m.inArray(m.valHooks.option.get(d),f)>=0)try{d.selected=c=!0}catch(h){d.scrollHeight}else d.selected=!1;return c||(a.selectedIndex=-1),e}}}}),m.each(["radio","checkbox"],function(){m.valHooks[this]={set:function(a,b){return m.isArray(b)?a.checked=m.inArray(m(a).val(),b)>=0:void 0}},k.checkOn||(m.valHooks[this].get=function(a){return null===a.getAttribute("value")?"on":a.value})});var mc,nc,oc=m.expr.attrHandle,pc=/^(?:checked|selected)$/i,qc=k.getSetAttribute,rc=k.input;m.fn.extend({attr:function(a,b){return V(this,m.attr,a,b,arguments.length>1)},removeAttr:function(a){return this.each(function(){m.removeAttr(this,a)})}}),m.extend({attr:function(a,b,c){var d,e,f=a.nodeType;if(a&&3!==f&&8!==f&&2!==f)return typeof a.getAttribute===K?m.prop(a,b,c):(1===f&&m.isXMLDoc(a)||(b=b.toLowerCase(),d=m.attrHooks[b]||(m.expr.match.bool.test(b)?nc:mc)),void 0===c?d&&"get"in d&&null!==(e=d.get(a,b))?e:(e=m.find.attr(a,b),null==e?void 0:e):null!==c?d&&"set"in d&&void 0!==(e=d.set(a,c,b))?e:(a.setAttribute(b,c+""),c):void m.removeAttr(a,b))},removeAttr:function(a,b){var c,d,e=0,f=b&&b.match(E);if(f&&1===a.nodeType)while(c=f[e++])d=m.propFix[c]||c,m.expr.match.bool.test(c)?rc&&qc||!pc.test(c)?a[d]=!1:a[m.camelCase("default-"+c)]=a[d]=!1:m.attr(a,c,""),a.removeAttribute(qc?c:d)},attrHooks:{type:{set:function(a,b){if(!k.radioValue&&"radio"===b&&m.nodeName(a,"input")){var c=a.value;return a.setAttribute("type",b),c&&(a.value=c),b}}}}}),nc={set:function(a,b,c){return b===!1?m.removeAttr(a,c):rc&&qc||!pc.test(c)?a.setAttribute(!qc&&m.propFix[c]||c,c):a[m.camelCase("default-"+c)]=a[c]=!0,c}},m.each(m.expr.match.bool.source.match(/\w+/g),function(a,b){var c=oc[b]||m.find.attr;oc[b]=rc&&qc||!pc.test(b)?function(a,b,d){var e,f;return d||(f=oc[b],oc[b]=e,e=null!=c(a,b,d)?b.toLowerCase():null,oc[b]=f),e}:function(a,b,c){return c?void 0:a[m.camelCase("default-"+b)]?b.toLowerCase():null}}),rc&&qc||(m.attrHooks.value={set:function(a,b,c){return m.nodeName(a,"input")?void(a.defaultValue=b):mc&&mc.set(a,b,c)}}),qc||(mc={set:function(a,b,c){var d=a.getAttributeNode(c);return d||a.setAttributeNode(d=a.ownerDocument.createAttribute(c)),d.value=b+="","value"===c||b===a.getAttribute(c)?b:void 0}},oc.id=oc.name=oc.coords=function(a,b,c){var d;return c?void 0:(d=a.getAttributeNode(b))&&""!==d.value?d.value:null},m.valHooks.button={get:function(a,b){var c=a.getAttributeNode(b);return c&&c.specified?c.value:void 0},set:mc.set},m.attrHooks.contenteditable={set:function(a,b,c){mc.set(a,""===b?!1:b,c)}},m.each(["width","height"],function(a,b){m.attrHooks[b]={set:function(a,c){return""===c?(a.setAttribute(b,"auto"),c):void 0}}})),k.style||(m.attrHooks.style={get:function(a){return a.style.cssText||void 0},set:function(a,b){return a.style.cssText=b+""}});var sc=/^(?:input|select|textarea|button|object)$/i,tc=/^(?:a|area)$/i;m.fn.extend({prop:function(a,b){return V(this,m.prop,a,b,arguments.length>1)},removeProp:function(a){return a=m.propFix[a]||a,this.each(function(){try{this[a]=void 0,delete this[a]}catch(b){}})}}),m.extend({propFix:{"for":"htmlFor","class":"className"},prop:function(a,b,c){var d,e,f,g=a.nodeType;if(a&&3!==g&&8!==g&&2!==g)return f=1!==g||!m.isXMLDoc(a),f&&(b=m.propFix[b]||b,e=m.propHooks[b]),void 0!==c?e&&"set"in e&&void 0!==(d=e.set(a,c,b))?d:a[b]=c:e&&"get"in e&&null!==(d=e.get(a,b))?d:a[b]},propHooks:{tabIndex:{get:function(a){var b=m.find.attr(a,"tabindex");return b?parseInt(b,10):sc.test(a.nodeName)||tc.test(a.nodeName)&&a.href?0:-1}}}}),k.hrefNormalized||m.each(["href","src"],function(a,b){m.propHooks[b]={get:function(a){return a.getAttribute(b,4)}}}),k.optSelected||(m.propHooks.selected={get:function(a){var b=a.parentNode;return b&&(b.selectedIndex,b.parentNode&&b.parentNode.selectedIndex),null}}),m.each(["tabIndex","readOnly","maxLength","cellSpacing","cellPadding","rowSpan","colSpan","useMap","frameBorder","contentEditable"],function(){m.propFix[this.toLowerCase()]=this}),k.enctype||(m.propFix.enctype="encoding");var uc=/[\t\r\n\f]/g;m.fn.extend({addClass:function(a){var b,c,d,e,f,g,h=0,i=this.length,j="string"==typeof a&&a;if(m.isFunction(a))return this.each(function(b){m(this).addClass(a.call(this,b,this.className))});if(j)for(b=(a||"").match(E)||[];i>h;h++)if(c=this[h],d=1===c.nodeType&&(c.className?(" "+c.className+" ").replace(uc," "):" ")){f=0;while(e=b[f++])d.indexOf(" "+e+" ")<0&&(d+=e+" ");g=m.trim(d),c.className!==g&&(c.className=g)}return this},removeClass:function(a){var b,c,d,e,f,g,h=0,i=this.length,j=0===arguments.length||"string"==typeof a&&a;if(m.isFunction(a))return this.each(function(b){m(this).removeClass(a.call(this,b,this.className))});if(j)for(b=(a||"").match(E)||[];i>h;h++)if(c=this[h],d=1===c.nodeType&&(c.className?(" "+c.className+" ").replace(uc," "):"")){f=0;while(e=b[f++])while(d.indexOf(" "+e+" ")>=0)d=d.replace(" "+e+" "," ");g=a?m.trim(d):"",c.className!==g&&(c.className=g)}return this},toggleClass:function(a,b){var c=typeof a;return"boolean"==typeof b&&"string"===c?b?this.addClass(a):this.removeClass(a):this.each(m.isFunction(a)?function(c){m(this).toggleClass(a.call(this,c,this.className,b),b)}:function(){if("string"===c){var b,d=0,e=m(this),f=a.match(E)||[];while(b=f[d++])e.hasClass(b)?e.removeClass(b):e.addClass(b)}else(c===K||"boolean"===c)&&(this.className&&m._data(this,"__className__",this.className),this.className=this.className||a===!1?"":m._data(this,"__className__")||"")})},hasClass:function(a){for(var b=" "+a+" ",c=0,d=this.length;d>c;c++)if(1===this[c].nodeType&&(" "+this[c].className+" ").replace(uc," ").indexOf(b)>=0)return!0;return!1}}),m.each("blur focus focusin focusout load resize scroll unload click dblclick mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave change select submit keydown keypress keyup error contextmenu".split(" "),function(a,b){m.fn[b]=function(a,c){return arguments.length>0?this.on(b,null,a,c):this.trigger(b)}}),m.fn.extend({hover:function(a,b){return this.mouseenter(a).mouseleave(b||a)},bind:function(a,b,c){return this.on(a,null,b,c)},unbind:function(a,b){return this.off(a,null,b)},delegate:function(a,b,c,d){return this.on(b,a,c,d)},undelegate:function(a,b,c){return 1===arguments.length?this.off(a,"**"):this.off(b,a||"**",c)}});var vc=m.now(),wc=/\?/,xc=/(,)|(\[|{)|(}|])|"(?:[^"\\\r\n]|\\["\\\/bfnrt]|\\u[\da-fA-F]{4})*"\s*:?|true|false|null|-?(?!0\d)\d+(?:\.\d+|)(?:[eE][+-]?\d+|)/g;m.parseJSON=function(b){if(a.JSON&&a.JSON.parse)return a.JSON.parse(b+"");var c,d=null,e=m.trim(b+"");return e&&!m.trim(e.replace(xc,function(a,b,e,f){return c&&b&&(d=0),0===d?a:(c=e||b,d+=!f-!e,"")}))?Function("return "+e)():m.error("Invalid JSON: "+b)},m.parseXML=function(b){var c,d;if(!b||"string"!=typeof b)return null;try{a.DOMParser?(d=new DOMParser,c=d.parseFromString(b,"text/xml")):(c=new ActiveXObject("Microsoft.XMLDOM"),c.async="false",c.loadXML(b))}catch(e){c=void 0}return c&&c.documentElement&&!c.getElementsByTagName("parsererror").length||m.error("Invalid XML: "+b),c};var yc,zc,Ac=/#.*$/,Bc=/([?&])_=[^&]*/,Cc=/^(.*?):[ \t]*([^\r\n]*)\r?$/gm,Dc=/^(?:about|app|app-storage|.+-extension|file|res|widget):$/,Ec=/^(?:GET|HEAD)$/,Fc=/^\/\//,Gc=/^([\w.+-]+:)(?:\/\/(?:[^\/?#]*@|)([^\/?#:]*)(?::(\d+)|)|)/,Hc={},Ic={},Jc="*/".concat("*");try{zc=location.href}catch(Kc){zc=y.createElement("a"),zc.href="",zc=zc.href}yc=Gc.exec(zc.toLowerCase())||[];function Lc(a){return function(b,c){"string"!=typeof b&&(c=b,b="*");var d,e=0,f=b.toLowerCase().match(E)||[];if(m.isFunction(c))while(d=f[e++])"+"===d.charAt(0)?(d=d.slice(1)||"*",(a[d]=a[d]||[]).unshift(c)):(a[d]=a[d]||[]).push(c)}}function Mc(a,b,c,d){var e={},f=a===Ic;function g(h){var i;return e[h]=!0,m.each(a[h]||[],function(a,h){var j=h(b,c,d);return"string"!=typeof j||f||e[j]?f?!(i=j):void 0:(b.dataTypes.unshift(j),g(j),!1)}),i}return g(b.dataTypes[0])||!e["*"]&&g("*")}function Nc(a,b){var c,d,e=m.ajaxSettings.flatOptions||{};for(d in b)void 0!==b[d]&&((e[d]?a:c||(c={}))[d]=b[d]);return c&&m.extend(!0,a,c),a}function Oc(a,b,c){var d,e,f,g,h=a.contents,i=a.dataTypes;while("*"===i[0])i.shift(),void 0===e&&(e=a.mimeType||b.getResponseHeader("Content-Type"));if(e)for(g in h)if(h[g]&&h[g].test(e)){i.unshift(g);break}if(i[0]in c)f=i[0];else{for(g in c){if(!i[0]||a.converters[g+" "+i[0]]){f=g;break}d||(d=g)}f=f||d}return f?(f!==i[0]&&i.unshift(f),c[f]):void 0}function Pc(a,b,c,d){var e,f,g,h,i,j={},k=a.dataTypes.slice();if(k[1])for(g in a.converters)j[g.toLowerCase()]=a.converters[g];f=k.shift();while(f)if(a.responseFields[f]&&(c[a.responseFields[f]]=b),!i&&d&&a.dataFilter&&(b=a.dataFilter(b,a.dataType)),i=f,f=k.shift())if("*"===f)f=i;else if("*"!==i&&i!==f){if(g=j[i+" "+f]||j["* "+f],!g)for(e in j)if(h=e.split(" "),h[1]===f&&(g=j[i+" "+h[0]]||j["* "+h[0]])){g===!0?g=j[e]:j[e]!==!0&&(f=h[0],k.unshift(h[1]));break}if(g!==!0)if(g&&a["throws"])b=g(b);else try{b=g(b)}catch(l){return{state:"parsererror",error:g?l:"No conversion from "+i+" to "+f}}}return{state:"success",data:b}}m.extend({active:0,lastModified:{},etag:{},ajaxSettings:{url:zc,type:"GET",isLocal:Dc.test(yc[1]),global:!0,processData:!0,async:!0,contentType:"application/x-www-form-urlencoded; charset=UTF-8",accepts:{"*":Jc,text:"text/plain",html:"text/html",xml:"application/xml, text/xml",json:"application/json, text/javascript"},contents:{xml:/xml/,html:/html/,json:/json/},responseFields:{xml:"responseXML",text:"responseText",json:"responseJSON"},converters:{"* text":String,"text html":!0,"text json":m.parseJSON,"text xml":m.parseXML},flatOptions:{url:!0,context:!0}},ajaxSetup:function(a,b){return b?Nc(Nc(a,m.ajaxSettings),b):Nc(m.ajaxSettings,a)},ajaxPrefilter:Lc(Hc),ajaxTransport:Lc(Ic),ajax:function(a,b){"object"==typeof a&&(b=a,a=void 0),b=b||{};var c,d,e,f,g,h,i,j,k=m.ajaxSetup({},b),l=k.context||k,n=k.context&&(l.nodeType||l.jquery)?m(l):m.event,o=m.Deferred(),p=m.Callbacks("once memory"),q=k.statusCode||{},r={},s={},t=0,u="canceled",v={readyState:0,getResponseHeader:function(a){var b;if(2===t){if(!j){j={};while(b=Cc.exec(f))j[b[1].toLowerCase()]=b[2]}b=j[a.toLowerCase()]}return null==b?null:b},getAllResponseHeaders:function(){return 2===t?f:null},setRequestHeader:function(a,b){var c=a.toLowerCase();return t||(a=s[c]=s[c]||a,r[a]=b),this},overrideMimeType:function(a){return t||(k.mimeType=a),this},statusCode:function(a){var b;if(a)if(2>t)for(b in a)q[b]=[q[b],a[b]];else v.always(a[v.status]);return this},abort:function(a){var b=a||u;return i&&i.abort(b),x(0,b),this}};if(o.promise(v).complete=p.add,v.success=v.done,v.error=v.fail,k.url=((a||k.url||zc)+"").replace(Ac,"").replace(Fc,yc[1]+"//"),k.type=b.method||b.type||k.method||k.type,k.dataTypes=m.trim(k.dataType||"*").toLowerCase().match(E)||[""],null==k.crossDomain&&(c=Gc.exec(k.url.toLowerCase()),k.crossDomain=!(!c||c[1]===yc[1]&&c[2]===yc[2]&&(c[3]||("http:"===c[1]?"80":"443"))===(yc[3]||("http:"===yc[1]?"80":"443")))),k.data&&k.processData&&"string"!=typeof k.data&&(k.data=m.param(k.data,k.traditional)),Mc(Hc,k,b,v),2===t)return v;h=k.global,h&&0===m.active++&&m.event.trigger("ajaxStart"),k.type=k.type.toUpperCase(),k.hasContent=!Ec.test(k.type),e=k.url,k.hasContent||(k.data&&(e=k.url+=(wc.test(e)?"&":"?")+k.data,delete k.data),k.cache===!1&&(k.url=Bc.test(e)?e.replace(Bc,"$1_="+vc++):e+(wc.test(e)?"&":"?")+"_="+vc++)),k.ifModified&&(m.lastModified[e]&&v.setRequestHeader("If-Modified-Since",m.lastModified[e]),m.etag[e]&&v.setRequestHeader("If-None-Match",m.etag[e])),(k.data&&k.hasContent&&k.contentType!==!1||b.contentType)&&v.setRequestHeader("Content-Type",k.contentType),v.setRequestHeader("Accept",k.dataTypes[0]&&k.accepts[k.dataTypes[0]]?k.accepts[k.dataTypes[0]]+("*"!==k.dataTypes[0]?", "+Jc+"; q=0.01":""):k.accepts["*"]);for(d in k.headers)v.setRequestHeader(d,k.headers[d]);if(k.beforeSend&&(k.beforeSend.call(l,v,k)===!1||2===t))return v.abort();u="abort";for(d in{success:1,error:1,complete:1})v[d](k[d]);if(i=Mc(Ic,k,b,v)){v.readyState=1,h&&n.trigger("ajaxSend",[v,k]),k.async&&k.timeout>0&&(g=setTimeout(function(){v.abort("timeout")},k.timeout));try{t=1,i.send(r,x)}catch(w){if(!(2>t))throw w;x(-1,w)}}else x(-1,"No Transport");function x(a,b,c,d){var j,r,s,u,w,x=b;2!==t&&(t=2,g&&clearTimeout(g),i=void 0,f=d||"",v.readyState=a>0?4:0,j=a>=200&&300>a||304===a,c&&(u=Oc(k,v,c)),u=Pc(k,u,v,j),j?(k.ifModified&&(w=v.getResponseHeader("Last-Modified"),w&&(m.lastModified[e]=w),w=v.getResponseHeader("etag"),w&&(m.etag[e]=w)),204===a||"HEAD"===k.type?x="nocontent":304===a?x="notmodified":(x=u.state,r=u.data,s=u.error,j=!s)):(s=x,(a||!x)&&(x="error",0>a&&(a=0))),v.status=a,v.statusText=(b||x)+"",j?o.resolveWith(l,[r,x,v]):o.rejectWith(l,[v,x,s]),v.statusCode(q),q=void 0,h&&n.trigger(j?"ajaxSuccess":"ajaxError",[v,k,j?r:s]),p.fireWith(l,[v,x]),h&&(n.trigger("ajaxComplete",[v,k]),--m.active||m.event.trigger("ajaxStop")))}return v},getJSON:function(a,b,c){return m.get(a,b,c,"json")},getScript:function(a,b){return m.get(a,void 0,b,"script")}}),m.each(["get","post"],function(a,b){m[b]=function(a,c,d,e){return m.isFunction(c)&&(e=e||d,d=c,c=void 0),m.ajax({url:a,type:b,dataType:e,data:c,success:d})}}),m.each(["ajaxStart","ajaxStop","ajaxComplete","ajaxError","ajaxSuccess","ajaxSend"],function(a,b){m.fn[b]=function(a){return this.on(b,a)}}),m._evalUrl=function(a){return m.ajax({url:a,type:"GET",dataType:"script",async:!1,global:!1,"throws":!0})},m.fn.extend({wrapAll:function(a){if(m.isFunction(a))return this.each(function(b){m(this).wrapAll(a.call(this,b))});if(this[0]){var b=m(a,this[0].ownerDocument).eq(0).clone(!0);this[0].parentNode&&b.insertBefore(this[0]),b.map(function(){var a=this;while(a.firstChild&&1===a.firstChild.nodeType)a=a.firstChild;return a}).append(this)}return this},wrapInner:function(a){return this.each(m.isFunction(a)?function(b){m(this).wrapInner(a.call(this,b))}:function(){var b=m(this),c=b.contents();c.length?c.wrapAll(a):b.append(a)})},wrap:function(a){var b=m.isFunction(a);return this.each(function(c){m(this).wrapAll(b?a.call(this,c):a)})},unwrap:function(){return this.parent().each(function(){m.nodeName(this,"body")||m(this).replaceWith(this.childNodes)}).end()}}),m.expr.filters.hidden=function(a){return a.offsetWidth<=0&&a.offsetHeight<=0||!k.reliableHiddenOffsets()&&"none"===(a.style&&a.style.display||m.css(a,"display"))},m.expr.filters.visible=function(a){return!m.expr.filters.hidden(a)};var Qc=/%20/g,Rc=/\[\]$/,Sc=/\r?\n/g,Tc=/^(?:submit|button|image|reset|file)$/i,Uc=/^(?:input|select|textarea|keygen)/i;function Vc(a,b,c,d){var e;if(m.isArray(b))m.each(b,function(b,e){c||Rc.test(a)?d(a,e):Vc(a+"["+("object"==typeof e?b:"")+"]",e,c,d)});else if(c||"object"!==m.type(b))d(a,b);else for(e in b)Vc(a+"["+e+"]",b[e],c,d)}m.param=function(a,b){var c,d=[],e=function(a,b){b=m.isFunction(b)?b():null==b?"":b,d[d.length]=encodeURIComponent(a)+"="+encodeURIComponent(b)};if(void 0===b&&(b=m.ajaxSettings&&m.ajaxSettings.traditional),m.isArray(a)||a.jquery&&!m.isPlainObject(a))m.each(a,function(){e(this.name,this.value)});else for(c in a)Vc(c,a[c],b,e);return d.join("&").replace(Qc,"+")},m.fn.extend({serialize:function(){return m.param(this.serializeArray())},serializeArray:function(){return this.map(function(){var a=m.prop(this,"elements");return a?m.makeArray(a):this}).filter(function(){var a=this.type;return this.name&&!m(this).is(":disabled")&&Uc.test(this.nodeName)&&!Tc.test(a)&&(this.checked||!W.test(a))}).map(function(a,b){var c=m(this).val();return null==c?null:m.isArray(c)?m.map(c,function(a){return{name:b.name,value:a.replace(Sc,"\r\n")}}):{name:b.name,value:c.replace(Sc,"\r\n")}}).get()}}),m.ajaxSettings.xhr=void 0!==a.ActiveXObject?function(){return!this.isLocal&&/^(get|post|head|put|delete|options)$/i.test(this.type)&&Zc()||$c()}:Zc;var Wc=0,Xc={},Yc=m.ajaxSettings.xhr();a.ActiveXObject&&m(a).on("unload",function(){for(var a in Xc)Xc[a](void 0,!0)}),k.cors=!!Yc&&"withCredentials"in Yc,Yc=k.ajax=!!Yc,Yc&&m.ajaxTransport(function(a){if(!a.crossDomain||k.cors){var b;return{send:function(c,d){var e,f=a.xhr(),g=++Wc;if(f.open(a.type,a.url,a.async,a.username,a.password),a.xhrFields)for(e in a.xhrFields)f[e]=a.xhrFields[e];a.mimeType&&f.overrideMimeType&&f.overrideMimeType(a.mimeType),a.crossDomain||c["X-Requested-With"]||(c["X-Requested-With"]="XMLHttpRequest");for(e in c)void 0!==c[e]&&f.setRequestHeader(e,c[e]+"");f.send(a.hasContent&&a.data||null),b=function(c,e){var h,i,j;if(b&&(e||4===f.readyState))if(delete Xc[g],b=void 0,f.onreadystatechange=m.noop,e)4!==f.readyState&&f.abort();else{j={},h=f.status,"string"==typeof f.responseText&&(j.text=f.responseText);try{i=f.statusText}catch(k){i=""}h||!a.isLocal||a.crossDomain?1223===h&&(h=204):h=j.text?200:404}j&&d(h,i,j,f.getAllResponseHeaders())},a.async?4===f.readyState?setTimeout(b):f.onreadystatechange=Xc[g]=b:b()},abort:function(){b&&b(void 0,!0)}}}});function Zc(){try{return new a.XMLHttpRequest}catch(b){}}function $c(){try{return new a.ActiveXObject("Microsoft.XMLHTTP")}catch(b){}}m.ajaxSetup({accepts:{script:"text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"},contents:{script:/(?:java|ecma)script/},converters:{"text script":function(a){return m.globalEval(a),a}}}),m.ajaxPrefilter("script",function(a){void 0===a.cache&&(a.cache=!1),a.crossDomain&&(a.type="GET",a.global=!1)}),m.ajaxTransport("script",function(a){if(a.crossDomain){var b,c=y.head||m("head")[0]||y.documentElement;return{send:function(d,e){b=y.createElement("script"),b.async=!0,a.scriptCharset&&(b.charset=a.scriptCharset),b.src=a.url,b.onload=b.onreadystatechange=function(a,c){(c||!b.readyState||/loaded|complete/.test(b.readyState))&&(b.onload=b.onreadystatechange=null,b.parentNode&&b.parentNode.removeChild(b),b=null,c||e(200,"success"))},c.insertBefore(b,c.firstChild)},abort:function(){b&&b.onload(void 0,!0)}}}});var _c=[],ad=/(=)\?(?=&|$)|\?\?/;m.ajaxSetup({jsonp:"callback",jsonpCallback:function(){var a=_c.pop()||m.expando+"_"+vc++;return this[a]=!0,a}}),m.ajaxPrefilter("json jsonp",function(b,c,d){var e,f,g,h=b.jsonp!==!1&&(ad.test(b.url)?"url":"string"==typeof b.data&&!(b.contentType||"").indexOf("application/x-www-form-urlencoded")&&ad.test(b.data)&&"data");return h||"jsonp"===b.dataTypes[0]?(e=b.jsonpCallback=m.isFunction(b.jsonpCallback)?b.jsonpCallback():b.jsonpCallback,h?b[h]=b[h].replace(ad,"$1"+e):b.jsonp!==!1&&(b.url+=(wc.test(b.url)?"&":"?")+b.jsonp+"="+e),b.converters["script json"]=function(){return g||m.error(e+" was not called"),g[0]},b.dataTypes[0]="json",f=a[e],a[e]=function(){g=arguments},d.always(function(){a[e]=f,b[e]&&(b.jsonpCallback=c.jsonpCallback,_c.push(e)),g&&m.isFunction(f)&&f(g[0]),g=f=void 0}),"script"):void 0}),m.parseHTML=function(a,b,c){if(!a||"string"!=typeof a)return null;"boolean"==typeof b&&(c=b,b=!1),b=b||y;var d=u.exec(a),e=!c&&[];return d?[b.createElement(d[1])]:(d=m.buildFragment([a],b,e),e&&e.length&&m(e).remove(),m.merge([],d.childNodes))};var bd=m.fn.load;m.fn.load=function(a,b,c){if("string"!=typeof a&&bd)return bd.apply(this,arguments);var d,e,f,g=this,h=a.indexOf(" ");return h>=0&&(d=m.trim(a.slice(h,a.length)),a=a.slice(0,h)),m.isFunction(b)?(c=b,b=void 0):b&&"object"==typeof b&&(f="POST"),g.length>0&&m.ajax({url:a,type:f,dataType:"html",data:b}).done(function(a){e=arguments,g.html(d?m("<div>").append(m.parseHTML(a)).find(d):a)}).complete(c&&function(a,b){g.each(c,e||[a.responseText,b,a])}),this},m.expr.filters.animated=function(a){return m.grep(m.timers,function(b){return a===b.elem}).length};var cd=a.document.documentElement;function dd(a){return m.isWindow(a)?a:9===a.nodeType?a.defaultView||a.parentWindow:!1}m.offset={setOffset:function(a,b,c){var d,e,f,g,h,i,j,k=m.css(a,"position"),l=m(a),n={};"static"===k&&(a.style.position="relative"),h=l.offset(),f=m.css(a,"top"),i=m.css(a,"left"),j=("absolute"===k||"fixed"===k)&&m.inArray("auto",[f,i])>-1,j?(d=l.position(),g=d.top,e=d.left):(g=parseFloat(f)||0,e=parseFloat(i)||0),m.isFunction(b)&&(b=b.call(a,c,h)),null!=b.top&&(n.top=b.top-h.top+g),null!=b.left&&(n.left=b.left-h.left+e),"using"in b?b.using.call(a,n):l.css(n)}},m.fn.extend({offset:function(a){if(arguments.length)return void 0===a?this:this.each(function(b){m.offset.setOffset(this,a,b)});var b,c,d={top:0,left:0},e=this[0],f=e&&e.ownerDocument;if(f)return b=f.documentElement,m.contains(b,e)?(typeof e.getBoundingClientRect!==K&&(d=e.getBoundingClientRect()),c=dd(f),{top:d.top+(c.pageYOffset||b.scrollTop)-(b.clientTop||0),left:d.left+(c.pageXOffset||b.scrollLeft)-(b.clientLeft||0)}):d},position:function(){if(this[0]){var a,b,c={top:0,left:0},d=this[0];return"fixed"===m.css(d,"position")?b=d.getBoundingClientRect():(a=this.offsetParent(),b=this.offset(),m.nodeName(a[0],"html")||(c=a.offset()),c.top+=m.css(a[0],"borderTopWidth",!0),c.left+=m.css(a[0],"borderLeftWidth",!0)),{top:b.top-c.top-m.css(d,"marginTop",!0),left:b.left-c.left-m.css(d,"marginLeft",!0)}}},offsetParent:function(){return this.map(function(){var a=this.offsetParent||cd;while(a&&!m.nodeName(a,"html")&&"static"===m.css(a,"position"))a=a.offsetParent;return a||cd})}}),m.each({scrollLeft:"pageXOffset",scrollTop:"pageYOffset"},function(a,b){var c=/Y/.test(b);m.fn[a]=function(d){return V(this,function(a,d,e){var f=dd(a);return void 0===e?f?b in f?f[b]:f.document.documentElement[d]:a[d]:void(f?f.scrollTo(c?m(f).scrollLeft():e,c?e:m(f).scrollTop()):a[d]=e)},a,d,arguments.length,null)}}),m.each(["top","left"],function(a,b){m.cssHooks[b]=Lb(k.pixelPosition,function(a,c){return c?(c=Jb(a,b),Hb.test(c)?m(a).position()[b]+"px":c):void 0})}),m.each({Height:"height",Width:"width"},function(a,b){m.each({padding:"inner"+a,content:b,"":"outer"+a},function(c,d){m.fn[d]=function(d,e){var f=arguments.length&&(c||"boolean"!=typeof d),g=c||(d===!0||e===!0?"margin":"border");return V(this,function(b,c,d){var e;return m.isWindow(b)?b.document.documentElement["client"+a]:9===b.nodeType?(e=b.documentElement,Math.max(b.body["scroll"+a],e["scroll"+a],b.body["offset"+a],e["offset"+a],e["client"+a])):void 0===d?m.css(b,c,g):m.style(b,c,d,g)},b,f?d:void 0,f,null)}})}),m.fn.size=function(){return this.length},m.fn.andSelf=m.fn.addBack,"function"==typeof define&&define.amd&&define("jquery",[],function(){return m});var ed=a.jQuery,fd=a.$;return m.noConflict=function(b){return a.$===m&&(a.$=fd),b&&a.jQuery===m&&(a.jQuery=ed),m},typeof b===K&&(a.jQuery=a.$=m),m});
+/*! jQuery v3.2.1 | (c) JS Foundation and other contributors | jquery.org/license */
+!function(a,b){"use strict";"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){"use strict";var c=[],d=a.document,e=Object.getPrototypeOf,f=c.slice,g=c.concat,h=c.push,i=c.indexOf,j={},k=j.toString,l=j.hasOwnProperty,m=l.toString,n=m.call(Object),o={};function p(a,b){b=b||d;var c=b.createElement("script");c.text=a,b.head.appendChild(c).parentNode.removeChild(c)}var q="3.2.1",r=function(a,b){return new r.fn.init(a,b)},s=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,t=/^-ms-/,u=/-([a-z])/g,v=function(a,b){return b.toUpperCase()};r.fn=r.prototype={jquery:q,constructor:r,length:0,toArray:function(){return f.call(this)},get:function(a){return null==a?f.call(this):a<0?this[a+this.length]:this[a]},pushStack:function(a){var b=r.merge(this.constructor(),a);return b.prevObject=this,b},each:function(a){return r.each(this,a)},map:function(a){return this.pushStack(r.map(this,function(b,c){return a.call(b,c,b)}))},slice:function(){return this.pushStack(f.apply(this,arguments))},first:function(){return this.eq(0)},last:function(){return this.eq(-1)},eq:function(a){var b=this.length,c=+a+(a<0?b:0);return this.pushStack(c>=0&&c<b?[this[c]]:[])},end:function(){return this.prevObject||this.constructor()},push:h,sort:c.sort,splice:c.splice},r.extend=r.fn.extend=function(){var a,b,c,d,e,f,g=arguments[0]||{},h=1,i=arguments.length,j=!1;for("boolean"==typeof g&&(j=g,g=arguments[h]||{},h++),"object"==typeof g||r.isFunction(g)||(g={}),h===i&&(g=this,h--);h<i;h++)if(null!=(a=arguments[h]))for(b in a)c=g[b],d=a[b],g!==d&&(j&&d&&(r.isPlainObject(d)||(e=Array.isArray(d)))?(e?(e=!1,f=c&&Array.isArray(c)?c:[]):f=c&&r.isPlainObject(c)?c:{},g[b]=r.extend(j,f,d)):void 0!==d&&(g[b]=d));return g},r.extend({expando:"jQuery"+(q+Math.random()).replace(/\D/g,""),isReady:!0,error:function(a){throw new Error(a)},noop:function(){},isFunction:function(a){return"function"===r.type(a)},isWindow:function(a){return null!=a&&a===a.window},isNumeric:function(a){var b=r.type(a);return("number"===b||"string"===b)&&!isNaN(a-parseFloat(a))},isPlainObject:function(a){var b,c;return!(!a||"[object Object]"!==k.call(a))&&(!(b=e(a))||(c=l.call(b,"constructor")&&b.constructor,"function"==typeof c&&m.call(c)===n))},isEmptyObject:function(a){var b;for(b in a)return!1;return!0},type:function(a){return null==a?a+"":"object"==typeof a||"function"==typeof a?j[k.call(a)]||"object":typeof a},globalEval:function(a){p(a)},camelCase:function(a){return a.replace(t,"ms-").replace(u,v)},each:function(a,b){var c,d=0;if(w(a)){for(c=a.length;d<c;d++)if(b.call(a[d],d,a[d])===!1)break}else for(d in a)if(b.call(a[d],d,a[d])===!1)break;return a},trim:function(a){return null==a?"":(a+"").replace(s,"")},makeArray:function(a,b){var c=b||[];return null!=a&&(w(Object(a))?r.merge(c,"string"==typeof a?[a]:a):h.call(c,a)),c},inArray:function(a,b,c){return null==b?-1:i.call(b,a,c)},merge:function(a,b){for(var c=+b.length,d=0,e=a.length;d<c;d++)a[e++]=b[d];return a.length=e,a},grep:function(a,b,c){for(var d,e=[],f=0,g=a.length,h=!c;f<g;f++)d=!b(a[f],f),d!==h&&e.push(a[f]);return e},map:function(a,b,c){var d,e,f=0,h=[];if(w(a))for(d=a.length;f<d;f++)e=b(a[f],f,c),null!=e&&h.push(e);else for(f in a)e=b(a[f],f,c),null!=e&&h.push(e);return g.apply([],h)},guid:1,proxy:function(a,b){var c,d,e;if("string"==typeof b&&(c=a[b],b=a,a=c),r.isFunction(a))return d=f.call(arguments,2),e=function(){return a.apply(b||this,d.concat(f.call(arguments)))},e.guid=a.guid=a.guid||r.guid++,e},now:Date.now,support:o}),"function"==typeof Symbol&&(r.fn[Symbol.iterator]=c[Symbol.iterator]),r.each("Boolean Number String Function Array Date RegExp Object Error Symbol".split(" "),function(a,b){j["[object "+b+"]"]=b.toLowerCase()});function w(a){var b=!!a&&"length"in a&&a.length,c=r.type(a);return"function"!==c&&!r.isWindow(a)&&("array"===c||0===b||"number"==typeof b&&b>0&&b-1 in a)}var x=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u="sizzle"+1*new Date,v=a.document,w=0,x=0,y=ha(),z=ha(),A=ha(),B=function(a,b){return a===b&&(l=!0),0},C={}.hasOwnProperty,D=[],E=D.pop,F=D.push,G=D.push,H=D.slice,I=function(a,b){for(var c=0,d=a.length;c<d;c++)if(a[c]===b)return c;return-1},J="checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",K="[\\x20\\t\\r\\n\\f]",L="(?:\\\\.|[\\w-]|[^\0-\\xa0])+",M="\\["+K+"*("+L+")(?:"+K+"*([*^$|!~]?=)"+K+"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|("+L+"))|)"+K+"*\\]",N=":("+L+")(?:\\((('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|((?:\\\\.|[^\\\\()[\\]]|"+M+")*)|.*)\\)|)",O=new RegExp(K+"+","g"),P=new RegExp("^"+K+"+|((?:^|[^\\\\])(?:\\\\.)*)"+K+"+$","g"),Q=new RegExp("^"+K+"*,"+K+"*"),R=new RegExp("^"+K+"*([>+~]|"+K+")"+K+"*"),S=new RegExp("="+K+"*([^\\]'\"]*?)"+K+"*\\]","g"),T=new RegExp(N),U=new RegExp("^"+L+"$"),V={ID:new RegExp("^#("+L+")"),CLASS:new RegExp("^\\.("+L+")"),TAG:new RegExp("^("+L+"|[*])"),ATTR:new RegExp("^"+M),PSEUDO:new RegExp("^"+N),CHILD:new RegExp("^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\("+K+"*(even|odd|(([+-]|)(\\d*)n|)"+K+"*(?:([+-]|)"+K+"*(\\d+)|))"+K+"*\\)|)","i"),bool:new RegExp("^(?:"+J+")$","i"),needsContext:new RegExp("^"+K+"*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\("+K+"*((?:-\\d)?\\d*)"+K+"*\\)|)(?=[^-]|$)","i")},W=/^(?:input|select|textarea|button)$/i,X=/^h\d$/i,Y=/^[^{]+\{\s*\[native \w/,Z=/^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,$=/[+~]/,_=new RegExp("\\\\([\\da-f]{1,6}"+K+"?|("+K+")|.)","ig"),aa=function(a,b,c){var d="0x"+b-65536;return d!==d||c?b:d<0?String.fromCharCode(d+65536):String.fromCharCode(d>>10|55296,1023&d|56320)},ba=/([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,ca=function(a,b){return b?"\0"===a?"\ufffd":a.slice(0,-1)+"\\"+a.charCodeAt(a.length-1).toString(16)+" ":"\\"+a},da=function(){m()},ea=ta(function(a){return a.disabled===!0&&("form"in a||"label"in a)},{dir:"parentNode",next:"legend"});try{G.apply(D=H.call(v.childNodes),v.childNodes),D[v.childNodes.length].nodeType}catch(fa){G={apply:D.length?function(a,b){F.apply(a,H.call(b))}:function(a,b){var c=a.length,d=0;while(a[c++]=b[d++]);a.length=c-1}}}function ga(a,b,d,e){var f,h,j,k,l,o,r,s=b&&b.ownerDocument,w=b?b.nodeType:9;if(d=d||[],"string"!=typeof a||!a||1!==w&&9!==w&&11!==w)return d;if(!e&&((b?b.ownerDocument||b:v)!==n&&m(b),b=b||n,p)){if(11!==w&&(l=Z.exec(a)))if(f=l[1]){if(9===w){if(!(j=b.getElementById(f)))return d;if(j.id===f)return d.push(j),d}else if(s&&(j=s.getElementById(f))&&t(b,j)&&j.id===f)return d.push(j),d}else{if(l[2])return G.apply(d,b.getElementsByTagName(a)),d;if((f=l[3])&&c.getElementsByClassName&&b.getElementsByClassName)return G.apply(d,b.getElementsByClassName(f)),d}if(c.qsa&&!A[a+" "]&&(!q||!q.test(a))){if(1!==w)s=b,r=a;else if("object"!==b.nodeName.toLowerCase()){(k=b.getAttribute("id"))?k=k.replace(ba,ca):b.setAttribute("id",k=u),o=g(a),h=o.length;while(h--)o[h]="#"+k+" "+sa(o[h]);r=o.join(","),s=$.test(a)&&qa(b.parentNode)||b}if(r)try{return G.apply(d,s.querySelectorAll(r)),d}catch(x){}finally{k===u&&b.removeAttribute("id")}}}return i(a.replace(P,"$1"),b,d,e)}function ha(){var a=[];function b(c,e){return a.push(c+" ")>d.cacheLength&&delete b[a.shift()],b[c+" "]=e}return b}function ia(a){return a[u]=!0,a}function ja(a){var b=n.createElement("fieldset");try{return!!a(b)}catch(c){return!1}finally{b.parentNode&&b.parentNode.removeChild(b),b=null}}function ka(a,b){var c=a.split("|"),e=c.length;while(e--)d.attrHandle[c[e]]=b}function la(a,b){var c=b&&a,d=c&&1===a.nodeType&&1===b.nodeType&&a.sourceIndex-b.sourceIndex;if(d)return d;if(c)while(c=c.nextSibling)if(c===b)return-1;return a?1:-1}function ma(a){return function(b){var c=b.nodeName.toLowerCase();return"input"===c&&b.type===a}}function na(a){return function(b){var c=b.nodeName.toLowerCase();return("input"===c||"button"===c)&&b.type===a}}function oa(a){return function(b){return"form"in b?b.parentNode&&b.disabled===!1?"label"in b?"label"in b.parentNode?b.parentNode.disabled===a:b.disabled===a:b.isDisabled===a||b.isDisabled!==!a&&ea(b)===a:b.disabled===a:"label"in b&&b.disabled===a}}function pa(a){return ia(function(b){return b=+b,ia(function(c,d){var e,f=a([],c.length,b),g=f.length;while(g--)c[e=f[g]]&&(c[e]=!(d[e]=c[e]))})})}function qa(a){return a&&"undefined"!=typeof a.getElementsByTagName&&a}c=ga.support={},f=ga.isXML=function(a){var b=a&&(a.ownerDocument||a).documentElement;return!!b&&"HTML"!==b.nodeName},m=ga.setDocument=function(a){var b,e,g=a?a.ownerDocument||a:v;return g!==n&&9===g.nodeType&&g.documentElement?(n=g,o=n.documentElement,p=!f(n),v!==n&&(e=n.defaultView)&&e.top!==e&&(e.addEventListener?e.addEventListener("unload",da,!1):e.attachEvent&&e.attachEvent("onunload",da)),c.attributes=ja(function(a){return a.className="i",!a.getAttribute("className")}),c.getElementsByTagName=ja(function(a){return a.appendChild(n.createComment("")),!a.getElementsByTagName("*").length}),c.getElementsByClassName=Y.test(n.getElementsByClassName),c.getById=ja(function(a){return o.appendChild(a).id=u,!n.getElementsByName||!n.getElementsByName(u).length}),c.getById?(d.filter.ID=function(a){var b=a.replace(_,aa);return function(a){return a.getAttribute("id")===b}},d.find.ID=function(a,b){if("undefined"!=typeof b.getElementById&&p){var c=b.getElementById(a);return c?[c]:[]}}):(d.filter.ID=function(a){var b=a.replace(_,aa);return function(a){var c="undefined"!=typeof a.getAttributeNode&&a.getAttributeNode("id");return c&&c.value===b}},d.find.ID=function(a,b){if("undefined"!=typeof b.getElementById&&p){var c,d,e,f=b.getElementById(a);if(f){if(c=f.getAttributeNode("id"),c&&c.value===a)return[f];e=b.getElementsByName(a),d=0;while(f=e[d++])if(c=f.getAttributeNode("id"),c&&c.value===a)return[f]}return[]}}),d.find.TAG=c.getElementsByTagName?function(a,b){return"undefined"!=typeof b.getElementsByTagName?b.getElementsByTagName(a):c.qsa?b.querySelectorAll(a):void 0}:function(a,b){var c,d=[],e=0,f=b.getElementsByTagName(a);if("*"===a){while(c=f[e++])1===c.nodeType&&d.push(c);return d}return f},d.find.CLASS=c.getElementsByClassName&&function(a,b){if("undefined"!=typeof b.getElementsByClassName&&p)return b.getElementsByClassName(a)},r=[],q=[],(c.qsa=Y.test(n.querySelectorAll))&&(ja(function(a){o.appendChild(a).innerHTML="<a id='"+u+"'></a><select id='"+u+"-\r\\' msallowcapture=''><option selected=''></option></select>",a.querySelectorAll("[msallowcapture^='']").length&&q.push("[*^$]="+K+"*(?:''|\"\")"),a.querySelectorAll("[selected]").length||q.push("\\["+K+"*(?:value|"+J+")"),a.querySelectorAll("[id~="+u+"-]").length||q.push("~="),a.querySelectorAll(":checked").length||q.push(":checked"),a.querySelectorAll("a#"+u+"+*").length||q.push(".#.+[+~]")}),ja(function(a){a.innerHTML="<a href='' disabled='disabled'></a><select disabled='disabled'><option/></select>";var b=n.createElement("input");b.setAttribute("type","hidden"),a.appendChild(b).setAttribute("name","D"),a.querySelectorAll("[name=d]").length&&q.push("name"+K+"*[*^$|!~]?="),2!==a.querySelectorAll(":enabled").length&&q.push(":enabled",":disabled"),o.appendChild(a).disabled=!0,2!==a.querySelectorAll(":disabled").length&&q.push(":enabled",":disabled"),a.querySelectorAll("*,:x"),q.push(",.*:")})),(c.matchesSelector=Y.test(s=o.matches||o.webkitMatchesSelector||o.mozMatchesSelector||o.oMatchesSelector||o.msMatchesSelector))&&ja(function(a){c.disconnectedMatch=s.call(a,"*"),s.call(a,"[s!='']:x"),r.push("!=",N)}),q=q.length&&new RegExp(q.join("|")),r=r.length&&new RegExp(r.join("|")),b=Y.test(o.compareDocumentPosition),t=b||Y.test(o.contains)?function(a,b){var c=9===a.nodeType?a.documentElement:a,d=b&&b.parentNode;return a===d||!(!d||1!==d.nodeType||!(c.contains?c.contains(d):a.compareDocumentPosition&&16&a.compareDocumentPosition(d)))}:function(a,b){if(b)while(b=b.parentNode)if(b===a)return!0;return!1},B=b?function(a,b){if(a===b)return l=!0,0;var d=!a.compareDocumentPosition-!b.compareDocumentPosition;return d?d:(d=(a.ownerDocument||a)===(b.ownerDocument||b)?a.compareDocumentPosition(b):1,1&d||!c.sortDetached&&b.compareDocumentPosition(a)===d?a===n||a.ownerDocument===v&&t(v,a)?-1:b===n||b.ownerDocument===v&&t(v,b)?1:k?I(k,a)-I(k,b):0:4&d?-1:1)}:function(a,b){if(a===b)return l=!0,0;var c,d=0,e=a.parentNode,f=b.parentNode,g=[a],h=[b];if(!e||!f)return a===n?-1:b===n?1:e?-1:f?1:k?I(k,a)-I(k,b):0;if(e===f)return la(a,b);c=a;while(c=c.parentNode)g.unshift(c);c=b;while(c=c.parentNode)h.unshift(c);while(g[d]===h[d])d++;return d?la(g[d],h[d]):g[d]===v?-1:h[d]===v?1:0},n):n},ga.matches=function(a,b){return ga(a,null,null,b)},ga.matchesSelector=function(a,b){if((a.ownerDocument||a)!==n&&m(a),b=b.replace(S,"='$1']"),c.matchesSelector&&p&&!A[b+" "]&&(!r||!r.test(b))&&(!q||!q.test(b)))try{var d=s.call(a,b);if(d||c.disconnectedMatch||a.document&&11!==a.document.nodeType)return d}catch(e){}return ga(b,n,null,[a]).length>0},ga.contains=function(a,b){return(a.ownerDocument||a)!==n&&m(a),t(a,b)},ga.attr=function(a,b){(a.ownerDocument||a)!==n&&m(a);var e=d.attrHandle[b.toLowerCase()],f=e&&C.call(d.attrHandle,b.toLowerCase())?e(a,b,!p):void 0;return void 0!==f?f:c.attributes||!p?a.getAttribute(b):(f=a.getAttributeNode(b))&&f.specified?f.value:null},ga.escape=function(a){return(a+"").replace(ba,ca)},ga.error=function(a){throw new Error("Syntax error, unrecognized expression: "+a)},ga.uniqueSort=function(a){var b,d=[],e=0,f=0;if(l=!c.detectDuplicates,k=!c.sortStable&&a.slice(0),a.sort(B),l){while(b=a[f++])b===a[f]&&(e=d.push(f));while(e--)a.splice(d[e],1)}return k=null,a},e=ga.getText=function(a){var b,c="",d=0,f=a.nodeType;if(f){if(1===f||9===f||11===f){if("string"==typeof a.textContent)return a.textContent;for(a=a.firstChild;a;a=a.nextSibling)c+=e(a)}else if(3===f||4===f)return a.nodeValue}else while(b=a[d++])c+=e(b);return c},d=ga.selectors={cacheLength:50,createPseudo:ia,match:V,attrHandle:{},find:{},relative:{">":{dir:"parentNode",first:!0}," ":{dir:"parentNode"},"+":{dir:"previousSibling",first:!0},"~":{dir:"previousSibling"}},preFilter:{ATTR:function(a){return a[1]=a[1].replace(_,aa),a[3]=(a[3]||a[4]||a[5]||"").replace(_,aa),"~="===a[2]&&(a[3]=" "+a[3]+" "),a.slice(0,4)},CHILD:function(a){return a[1]=a[1].toLowerCase(),"nth"===a[1].slice(0,3)?(a[3]||ga.error(a[0]),a[4]=+(a[4]?a[5]+(a[6]||1):2*("even"===a[3]||"odd"===a[3])),a[5]=+(a[7]+a[8]||"odd"===a[3])):a[3]&&ga.error(a[0]),a},PSEUDO:function(a){var b,c=!a[6]&&a[2];return V.CHILD.test(a[0])?null:(a[3]?a[2]=a[4]||a[5]||"":c&&T.test(c)&&(b=g(c,!0))&&(b=c.indexOf(")",c.length-b)-c.length)&&(a[0]=a[0].slice(0,b),a[2]=c.slice(0,b)),a.slice(0,3))}},filter:{TAG:function(a){var b=a.replace(_,aa).toLowerCase();return"*"===a?function(){return!0}:function(a){return a.nodeName&&a.nodeName.toLowerCase()===b}},CLASS:function(a){var b=y[a+" "];return b||(b=new RegExp("(^|"+K+")"+a+"("+K+"|$)"))&&y(a,function(a){return b.test("string"==typeof a.className&&a.className||"undefined"!=typeof a.getAttribute&&a.getAttribute("class")||"")})},ATTR:function(a,b,c){return function(d){var e=ga.attr(d,a);return null==e?"!="===b:!b||(e+="","="===b?e===c:"!="===b?e!==c:"^="===b?c&&0===e.indexOf(c):"*="===b?c&&e.indexOf(c)>-1:"$="===b?c&&e.slice(-c.length)===c:"~="===b?(" "+e.replace(O," ")+" ").indexOf(c)>-1:"|="===b&&(e===c||e.slice(0,c.length+1)===c+"-"))}},CHILD:function(a,b,c,d,e){var f="nth"!==a.slice(0,3),g="last"!==a.slice(-4),h="of-type"===b;return 1===d&&0===e?function(a){return!!a.parentNode}:function(b,c,i){var j,k,l,m,n,o,p=f!==g?"nextSibling":"previousSibling",q=b.parentNode,r=h&&b.nodeName.toLowerCase(),s=!i&&!h,t=!1;if(q){if(f){while(p){m=b;while(m=m[p])if(h?m.nodeName.toLowerCase()===r:1===m.nodeType)return!1;o=p="only"===a&&!o&&"nextSibling"}return!0}if(o=[g?q.firstChild:q.lastChild],g&&s){m=q,l=m[u]||(m[u]={}),k=l[m.uniqueID]||(l[m.uniqueID]={}),j=k[a]||[],n=j[0]===w&&j[1],t=n&&j[2],m=n&&q.childNodes[n];while(m=++n&&m&&m[p]||(t=n=0)||o.pop())if(1===m.nodeType&&++t&&m===b){k[a]=[w,n,t];break}}else if(s&&(m=b,l=m[u]||(m[u]={}),k=l[m.uniqueID]||(l[m.uniqueID]={}),j=k[a]||[],n=j[0]===w&&j[1],t=n),t===!1)while(m=++n&&m&&m[p]||(t=n=0)||o.pop())if((h?m.nodeName.toLowerCase()===r:1===m.nodeType)&&++t&&(s&&(l=m[u]||(m[u]={}),k=l[m.uniqueID]||(l[m.uniqueID]={}),k[a]=[w,t]),m===b))break;return t-=e,t===d||t%d===0&&t/d>=0}}},PSEUDO:function(a,b){var c,e=d.pseudos[a]||d.setFilters[a.toLowerCase()]||ga.error("unsupported pseudo: "+a);return e[u]?e(b):e.length>1?(c=[a,a,"",b],d.setFilters.hasOwnProperty(a.toLowerCase())?ia(function(a,c){var d,f=e(a,b),g=f.length;while(g--)d=I(a,f[g]),a[d]=!(c[d]=f[g])}):function(a){return e(a,0,c)}):e}},pseudos:{not:ia(function(a){var b=[],c=[],d=h(a.replace(P,"$1"));return d[u]?ia(function(a,b,c,e){var f,g=d(a,null,e,[]),h=a.length;while(h--)(f=g[h])&&(a[h]=!(b[h]=f))}):function(a,e,f){return b[0]=a,d(b,null,f,c),b[0]=null,!c.pop()}}),has:ia(function(a){return function(b){return ga(a,b).length>0}}),contains:ia(function(a){return a=a.replace(_,aa),function(b){return(b.textContent||b.innerText||e(b)).indexOf(a)>-1}}),lang:ia(function(a){return U.test(a||"")||ga.error("unsupported lang: "+a),a=a.replace(_,aa).toLowerCase(),function(b){var c;do if(c=p?b.lang:b.getAttribute("xml:lang")||b.getAttribute("lang"))return c=c.toLowerCase(),c===a||0===c.indexOf(a+"-");while((b=b.parentNode)&&1===b.nodeType);return!1}}),target:function(b){var c=a.location&&a.location.hash;return c&&c.slice(1)===b.id},root:function(a){return a===o},focus:function(a){return a===n.activeElement&&(!n.hasFocus||n.hasFocus())&&!!(a.type||a.href||~a.tabIndex)},enabled:oa(!1),disabled:oa(!0),checked:function(a){var b=a.nodeName.toLowerCase();return"input"===b&&!!a.checked||"option"===b&&!!a.selected},selected:function(a){return a.parentNode&&a.parentNode.selectedIndex,a.selected===!0},empty:function(a){for(a=a.firstChild;a;a=a.nextSibling)if(a.nodeType<6)return!1;return!0},parent:function(a){return!d.pseudos.empty(a)},header:function(a){return X.test(a.nodeName)},input:function(a){return W.test(a.nodeName)},button:function(a){var b=a.nodeName.toLowerCase();return"input"===b&&"button"===a.type||"button"===b},text:function(a){var b;return"input"===a.nodeName.toLowerCase()&&"text"===a.type&&(null==(b=a.getAttribute("type"))||"text"===b.toLowerCase())},first:pa(function(){return[0]}),last:pa(function(a,b){return[b-1]}),eq:pa(function(a,b,c){return[c<0?c+b:c]}),even:pa(function(a,b){for(var c=0;c<b;c+=2)a.push(c);return a}),odd:pa(function(a,b){for(var c=1;c<b;c+=2)a.push(c);return a}),lt:pa(function(a,b,c){for(var d=c<0?c+b:c;--d>=0;)a.push(d);return a}),gt:pa(function(a,b,c){for(var d=c<0?c+b:c;++d<b;)a.push(d);return a})}},d.pseudos.nth=d.pseudos.eq;for(b in{radio:!0,checkbox:!0,file:!0,password:!0,image:!0})d.pseudos[b]=ma(b);for(b in{submit:!0,reset:!0})d.pseudos[b]=na(b);function ra(){}ra.prototype=d.filters=d.pseudos,d.setFilters=new ra,g=ga.tokenize=function(a,b){var c,e,f,g,h,i,j,k=z[a+" "];if(k)return b?0:k.slice(0);h=a,i=[],j=d.preFilter;while(h){c&&!(e=Q.exec(h))||(e&&(h=h.slice(e[0].length)||h),i.push(f=[])),c=!1,(e=R.exec(h))&&(c=e.shift(),f.push({value:c,type:e[0].replace(P," ")}),h=h.slice(c.length));for(g in d.filter)!(e=V[g].exec(h))||j[g]&&!(e=j[g](e))||(c=e.shift(),f.push({value:c,type:g,matches:e}),h=h.slice(c.length));if(!c)break}return b?h.length:h?ga.error(a):z(a,i).slice(0)};function sa(a){for(var b=0,c=a.length,d="";b<c;b++)d+=a[b].value;return d}function ta(a,b,c){var d=b.dir,e=b.next,f=e||d,g=c&&"parentNode"===f,h=x++;return b.first?function(b,c,e){while(b=b[d])if(1===b.nodeType||g)return a(b,c,e);return!1}:function(b,c,i){var j,k,l,m=[w,h];if(i){while(b=b[d])if((1===b.nodeType||g)&&a(b,c,i))return!0}else while(b=b[d])if(1===b.nodeType||g)if(l=b[u]||(b[u]={}),k=l[b.uniqueID]||(l[b.uniqueID]={}),e&&e===b.nodeName.toLowerCase())b=b[d]||b;else{if((j=k[f])&&j[0]===w&&j[1]===h)return m[2]=j[2];if(k[f]=m,m[2]=a(b,c,i))return!0}return!1}}function ua(a){return a.length>1?function(b,c,d){var e=a.length;while(e--)if(!a[e](b,c,d))return!1;return!0}:a[0]}function va(a,b,c){for(var d=0,e=b.length;d<e;d++)ga(a,b[d],c);return c}function wa(a,b,c,d,e){for(var f,g=[],h=0,i=a.length,j=null!=b;h<i;h++)(f=a[h])&&(c&&!c(f,d,e)||(g.push(f),j&&b.push(h)));return g}function xa(a,b,c,d,e,f){return d&&!d[u]&&(d=xa(d)),e&&!e[u]&&(e=xa(e,f)),ia(function(f,g,h,i){var j,k,l,m=[],n=[],o=g.length,p=f||va(b||"*",h.nodeType?[h]:h,[]),q=!a||!f&&b?p:wa(p,m,a,h,i),r=c?e||(f?a:o||d)?[]:g:q;if(c&&c(q,r,h,i),d){j=wa(r,n),d(j,[],h,i),k=j.length;while(k--)(l=j[k])&&(r[n[k]]=!(q[n[k]]=l))}if(f){if(e||a){if(e){j=[],k=r.length;while(k--)(l=r[k])&&j.push(q[k]=l);e(null,r=[],j,i)}k=r.length;while(k--)(l=r[k])&&(j=e?I(f,l):m[k])>-1&&(f[j]=!(g[j]=l))}}else r=wa(r===g?r.splice(o,r.length):r),e?e(null,g,r,i):G.apply(g,r)})}function ya(a){for(var b,c,e,f=a.length,g=d.relative[a[0].type],h=g||d.relative[" "],i=g?1:0,k=ta(function(a){return a===b},h,!0),l=ta(function(a){return I(b,a)>-1},h,!0),m=[function(a,c,d){var e=!g&&(d||c!==j)||((b=c).nodeType?k(a,c,d):l(a,c,d));return b=null,e}];i<f;i++)if(c=d.relative[a[i].type])m=[ta(ua(m),c)];else{if(c=d.filter[a[i].type].apply(null,a[i].matches),c[u]){for(e=++i;e<f;e++)if(d.relative[a[e].type])break;return xa(i>1&&ua(m),i>1&&sa(a.slice(0,i-1).concat({value:" "===a[i-2].type?"*":""})).replace(P,"$1"),c,i<e&&ya(a.slice(i,e)),e<f&&ya(a=a.slice(e)),e<f&&sa(a))}m.push(c)}return ua(m)}function za(a,b){var c=b.length>0,e=a.length>0,f=function(f,g,h,i,k){var l,o,q,r=0,s="0",t=f&&[],u=[],v=j,x=f||e&&d.find.TAG("*",k),y=w+=null==v?1:Math.random()||.1,z=x.length;for(k&&(j=g===n||g||k);s!==z&&null!=(l=x[s]);s++){if(e&&l){o=0,g||l.ownerDocument===n||(m(l),h=!p);while(q=a[o++])if(q(l,g||n,h)){i.push(l);break}k&&(w=y)}c&&((l=!q&&l)&&r--,f&&t.push(l))}if(r+=s,c&&s!==r){o=0;while(q=b[o++])q(t,u,g,h);if(f){if(r>0)while(s--)t[s]||u[s]||(u[s]=E.call(i));u=wa(u)}G.apply(i,u),k&&!f&&u.length>0&&r+b.length>1&&ga.uniqueSort(i)}return k&&(w=y,j=v),t};return c?ia(f):f}return h=ga.compile=function(a,b){var c,d=[],e=[],f=A[a+" "];if(!f){b||(b=g(a)),c=b.length;while(c--)f=ya(b[c]),f[u]?d.push(f):e.push(f);f=A(a,za(e,d)),f.selector=a}return f},i=ga.select=function(a,b,c,e){var f,i,j,k,l,m="function"==typeof a&&a,n=!e&&g(a=m.selector||a);if(c=c||[],1===n.length){if(i=n[0]=n[0].slice(0),i.length>2&&"ID"===(j=i[0]).type&&9===b.nodeType&&p&&d.relative[i[1].type]){if(b=(d.find.ID(j.matches[0].replace(_,aa),b)||[])[0],!b)return c;m&&(b=b.parentNode),a=a.slice(i.shift().value.length)}f=V.needsContext.test(a)?0:i.length;while(f--){if(j=i[f],d.relative[k=j.type])break;if((l=d.find[k])&&(e=l(j.matches[0].replace(_,aa),$.test(i[0].type)&&qa(b.parentNode)||b))){if(i.splice(f,1),a=e.length&&sa(i),!a)return G.apply(c,e),c;break}}}return(m||h(a,n))(e,b,!p,c,!b||$.test(a)&&qa(b.parentNode)||b),c},c.sortStable=u.split("").sort(B).join("")===u,c.detectDuplicates=!!l,m(),c.sortDetached=ja(function(a){return 1&a.compareDocumentPosition(n.createElement("fieldset"))}),ja(function(a){return a.innerHTML="<a href='#'></a>","#"===a.firstChild.getAttribute("href")})||ka("type|href|height|width",function(a,b,c){if(!c)return a.getAttribute(b,"type"===b.toLowerCase()?1:2)}),c.attributes&&ja(function(a){return a.innerHTML="<input/>",a.firstChild.setAttribute("value",""),""===a.firstChild.getAttribute("value")})||ka("value",function(a,b,c){if(!c&&"input"===a.nodeName.toLowerCase())return a.defaultValue}),ja(function(a){return null==a.getAttribute("disabled")})||ka(J,function(a,b,c){var d;if(!c)return a[b]===!0?b.toLowerCase():(d=a.getAttributeNode(b))&&d.specified?d.value:null}),ga}(a);r.find=x,r.expr=x.selectors,r.expr[":"]=r.expr.pseudos,r.uniqueSort=r.unique=x.uniqueSort,r.text=x.getText,r.isXMLDoc=x.isXML,r.contains=x.contains,r.escapeSelector=x.escape;var y=function(a,b,c){var d=[],e=void 0!==c;while((a=a[b])&&9!==a.nodeType)if(1===a.nodeType){if(e&&r(a).is(c))break;d.push(a)}return d},z=function(a,b){for(var c=[];a;a=a.nextSibling)1===a.nodeType&&a!==b&&c.push(a);return c},A=r.expr.match.needsContext;function B(a,b){return a.nodeName&&a.nodeName.toLowerCase()===b.toLowerCase()}var C=/^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i,D=/^.[^:#\[\.,]*$/;function E(a,b,c){return r.isFunction(b)?r.grep(a,function(a,d){return!!b.call(a,d,a)!==c}):b.nodeType?r.grep(a,function(a){return a===b!==c}):"string"!=typeof b?r.grep(a,function(a){return i.call(b,a)>-1!==c}):D.test(b)?r.filter(b,a,c):(b=r.filter(b,a),r.grep(a,function(a){return i.call(b,a)>-1!==c&&1===a.nodeType}))}r.filter=function(a,b,c){var d=b[0];return c&&(a=":not("+a+")"),1===b.length&&1===d.nodeType?r.find.matchesSelector(d,a)?[d]:[]:r.find.matches(a,r.grep(b,function(a){return 1===a.nodeType}))},r.fn.extend({find:function(a){var b,c,d=this.length,e=this;if("string"!=typeof a)return this.pushStack(r(a).filter(function(){for(b=0;b<d;b++)if(r.contains(e[b],this))return!0}));for(c=this.pushStack([]),b=0;b<d;b++)r.find(a,e[b],c);return d>1?r.uniqueSort(c):c},filter:function(a){return this.pushStack(E(this,a||[],!1))},not:function(a){return this.pushStack(E(this,a||[],!0))},is:function(a){return!!E(this,"string"==typeof a&&A.test(a)?r(a):a||[],!1).length}});var F,G=/^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/,H=r.fn.init=function(a,b,c){var e,f;if(!a)return this;if(c=c||F,"string"==typeof a){if(e="<"===a[0]&&">"===a[a.length-1]&&a.length>=3?[null,a,null]:G.exec(a),!e||!e[1]&&b)return!b||b.jquery?(b||c).find(a):this.constructor(b).find(a);if(e[1]){if(b=b instanceof r?b[0]:b,r.merge(this,r.parseHTML(e[1],b&&b.nodeType?b.ownerDocument||b:d,!0)),C.test(e[1])&&r.isPlainObject(b))for(e in b)r.isFunction(this[e])?this[e](b[e]):this.attr(e,b[e]);return this}return f=d.getElementById(e[2]),f&&(this[0]=f,this.length=1),this}return a.nodeType?(this[0]=a,this.length=1,this):r.isFunction(a)?void 0!==c.ready?c.ready(a):a(r):r.makeArray(a,this)};H.prototype=r.fn,F=r(d);var I=/^(?:parents|prev(?:Until|All))/,J={children:!0,contents:!0,next:!0,prev:!0};r.fn.extend({has:function(a){var b=r(a,this),c=b.length;return this.filter(function(){for(var a=0;a<c;a++)if(r.contains(this,b[a]))return!0})},closest:function(a,b){var c,d=0,e=this.length,f=[],g="string"!=typeof a&&r(a);if(!A.test(a))for(;d<e;d++)for(c=this[d];c&&c!==b;c=c.parentNode)if(c.nodeType<11&&(g?g.index(c)>-1:1===c.nodeType&&r.find.matchesSelector(c,a))){f.push(c);break}return this.pushStack(f.length>1?r.uniqueSort(f):f)},index:function(a){return a?"string"==typeof a?i.call(r(a),this[0]):i.call(this,a.jquery?a[0]:a):this[0]&&this[0].parentNode?this.first().prevAll().length:-1},add:function(a,b){return this.pushStack(r.uniqueSort(r.merge(this.get(),r(a,b))))},addBack:function(a){return this.add(null==a?this.prevObject:this.prevObject.filter(a))}});function K(a,b){while((a=a[b])&&1!==a.nodeType);return a}r.each({parent:function(a){var b=a.parentNode;return b&&11!==b.nodeType?b:null},parents:function(a){return y(a,"parentNode")},parentsUntil:function(a,b,c){return y(a,"parentNode",c)},next:function(a){return K(a,"nextSibling")},prev:function(a){return K(a,"previousSibling")},nextAll:function(a){return y(a,"nextSibling")},prevAll:function(a){return y(a,"previousSibling")},nextUntil:function(a,b,c){return y(a,"nextSibling",c)},prevUntil:function(a,b,c){return y(a,"previousSibling",c)},siblings:function(a){return z((a.parentNode||{}).firstChild,a)},children:function(a){return z(a.firstChild)},contents:function(a){return B(a,"iframe")?a.contentDocument:(B(a,"template")&&(a=a.content||a),r.merge([],a.childNodes))}},function(a,b){r.fn[a]=function(c,d){var e=r.map(this,b,c);return"Until"!==a.slice(-5)&&(d=c),d&&"string"==typeof d&&(e=r.filter(d,e)),this.length>1&&(J[a]||r.uniqueSort(e),I.test(a)&&e.reverse()),this.pushStack(e)}});var L=/[^\x20\t\r\n\f]+/g;function M(a){var b={};return r.each(a.match(L)||[],function(a,c){b[c]=!0}),b}r.Callbacks=function(a){a="string"==typeof a?M(a):r.extend({},a);var b,c,d,e,f=[],g=[],h=-1,i=function(){for(e=e||a.once,d=b=!0;g.length;h=-1){c=g.shift();while(++h<f.length)f[h].apply(c[0],c[1])===!1&&a.stopOnFalse&&(h=f.length,c=!1)}a.memory||(c=!1),b=!1,e&&(f=c?[]:"")},j={add:function(){return f&&(c&&!b&&(h=f.length-1,g.push(c)),function d(b){r.each(b,function(b,c){r.isFunction(c)?a.unique&&j.has(c)||f.push(c):c&&c.length&&"string"!==r.type(c)&&d(c)})}(arguments),c&&!b&&i()),this},remove:function(){return r.each(arguments,function(a,b){var c;while((c=r.inArray(b,f,c))>-1)f.splice(c,1),c<=h&&h--}),this},has:function(a){return a?r.inArray(a,f)>-1:f.length>0},empty:function(){return f&&(f=[]),this},disable:function(){return e=g=[],f=c="",this},disabled:function(){return!f},lock:function(){return e=g=[],c||b||(f=c=""),this},locked:function(){return!!e},fireWith:function(a,c){return e||(c=c||[],c=[a,c.slice?c.slice():c],g.push(c),b||i()),this},fire:function(){return j.fireWith(this,arguments),this},fired:function(){return!!d}};return j};function N(a){return a}function O(a){throw a}function P(a,b,c,d){var e;try{a&&r.isFunction(e=a.promise)?e.call(a).done(b).fail(c):a&&r.isFunction(e=a.then)?e.call(a,b,c):b.apply(void 0,[a].slice(d))}catch(a){c.apply(void 0,[a])}}r.extend({Deferred:function(b){var c=[["notify","progress",r.Callbacks("memory"),r.Callbacks("memory"),2],["resolve","done",r.Callbacks("once memory"),r.Callbacks("once memory"),0,"resolved"],["reject","fail",r.Callbacks("once memory"),r.Callbacks("once memory"),1,"rejected"]],d="pending",e={state:function(){return d},always:function(){return f.done(arguments).fail(arguments),this},"catch":function(a){return e.then(null,a)},pipe:function(){var a=arguments;return r.Deferred(function(b){r.each(c,function(c,d){var e=r.isFunction(a[d[4]])&&a[d[4]];f[d[1]](function(){var a=e&&e.apply(this,arguments);a&&r.isFunction(a.promise)?a.promise().progress(b.notify).done(b.resolve).fail(b.reject):b[d[0]+"With"](this,e?[a]:arguments)})}),a=null}).promise()},then:function(b,d,e){var f=0;function g(b,c,d,e){return function(){var h=this,i=arguments,j=function(){var a,j;if(!(b<f)){if(a=d.apply(h,i),a===c.promise())throw new TypeError("Thenable self-resolution");j=a&&("object"==typeof a||"function"==typeof a)&&a.then,r.isFunction(j)?e?j.call(a,g(f,c,N,e),g(f,c,O,e)):(f++,j.call(a,g(f,c,N,e),g(f,c,O,e),g(f,c,N,c.notifyWith))):(d!==N&&(h=void 0,i=[a]),(e||c.resolveWith)(h,i))}},k=e?j:function(){try{j()}catch(a){r.Deferred.exceptionHook&&r.Deferred.exceptionHook(a,k.stackTrace),b+1>=f&&(d!==O&&(h=void 0,i=[a]),c.rejectWith(h,i))}};b?k():(r.Deferred.getStackHook&&(k.stackTrace=r.Deferred.getStackHook()),a.setTimeout(k))}}return r.Deferred(function(a){c[0][3].add(g(0,a,r.isFunction(e)?e:N,a.notifyWith)),c[1][3].add(g(0,a,r.isFunction(b)?b:N)),c[2][3].add(g(0,a,r.isFunction(d)?d:O))}).promise()},promise:function(a){return null!=a?r.extend(a,e):e}},f={};return r.each(c,function(a,b){var g=b[2],h=b[5];e[b[1]]=g.add,h&&g.add(function(){d=h},c[3-a][2].disable,c[0][2].lock),g.add(b[3].fire),f[b[0]]=function(){return f[b[0]+"With"](this===f?void 0:this,arguments),this},f[b[0]+"With"]=g.fireWith}),e.promise(f),b&&b.call(f,f),f},when:function(a){var b=arguments.length,c=b,d=Array(c),e=f.call(arguments),g=r.Deferred(),h=function(a){return function(c){d[a]=this,e[a]=arguments.length>1?f.call(arguments):c,--b||g.resolveWith(d,e)}};if(b<=1&&(P(a,g.done(h(c)).resolve,g.reject,!b),"pending"===g.state()||r.isFunction(e[c]&&e[c].then)))return g.then();while(c--)P(e[c],h(c),g.reject);return g.promise()}});var Q=/^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/;r.Deferred.exceptionHook=function(b,c){a.console&&a.console.warn&&b&&Q.test(b.name)&&a.console.warn("jQuery.Deferred exception: "+b.message,b.stack,c)},r.readyException=function(b){a.setTimeout(function(){throw b})};var R=r.Deferred();r.fn.ready=function(a){return R.then(a)["catch"](function(a){r.readyException(a)}),this},r.extend({isReady:!1,readyWait:1,ready:function(a){(a===!0?--r.readyWait:r.isReady)||(r.isReady=!0,a!==!0&&--r.readyWait>0||R.resolveWith(d,[r]))}}),r.ready.then=R.then;function S(){d.removeEventListener("DOMContentLoaded",S),
+a.removeEventListener("load",S),r.ready()}"complete"===d.readyState||"loading"!==d.readyState&&!d.documentElement.doScroll?a.setTimeout(r.ready):(d.addEventListener("DOMContentLoaded",S),a.addEventListener("load",S));var T=function(a,b,c,d,e,f,g){var h=0,i=a.length,j=null==c;if("object"===r.type(c)){e=!0;for(h in c)T(a,b,h,c[h],!0,f,g)}else if(void 0!==d&&(e=!0,r.isFunction(d)||(g=!0),j&&(g?(b.call(a,d),b=null):(j=b,b=function(a,b,c){return j.call(r(a),c)})),b))for(;h<i;h++)b(a[h],c,g?d:d.call(a[h],h,b(a[h],c)));return e?a:j?b.call(a):i?b(a[0],c):f},U=function(a){return 1===a.nodeType||9===a.nodeType||!+a.nodeType};function V(){this.expando=r.expando+V.uid++}V.uid=1,V.prototype={cache:function(a){var b=a[this.expando];return b||(b={},U(a)&&(a.nodeType?a[this.expando]=b:Object.defineProperty(a,this.expando,{value:b,configurable:!0}))),b},set:function(a,b,c){var d,e=this.cache(a);if("string"==typeof b)e[r.camelCase(b)]=c;else for(d in b)e[r.camelCase(d)]=b[d];return e},get:function(a,b){return void 0===b?this.cache(a):a[this.expando]&&a[this.expando][r.camelCase(b)]},access:function(a,b,c){return void 0===b||b&&"string"==typeof b&&void 0===c?this.get(a,b):(this.set(a,b,c),void 0!==c?c:b)},remove:function(a,b){var c,d=a[this.expando];if(void 0!==d){if(void 0!==b){Array.isArray(b)?b=b.map(r.camelCase):(b=r.camelCase(b),b=b in d?[b]:b.match(L)||[]),c=b.length;while(c--)delete d[b[c]]}(void 0===b||r.isEmptyObject(d))&&(a.nodeType?a[this.expando]=void 0:delete a[this.expando])}},hasData:function(a){var b=a[this.expando];return void 0!==b&&!r.isEmptyObject(b)}};var W=new V,X=new V,Y=/^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,Z=/[A-Z]/g;function $(a){return"true"===a||"false"!==a&&("null"===a?null:a===+a+""?+a:Y.test(a)?JSON.parse(a):a)}function _(a,b,c){var d;if(void 0===c&&1===a.nodeType)if(d="data-"+b.replace(Z,"-$&").toLowerCase(),c=a.getAttribute(d),"string"==typeof c){try{c=$(c)}catch(e){}X.set(a,b,c)}else c=void 0;return c}r.extend({hasData:function(a){return X.hasData(a)||W.hasData(a)},data:function(a,b,c){return X.access(a,b,c)},removeData:function(a,b){X.remove(a,b)},_data:function(a,b,c){return W.access(a,b,c)},_removeData:function(a,b){W.remove(a,b)}}),r.fn.extend({data:function(a,b){var c,d,e,f=this[0],g=f&&f.attributes;if(void 0===a){if(this.length&&(e=X.get(f),1===f.nodeType&&!W.get(f,"hasDataAttrs"))){c=g.length;while(c--)g[c]&&(d=g[c].name,0===d.indexOf("data-")&&(d=r.camelCase(d.slice(5)),_(f,d,e[d])));W.set(f,"hasDataAttrs",!0)}return e}return"object"==typeof a?this.each(function(){X.set(this,a)}):T(this,function(b){var c;if(f&&void 0===b){if(c=X.get(f,a),void 0!==c)return c;if(c=_(f,a),void 0!==c)return c}else this.each(function(){X.set(this,a,b)})},null,b,arguments.length>1,null,!0)},removeData:function(a){return this.each(function(){X.remove(this,a)})}}),r.extend({queue:function(a,b,c){var d;if(a)return b=(b||"fx")+"queue",d=W.get(a,b),c&&(!d||Array.isArray(c)?d=W.access(a,b,r.makeArray(c)):d.push(c)),d||[]},dequeue:function(a,b){b=b||"fx";var c=r.queue(a,b),d=c.length,e=c.shift(),f=r._queueHooks(a,b),g=function(){r.dequeue(a,b)};"inprogress"===e&&(e=c.shift(),d--),e&&("fx"===b&&c.unshift("inprogress"),delete f.stop,e.call(a,g,f)),!d&&f&&f.empty.fire()},_queueHooks:function(a,b){var c=b+"queueHooks";return W.get(a,c)||W.access(a,c,{empty:r.Callbacks("once memory").add(function(){W.remove(a,[b+"queue",c])})})}}),r.fn.extend({queue:function(a,b){var c=2;return"string"!=typeof a&&(b=a,a="fx",c--),arguments.length<c?r.queue(this[0],a):void 0===b?this:this.each(function(){var c=r.queue(this,a,b);r._queueHooks(this,a),"fx"===a&&"inprogress"!==c[0]&&r.dequeue(this,a)})},dequeue:function(a){return this.each(function(){r.dequeue(this,a)})},clearQueue:function(a){return this.queue(a||"fx",[])},promise:function(a,b){var c,d=1,e=r.Deferred(),f=this,g=this.length,h=function(){--d||e.resolveWith(f,[f])};"string"!=typeof a&&(b=a,a=void 0),a=a||"fx";while(g--)c=W.get(f[g],a+"queueHooks"),c&&c.empty&&(d++,c.empty.add(h));return h(),e.promise(b)}});var aa=/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/.source,ba=new RegExp("^(?:([+-])=|)("+aa+")([a-z%]*)$","i"),ca=["Top","Right","Bottom","Left"],da=function(a,b){return a=b||a,"none"===a.style.display||""===a.style.display&&r.contains(a.ownerDocument,a)&&"none"===r.css(a,"display")},ea=function(a,b,c,d){var e,f,g={};for(f in b)g[f]=a.style[f],a.style[f]=b[f];e=c.apply(a,d||[]);for(f in b)a.style[f]=g[f];return e};function fa(a,b,c,d){var e,f=1,g=20,h=d?function(){return d.cur()}:function(){return r.css(a,b,"")},i=h(),j=c&&c[3]||(r.cssNumber[b]?"":"px"),k=(r.cssNumber[b]||"px"!==j&&+i)&&ba.exec(r.css(a,b));if(k&&k[3]!==j){j=j||k[3],c=c||[],k=+i||1;do f=f||".5",k/=f,r.style(a,b,k+j);while(f!==(f=h()/i)&&1!==f&&--g)}return c&&(k=+k||+i||0,e=c[1]?k+(c[1]+1)*c[2]:+c[2],d&&(d.unit=j,d.start=k,d.end=e)),e}var ga={};function ha(a){var b,c=a.ownerDocument,d=a.nodeName,e=ga[d];return e?e:(b=c.body.appendChild(c.createElement(d)),e=r.css(b,"display"),b.parentNode.removeChild(b),"none"===e&&(e="block"),ga[d]=e,e)}function ia(a,b){for(var c,d,e=[],f=0,g=a.length;f<g;f++)d=a[f],d.style&&(c=d.style.display,b?("none"===c&&(e[f]=W.get(d,"display")||null,e[f]||(d.style.display="")),""===d.style.display&&da(d)&&(e[f]=ha(d))):"none"!==c&&(e[f]="none",W.set(d,"display",c)));for(f=0;f<g;f++)null!=e[f]&&(a[f].style.display=e[f]);return a}r.fn.extend({show:function(){return ia(this,!0)},hide:function(){return ia(this)},toggle:function(a){return"boolean"==typeof a?a?this.show():this.hide():this.each(function(){da(this)?r(this).show():r(this).hide()})}});var ja=/^(?:checkbox|radio)$/i,ka=/<([a-z][^\/\0>\x20\t\r\n\f]+)/i,la=/^$|\/(?:java|ecma)script/i,ma={option:[1,"<select multiple='multiple'>","</select>"],thead:[1,"<table>","</table>"],col:[2,"<table><colgroup>","</colgroup></table>"],tr:[2,"<table><tbody>","</tbody></table>"],td:[3,"<table><tbody><tr>","</tr></tbody></table>"],_default:[0,"",""]};ma.optgroup=ma.option,ma.tbody=ma.tfoot=ma.colgroup=ma.caption=ma.thead,ma.th=ma.td;function na(a,b){var c;return c="undefined"!=typeof a.getElementsByTagName?a.getElementsByTagName(b||"*"):"undefined"!=typeof a.querySelectorAll?a.querySelectorAll(b||"*"):[],void 0===b||b&&B(a,b)?r.merge([a],c):c}function oa(a,b){for(var c=0,d=a.length;c<d;c++)W.set(a[c],"globalEval",!b||W.get(b[c],"globalEval"))}var pa=/<|&#?\w+;/;function qa(a,b,c,d,e){for(var f,g,h,i,j,k,l=b.createDocumentFragment(),m=[],n=0,o=a.length;n<o;n++)if(f=a[n],f||0===f)if("object"===r.type(f))r.merge(m,f.nodeType?[f]:f);else if(pa.test(f)){g=g||l.appendChild(b.createElement("div")),h=(ka.exec(f)||["",""])[1].toLowerCase(),i=ma[h]||ma._default,g.innerHTML=i[1]+r.htmlPrefilter(f)+i[2],k=i[0];while(k--)g=g.lastChild;r.merge(m,g.childNodes),g=l.firstChild,g.textContent=""}else m.push(b.createTextNode(f));l.textContent="",n=0;while(f=m[n++])if(d&&r.inArray(f,d)>-1)e&&e.push(f);else if(j=r.contains(f.ownerDocument,f),g=na(l.appendChild(f),"script"),j&&oa(g),c){k=0;while(f=g[k++])la.test(f.type||"")&&c.push(f)}return l}!function(){var a=d.createDocumentFragment(),b=a.appendChild(d.createElement("div")),c=d.createElement("input");c.setAttribute("type","radio"),c.setAttribute("checked","checked"),c.setAttribute("name","t"),b.appendChild(c),o.checkClone=b.cloneNode(!0).cloneNode(!0).lastChild.checked,b.innerHTML="<textarea>x</textarea>",o.noCloneChecked=!!b.cloneNode(!0).lastChild.defaultValue}();var ra=d.documentElement,sa=/^key/,ta=/^(?:mouse|pointer|contextmenu|drag|drop)|click/,ua=/^([^.]*)(?:\.(.+)|)/;function va(){return!0}function wa(){return!1}function xa(){try{return d.activeElement}catch(a){}}function ya(a,b,c,d,e,f){var g,h;if("object"==typeof b){"string"!=typeof c&&(d=d||c,c=void 0);for(h in b)ya(a,h,c,d,b[h],f);return a}if(null==d&&null==e?(e=c,d=c=void 0):null==e&&("string"==typeof c?(e=d,d=void 0):(e=d,d=c,c=void 0)),e===!1)e=wa;else if(!e)return a;return 1===f&&(g=e,e=function(a){return r().off(a),g.apply(this,arguments)},e.guid=g.guid||(g.guid=r.guid++)),a.each(function(){r.event.add(this,b,e,d,c)})}r.event={global:{},add:function(a,b,c,d,e){var f,g,h,i,j,k,l,m,n,o,p,q=W.get(a);if(q){c.handler&&(f=c,c=f.handler,e=f.selector),e&&r.find.matchesSelector(ra,e),c.guid||(c.guid=r.guid++),(i=q.events)||(i=q.events={}),(g=q.handle)||(g=q.handle=function(b){return"undefined"!=typeof r&&r.event.triggered!==b.type?r.event.dispatch.apply(a,arguments):void 0}),b=(b||"").match(L)||[""],j=b.length;while(j--)h=ua.exec(b[j])||[],n=p=h[1],o=(h[2]||"").split(".").sort(),n&&(l=r.event.special[n]||{},n=(e?l.delegateType:l.bindType)||n,l=r.event.special[n]||{},k=r.extend({type:n,origType:p,data:d,handler:c,guid:c.guid,selector:e,needsContext:e&&r.expr.match.needsContext.test(e),namespace:o.join(".")},f),(m=i[n])||(m=i[n]=[],m.delegateCount=0,l.setup&&l.setup.call(a,d,o,g)!==!1||a.addEventListener&&a.addEventListener(n,g)),l.add&&(l.add.call(a,k),k.handler.guid||(k.handler.guid=c.guid)),e?m.splice(m.delegateCount++,0,k):m.push(k),r.event.global[n]=!0)}},remove:function(a,b,c,d,e){var f,g,h,i,j,k,l,m,n,o,p,q=W.hasData(a)&&W.get(a);if(q&&(i=q.events)){b=(b||"").match(L)||[""],j=b.length;while(j--)if(h=ua.exec(b[j])||[],n=p=h[1],o=(h[2]||"").split(".").sort(),n){l=r.event.special[n]||{},n=(d?l.delegateType:l.bindType)||n,m=i[n]||[],h=h[2]&&new RegExp("(^|\\.)"+o.join("\\.(?:.*\\.|)")+"(\\.|$)"),g=f=m.length;while(f--)k=m[f],!e&&p!==k.origType||c&&c.guid!==k.guid||h&&!h.test(k.namespace)||d&&d!==k.selector&&("**"!==d||!k.selector)||(m.splice(f,1),k.selector&&m.delegateCount--,l.remove&&l.remove.call(a,k));g&&!m.length&&(l.teardown&&l.teardown.call(a,o,q.handle)!==!1||r.removeEvent(a,n,q.handle),delete i[n])}else for(n in i)r.event.remove(a,n+b[j],c,d,!0);r.isEmptyObject(i)&&W.remove(a,"handle events")}},dispatch:function(a){var b=r.event.fix(a),c,d,e,f,g,h,i=new Array(arguments.length),j=(W.get(this,"events")||{})[b.type]||[],k=r.event.special[b.type]||{};for(i[0]=b,c=1;c<arguments.length;c++)i[c]=arguments[c];if(b.delegateTarget=this,!k.preDispatch||k.preDispatch.call(this,b)!==!1){h=r.event.handlers.call(this,b,j),c=0;while((f=h[c++])&&!b.isPropagationStopped()){b.currentTarget=f.elem,d=0;while((g=f.handlers[d++])&&!b.isImmediatePropagationStopped())b.rnamespace&&!b.rnamespace.test(g.namespace)||(b.handleObj=g,b.data=g.data,e=((r.event.special[g.origType]||{}).handle||g.handler).apply(f.elem,i),void 0!==e&&(b.result=e)===!1&&(b.preventDefault(),b.stopPropagation()))}return k.postDispatch&&k.postDispatch.call(this,b),b.result}},handlers:function(a,b){var c,d,e,f,g,h=[],i=b.delegateCount,j=a.target;if(i&&j.nodeType&&!("click"===a.type&&a.button>=1))for(;j!==this;j=j.parentNode||this)if(1===j.nodeType&&("click"!==a.type||j.disabled!==!0)){for(f=[],g={},c=0;c<i;c++)d=b[c],e=d.selector+" ",void 0===g[e]&&(g[e]=d.needsContext?r(e,this).index(j)>-1:r.find(e,this,null,[j]).length),g[e]&&f.push(d);f.length&&h.push({elem:j,handlers:f})}return j=this,i<b.length&&h.push({elem:j,handlers:b.slice(i)}),h},addProp:function(a,b){Object.defineProperty(r.Event.prototype,a,{enumerable:!0,configurable:!0,get:r.isFunction(b)?function(){if(this.originalEvent)return b(this.originalEvent)}:function(){if(this.originalEvent)return this.originalEvent[a]},set:function(b){Object.defineProperty(this,a,{enumerable:!0,configurable:!0,writable:!0,value:b})}})},fix:function(a){return a[r.expando]?a:new r.Event(a)},special:{load:{noBubble:!0},focus:{trigger:function(){if(this!==xa()&&this.focus)return this.focus(),!1},delegateType:"focusin"},blur:{trigger:function(){if(this===xa()&&this.blur)return this.blur(),!1},delegateType:"focusout"},click:{trigger:function(){if("checkbox"===this.type&&this.click&&B(this,"input"))return this.click(),!1},_default:function(a){return B(a.target,"a")}},beforeunload:{postDispatch:function(a){void 0!==a.result&&a.originalEvent&&(a.originalEvent.returnValue=a.result)}}}},r.removeEvent=function(a,b,c){a.removeEventListener&&a.removeEventListener(b,c)},r.Event=function(a,b){return this instanceof r.Event?(a&&a.type?(this.originalEvent=a,this.type=a.type,this.isDefaultPrevented=a.defaultPrevented||void 0===a.defaultPrevented&&a.returnValue===!1?va:wa,this.target=a.target&&3===a.target.nodeType?a.target.parentNode:a.target,this.currentTarget=a.currentTarget,this.relatedTarget=a.relatedTarget):this.type=a,b&&r.extend(this,b),this.timeStamp=a&&a.timeStamp||r.now(),void(this[r.expando]=!0)):new r.Event(a,b)},r.Event.prototype={constructor:r.Event,isDefaultPrevented:wa,isPropagationStopped:wa,isImmediatePropagationStopped:wa,isSimulated:!1,preventDefault:function(){var a=this.originalEvent;this.isDefaultPrevented=va,a&&!this.isSimulated&&a.preventDefault()},stopPropagation:function(){var a=this.originalEvent;this.isPropagationStopped=va,a&&!this.isSimulated&&a.stopPropagation()},stopImmediatePropagation:function(){var a=this.originalEvent;this.isImmediatePropagationStopped=va,a&&!this.isSimulated&&a.stopImmediatePropagation(),this.stopPropagation()}},r.each({altKey:!0,bubbles:!0,cancelable:!0,changedTouches:!0,ctrlKey:!0,detail:!0,eventPhase:!0,metaKey:!0,pageX:!0,pageY:!0,shiftKey:!0,view:!0,"char":!0,charCode:!0,key:!0,keyCode:!0,button:!0,buttons:!0,clientX:!0,clientY:!0,offsetX:!0,offsetY:!0,pointerId:!0,pointerType:!0,screenX:!0,screenY:!0,targetTouches:!0,toElement:!0,touches:!0,which:function(a){var b=a.button;return null==a.which&&sa.test(a.type)?null!=a.charCode?a.charCode:a.keyCode:!a.which&&void 0!==b&&ta.test(a.type)?1&b?1:2&b?3:4&b?2:0:a.which}},r.event.addProp),r.each({mouseenter:"mouseover",mouseleave:"mouseout",pointerenter:"pointerover",pointerleave:"pointerout"},function(a,b){r.event.special[a]={delegateType:b,bindType:b,handle:function(a){var c,d=this,e=a.relatedTarget,f=a.handleObj;return e&&(e===d||r.contains(d,e))||(a.type=f.origType,c=f.handler.apply(this,arguments),a.type=b),c}}}),r.fn.extend({on:function(a,b,c,d){return ya(this,a,b,c,d)},one:function(a,b,c,d){return ya(this,a,b,c,d,1)},off:function(a,b,c){var d,e;if(a&&a.preventDefault&&a.handleObj)return d=a.handleObj,r(a.delegateTarget).off(d.namespace?d.origType+"."+d.namespace:d.origType,d.selector,d.handler),this;if("object"==typeof a){for(e in a)this.off(e,b,a[e]);return this}return b!==!1&&"function"!=typeof b||(c=b,b=void 0),c===!1&&(c=wa),this.each(function(){r.event.remove(this,a,c,b)})}});var za=/<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi,Aa=/<script|<style|<link/i,Ba=/checked\s*(?:[^=]|=\s*.checked.)/i,Ca=/^true\/(.*)/,Da=/^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g;function Ea(a,b){return B(a,"table")&&B(11!==b.nodeType?b:b.firstChild,"tr")?r(">tbody",a)[0]||a:a}function Fa(a){return a.type=(null!==a.getAttribute("type"))+"/"+a.type,a}function Ga(a){var b=Ca.exec(a.type);return b?a.type=b[1]:a.removeAttribute("type"),a}function Ha(a,b){var c,d,e,f,g,h,i,j;if(1===b.nodeType){if(W.hasData(a)&&(f=W.access(a),g=W.set(b,f),j=f.events)){delete g.handle,g.events={};for(e in j)for(c=0,d=j[e].length;c<d;c++)r.event.add(b,e,j[e][c])}X.hasData(a)&&(h=X.access(a),i=r.extend({},h),X.set(b,i))}}function Ia(a,b){var c=b.nodeName.toLowerCase();"input"===c&&ja.test(a.type)?b.checked=a.checked:"input"!==c&&"textarea"!==c||(b.defaultValue=a.defaultValue)}function Ja(a,b,c,d){b=g.apply([],b);var e,f,h,i,j,k,l=0,m=a.length,n=m-1,q=b[0],s=r.isFunction(q);if(s||m>1&&"string"==typeof q&&!o.checkClone&&Ba.test(q))return a.each(function(e){var f=a.eq(e);s&&(b[0]=q.call(this,e,f.html())),Ja(f,b,c,d)});if(m&&(e=qa(b,a[0].ownerDocument,!1,a,d),f=e.firstChild,1===e.childNodes.length&&(e=f),f||d)){for(h=r.map(na(e,"script"),Fa),i=h.length;l<m;l++)j=e,l!==n&&(j=r.clone(j,!0,!0),i&&r.merge(h,na(j,"script"))),c.call(a[l],j,l);if(i)for(k=h[h.length-1].ownerDocument,r.map(h,Ga),l=0;l<i;l++)j=h[l],la.test(j.type||"")&&!W.access(j,"globalEval")&&r.contains(k,j)&&(j.src?r._evalUrl&&r._evalUrl(j.src):p(j.textContent.replace(Da,""),k))}return a}function Ka(a,b,c){for(var d,e=b?r.filter(b,a):a,f=0;null!=(d=e[f]);f++)c||1!==d.nodeType||r.cleanData(na(d)),d.parentNode&&(c&&r.contains(d.ownerDocument,d)&&oa(na(d,"script")),d.parentNode.removeChild(d));return a}r.extend({htmlPrefilter:function(a){return a.replace(za,"<$1></$2>")},clone:function(a,b,c){var d,e,f,g,h=a.cloneNode(!0),i=r.contains(a.ownerDocument,a);if(!(o.noCloneChecked||1!==a.nodeType&&11!==a.nodeType||r.isXMLDoc(a)))for(g=na(h),f=na(a),d=0,e=f.length;d<e;d++)Ia(f[d],g[d]);if(b)if(c)for(f=f||na(a),g=g||na(h),d=0,e=f.length;d<e;d++)Ha(f[d],g[d]);else Ha(a,h);return g=na(h,"script"),g.length>0&&oa(g,!i&&na(a,"script")),h},cleanData:function(a){for(var b,c,d,e=r.event.special,f=0;void 0!==(c=a[f]);f++)if(U(c)){if(b=c[W.expando]){if(b.events)for(d in b.events)e[d]?r.event.remove(c,d):r.removeEvent(c,d,b.handle);c[W.expando]=void 0}c[X.expando]&&(c[X.expando]=void 0)}}}),r.fn.extend({detach:function(a){return Ka(this,a,!0)},remove:function(a){return Ka(this,a)},text:function(a){return T(this,function(a){return void 0===a?r.text(this):this.empty().each(function(){1!==this.nodeType&&11!==this.nodeType&&9!==this.nodeType||(this.textContent=a)})},null,a,arguments.length)},append:function(){return Ja(this,arguments,function(a){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var b=Ea(this,a);b.appendChild(a)}})},prepend:function(){return Ja(this,arguments,function(a){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var b=Ea(this,a);b.insertBefore(a,b.firstChild)}})},before:function(){return Ja(this,arguments,function(a){this.parentNode&&this.parentNode.insertBefore(a,this)})},after:function(){return Ja(this,arguments,function(a){this.parentNode&&this.parentNode.insertBefore(a,this.nextSibling)})},empty:function(){for(var a,b=0;null!=(a=this[b]);b++)1===a.nodeType&&(r.cleanData(na(a,!1)),a.textContent="");return this},clone:function(a,b){return a=null!=a&&a,b=null==b?a:b,this.map(function(){return r.clone(this,a,b)})},html:function(a){return T(this,function(a){var b=this[0]||{},c=0,d=this.length;if(void 0===a&&1===b.nodeType)return b.innerHTML;if("string"==typeof a&&!Aa.test(a)&&!ma[(ka.exec(a)||["",""])[1].toLowerCase()]){a=r.htmlPrefilter(a);try{for(;c<d;c++)b=this[c]||{},1===b.nodeType&&(r.cleanData(na(b,!1)),b.innerHTML=a);b=0}catch(e){}}b&&this.empty().append(a)},null,a,arguments.length)},replaceWith:function(){var a=[];return Ja(this,arguments,function(b){var c=this.parentNode;r.inArray(this,a)<0&&(r.cleanData(na(this)),c&&c.replaceChild(b,this))},a)}}),r.each({appendTo:"append",prependTo:"prepend",insertBefore:"before",insertAfter:"after",replaceAll:"replaceWith"},function(a,b){r.fn[a]=function(a){for(var c,d=[],e=r(a),f=e.length-1,g=0;g<=f;g++)c=g===f?this:this.clone(!0),r(e[g])[b](c),h.apply(d,c.get());return this.pushStack(d)}});var La=/^margin/,Ma=new RegExp("^("+aa+")(?!px)[a-z%]+$","i"),Na=function(b){var c=b.ownerDocument.defaultView;return c&&c.opener||(c=a),c.getComputedStyle(b)};!function(){function b(){if(i){i.style.cssText="box-sizing:border-box;position:relative;display:block;margin:auto;border:1px;padding:1px;top:1%;width:50%",i.innerHTML="",ra.appendChild(h);var b=a.getComputedStyle(i);c="1%"!==b.top,g="2px"===b.marginLeft,e="4px"===b.width,i.style.marginRight="50%",f="4px"===b.marginRight,ra.removeChild(h),i=null}}var c,e,f,g,h=d.createElement("div"),i=d.createElement("div");i.style&&(i.style.backgroundClip="content-box",i.cloneNode(!0).style.backgroundClip="",o.clearCloneStyle="content-box"===i.style.backgroundClip,h.style.cssText="border:0;width:8px;height:0;top:0;left:-9999px;padding:0;margin-top:1px;position:absolute",h.appendChild(i),r.extend(o,{pixelPosition:function(){return b(),c},boxSizingReliable:function(){return b(),e},pixelMarginRight:function(){return b(),f},reliableMarginLeft:function(){return b(),g}}))}();function Oa(a,b,c){var d,e,f,g,h=a.style;return c=c||Na(a),c&&(g=c.getPropertyValue(b)||c[b],""!==g||r.contains(a.ownerDocument,a)||(g=r.style(a,b)),!o.pixelMarginRight()&&Ma.test(g)&&La.test(b)&&(d=h.width,e=h.minWidth,f=h.maxWidth,h.minWidth=h.maxWidth=h.width=g,g=c.width,h.width=d,h.minWidth=e,h.maxWidth=f)),void 0!==g?g+"":g}function Pa(a,b){return{get:function(){return a()?void delete this.get:(this.get=b).apply(this,arguments)}}}var Qa=/^(none|table(?!-c[ea]).+)/,Ra=/^--/,Sa={position:"absolute",visibility:"hidden",display:"block"},Ta={letterSpacing:"0",fontWeight:"400"},Ua=["Webkit","Moz","ms"],Va=d.createElement("div").style;function Wa(a){if(a in Va)return a;var b=a[0].toUpperCase()+a.slice(1),c=Ua.length;while(c--)if(a=Ua[c]+b,a in Va)return a}function Xa(a){var b=r.cssProps[a];return b||(b=r.cssProps[a]=Wa(a)||a),b}function Ya(a,b,c){var d=ba.exec(b);return d?Math.max(0,d[2]-(c||0))+(d[3]||"px"):b}function Za(a,b,c,d,e){var f,g=0;for(f=c===(d?"border":"content")?4:"width"===b?1:0;f<4;f+=2)"margin"===c&&(g+=r.css(a,c+ca[f],!0,e)),d?("content"===c&&(g-=r.css(a,"padding"+ca[f],!0,e)),"margin"!==c&&(g-=r.css(a,"border"+ca[f]+"Width",!0,e))):(g+=r.css(a,"padding"+ca[f],!0,e),"padding"!==c&&(g+=r.css(a,"border"+ca[f]+"Width",!0,e)));return g}function $a(a,b,c){var d,e=Na(a),f=Oa(a,b,e),g="border-box"===r.css(a,"boxSizing",!1,e);return Ma.test(f)?f:(d=g&&(o.boxSizingReliable()||f===a.style[b]),"auto"===f&&(f=a["offset"+b[0].toUpperCase()+b.slice(1)]),f=parseFloat(f)||0,f+Za(a,b,c||(g?"border":"content"),d,e)+"px")}r.extend({cssHooks:{opacity:{get:function(a,b){if(b){var c=Oa(a,"opacity");return""===c?"1":c}}}},cssNumber:{animationIterationCount:!0,columnCount:!0,fillOpacity:!0,flexGrow:!0,flexShrink:!0,fontWeight:!0,lineHeight:!0,opacity:!0,order:!0,orphans:!0,widows:!0,zIndex:!0,zoom:!0},cssProps:{"float":"cssFloat"},style:function(a,b,c,d){if(a&&3!==a.nodeType&&8!==a.nodeType&&a.style){var e,f,g,h=r.camelCase(b),i=Ra.test(b),j=a.style;return i||(b=Xa(h)),g=r.cssHooks[b]||r.cssHooks[h],void 0===c?g&&"get"in g&&void 0!==(e=g.get(a,!1,d))?e:j[b]:(f=typeof c,"string"===f&&(e=ba.exec(c))&&e[1]&&(c=fa(a,b,e),f="number"),null!=c&&c===c&&("number"===f&&(c+=e&&e[3]||(r.cssNumber[h]?"":"px")),o.clearCloneStyle||""!==c||0!==b.indexOf("background")||(j[b]="inherit"),g&&"set"in g&&void 0===(c=g.set(a,c,d))||(i?j.setProperty(b,c):j[b]=c)),void 0)}},css:function(a,b,c,d){var e,f,g,h=r.camelCase(b),i=Ra.test(b);return i||(b=Xa(h)),g=r.cssHooks[b]||r.cssHooks[h],g&&"get"in g&&(e=g.get(a,!0,c)),void 0===e&&(e=Oa(a,b,d)),"normal"===e&&b in Ta&&(e=Ta[b]),""===c||c?(f=parseFloat(e),c===!0||isFinite(f)?f||0:e):e}}),r.each(["height","width"],function(a,b){r.cssHooks[b]={get:function(a,c,d){if(c)return!Qa.test(r.css(a,"display"))||a.getClientRects().length&&a.getBoundingClientRect().width?$a(a,b,d):ea(a,Sa,function(){return $a(a,b,d)})},set:function(a,c,d){var e,f=d&&Na(a),g=d&&Za(a,b,d,"border-box"===r.css(a,"boxSizing",!1,f),f);return g&&(e=ba.exec(c))&&"px"!==(e[3]||"px")&&(a.style[b]=c,c=r.css(a,b)),Ya(a,c,g)}}}),r.cssHooks.marginLeft=Pa(o.reliableMarginLeft,function(a,b){if(b)return(parseFloat(Oa(a,"marginLeft"))||a.getBoundingClientRect().left-ea(a,{marginLeft:0},function(){return a.getBoundingClientRect().left}))+"px"}),r.each({margin:"",padding:"",border:"Width"},function(a,b){r.cssHooks[a+b]={expand:function(c){for(var d=0,e={},f="string"==typeof c?c.split(" "):[c];d<4;d++)e[a+ca[d]+b]=f[d]||f[d-2]||f[0];return e}},La.test(a)||(r.cssHooks[a+b].set=Ya)}),r.fn.extend({css:function(a,b){return T(this,function(a,b,c){var d,e,f={},g=0;if(Array.isArray(b)){for(d=Na(a),e=b.length;g<e;g++)f[b[g]]=r.css(a,b[g],!1,d);return f}return void 0!==c?r.style(a,b,c):r.css(a,b)},a,b,arguments.length>1)}});function _a(a,b,c,d,e){return new _a.prototype.init(a,b,c,d,e)}r.Tween=_a,_a.prototype={constructor:_a,init:function(a,b,c,d,e,f){this.elem=a,this.prop=c,this.easing=e||r.easing._default,this.options=b,this.start=this.now=this.cur(),this.end=d,this.unit=f||(r.cssNumber[c]?"":"px")},cur:function(){var a=_a.propHooks[this.prop];return a&&a.get?a.get(this):_a.propHooks._default.get(this)},run:function(a){var b,c=_a.propHooks[this.prop];return this.options.duration?this.pos=b=r.easing[this.easing](a,this.options.duration*a,0,1,this.options.duration):this.pos=b=a,this.now=(this.end-this.start)*b+this.start,this.options.step&&this.options.step.call(this.elem,this.now,this),c&&c.set?c.set(this):_a.propHooks._default.set(this),this}},_a.prototype.init.prototype=_a.prototype,_a.propHooks={_default:{get:function(a){var b;return 1!==a.elem.nodeType||null!=a.elem[a.prop]&&null==a.elem.style[a.prop]?a.elem[a.prop]:(b=r.css(a.elem,a.prop,""),b&&"auto"!==b?b:0)},set:function(a){r.fx.step[a.prop]?r.fx.step[a.prop](a):1!==a.elem.nodeType||null==a.elem.style[r.cssProps[a.prop]]&&!r.cssHooks[a.prop]?a.elem[a.prop]=a.now:r.style(a.elem,a.prop,a.now+a.unit)}}},_a.propHooks.scrollTop=_a.propHooks.scrollLeft={set:function(a){a.elem.nodeType&&a.elem.parentNode&&(a.elem[a.prop]=a.now)}},r.easing={linear:function(a){return a},swing:function(a){return.5-Math.cos(a*Math.PI)/2},_default:"swing"},r.fx=_a.prototype.init,r.fx.step={};var ab,bb,cb=/^(?:toggle|show|hide)$/,db=/queueHooks$/;function eb(){bb&&(d.hidden===!1&&a.requestAnimationFrame?a.requestAnimationFrame(eb):a.setTimeout(eb,r.fx.interval),r.fx.tick())}function fb(){return a.setTimeout(function(){ab=void 0}),ab=r.now()}function gb(a,b){var c,d=0,e={height:a};for(b=b?1:0;d<4;d+=2-b)c=ca[d],e["margin"+c]=e["padding"+c]=a;return b&&(e.opacity=e.width=a),e}function hb(a,b,c){for(var d,e=(kb.tweeners[b]||[]).concat(kb.tweeners["*"]),f=0,g=e.length;f<g;f++)if(d=e[f].call(c,b,a))return d}function ib(a,b,c){var d,e,f,g,h,i,j,k,l="width"in b||"height"in b,m=this,n={},o=a.style,p=a.nodeType&&da(a),q=W.get(a,"fxshow");c.queue||(g=r._queueHooks(a,"fx"),null==g.unqueued&&(g.unqueued=0,h=g.empty.fire,g.empty.fire=function(){g.unqueued||h()}),g.unqueued++,m.always(function(){m.always(function(){g.unqueued--,r.queue(a,"fx").length||g.empty.fire()})}));for(d in b)if(e=b[d],cb.test(e)){if(delete b[d],f=f||"toggle"===e,e===(p?"hide":"show")){if("show"!==e||!q||void 0===q[d])continue;p=!0}n[d]=q&&q[d]||r.style(a,d)}if(i=!r.isEmptyObject(b),i||!r.isEmptyObject(n)){l&&1===a.nodeType&&(c.overflow=[o.overflow,o.overflowX,o.overflowY],j=q&&q.display,null==j&&(j=W.get(a,"display")),k=r.css(a,"display"),"none"===k&&(j?k=j:(ia([a],!0),j=a.style.display||j,k=r.css(a,"display"),ia([a]))),("inline"===k||"inline-block"===k&&null!=j)&&"none"===r.css(a,"float")&&(i||(m.done(function(){o.display=j}),null==j&&(k=o.display,j="none"===k?"":k)),o.display="inline-block")),c.overflow&&(o.overflow="hidden",m.always(function(){o.overflow=c.overflow[0],o.overflowX=c.overflow[1],o.overflowY=c.overflow[2]})),i=!1;for(d in n)i||(q?"hidden"in q&&(p=q.hidden):q=W.access(a,"fxshow",{display:j}),f&&(q.hidden=!p),p&&ia([a],!0),m.done(function(){p||ia([a]),W.remove(a,"fxshow");for(d in n)r.style(a,d,n[d])})),i=hb(p?q[d]:0,d,m),d in q||(q[d]=i.start,p&&(i.end=i.start,i.start=0))}}function jb(a,b){var c,d,e,f,g;for(c in a)if(d=r.camelCase(c),e=b[d],f=a[c],Array.isArray(f)&&(e=f[1],f=a[c]=f[0]),c!==d&&(a[d]=f,delete a[c]),g=r.cssHooks[d],g&&"expand"in g){f=g.expand(f),delete a[d];for(c in f)c in a||(a[c]=f[c],b[c]=e)}else b[d]=e}function kb(a,b,c){var d,e,f=0,g=kb.prefilters.length,h=r.Deferred().always(function(){delete i.elem}),i=function(){if(e)return!1;for(var b=ab||fb(),c=Math.max(0,j.startTime+j.duration-b),d=c/j.duration||0,f=1-d,g=0,i=j.tweens.length;g<i;g++)j.tweens[g].run(f);return h.notifyWith(a,[j,f,c]),f<1&&i?c:(i||h.notifyWith(a,[j,1,0]),h.resolveWith(a,[j]),!1)},j=h.promise({elem:a,props:r.extend({},b),opts:r.extend(!0,{specialEasing:{},easing:r.easing._default},c),originalProperties:b,originalOptions:c,startTime:ab||fb(),duration:c.duration,tweens:[],createTween:function(b,c){var d=r.Tween(a,j.opts,b,c,j.opts.specialEasing[b]||j.opts.easing);return j.tweens.push(d),d},stop:function(b){var c=0,d=b?j.tweens.length:0;if(e)return this;for(e=!0;c<d;c++)j.tweens[c].run(1);return b?(h.notifyWith(a,[j,1,0]),h.resolveWith(a,[j,b])):h.rejectWith(a,[j,b]),this}}),k=j.props;for(jb(k,j.opts.specialEasing);f<g;f++)if(d=kb.prefilters[f].call(j,a,k,j.opts))return r.isFunction(d.stop)&&(r._queueHooks(j.elem,j.opts.queue).stop=r.proxy(d.stop,d)),d;return r.map(k,hb,j),r.isFunction(j.opts.start)&&j.opts.start.call(a,j),j.progress(j.opts.progress).done(j.opts.done,j.opts.complete).fail(j.opts.fail).always(j.opts.always),r.fx.timer(r.extend(i,{elem:a,anim:j,queue:j.opts.queue})),j}r.Animation=r.extend(kb,{tweeners:{"*":[function(a,b){var c=this.createTween(a,b);return fa(c.elem,a,ba.exec(b),c),c}]},tweener:function(a,b){r.isFunction(a)?(b=a,a=["*"]):a=a.match(L);for(var c,d=0,e=a.length;d<e;d++)c=a[d],kb.tweeners[c]=kb.tweeners[c]||[],kb.tweeners[c].unshift(b)},prefilters:[ib],prefilter:function(a,b){b?kb.prefilters.unshift(a):kb.prefilters.push(a)}}),r.speed=function(a,b,c){var d=a&&"object"==typeof a?r.extend({},a):{complete:c||!c&&b||r.isFunction(a)&&a,duration:a,easing:c&&b||b&&!r.isFunction(b)&&b};return r.fx.off?d.duration=0:"number"!=typeof d.duration&&(d.duration in r.fx.speeds?d.duration=r.fx.speeds[d.duration]:d.duration=r.fx.speeds._default),null!=d.queue&&d.queue!==!0||(d.queue="fx"),d.old=d.complete,d.complete=function(){r.isFunction(d.old)&&d.old.call(this),d.queue&&r.dequeue(this,d.queue)},d},r.fn.extend({fadeTo:function(a,b,c,d){return this.filter(da).css("opacity",0).show().end().animate({opacity:b},a,c,d)},animate:function(a,b,c,d){var e=r.isEmptyObject(a),f=r.speed(b,c,d),g=function(){var b=kb(this,r.extend({},a),f);(e||W.get(this,"finish"))&&b.stop(!0)};return g.finish=g,e||f.queue===!1?this.each(g):this.queue(f.queue,g)},stop:function(a,b,c){var d=function(a){var b=a.stop;delete a.stop,b(c)};return"string"!=typeof a&&(c=b,b=a,a=void 0),b&&a!==!1&&this.queue(a||"fx",[]),this.each(function(){var b=!0,e=null!=a&&a+"queueHooks",f=r.timers,g=W.get(this);if(e)g[e]&&g[e].stop&&d(g[e]);else for(e in g)g[e]&&g[e].stop&&db.test(e)&&d(g[e]);for(e=f.length;e--;)f[e].elem!==this||null!=a&&f[e].queue!==a||(f[e].anim.stop(c),b=!1,f.splice(e,1));!b&&c||r.dequeue(this,a)})},finish:function(a){return a!==!1&&(a=a||"fx"),this.each(function(){var b,c=W.get(this),d=c[a+"queue"],e=c[a+"queueHooks"],f=r.timers,g=d?d.length:0;for(c.finish=!0,r.queue(this,a,[]),e&&e.stop&&e.stop.call(this,!0),b=f.length;b--;)f[b].elem===this&&f[b].queue===a&&(f[b].anim.stop(!0),f.splice(b,1));for(b=0;b<g;b++)d[b]&&d[b].finish&&d[b].finish.call(this);delete c.finish})}}),r.each(["toggle","show","hide"],function(a,b){var c=r.fn[b];r.fn[b]=function(a,d,e){return null==a||"boolean"==typeof a?c.apply(this,arguments):this.animate(gb(b,!0),a,d,e)}}),r.each({slideDown:gb("show"),slideUp:gb("hide"),slideToggle:gb("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(a,b){r.fn[a]=function(a,c,d){return this.animate(b,a,c,d)}}),r.timers=[],r.fx.tick=function(){var a,b=0,c=r.timers;for(ab=r.now();b<c.length;b++)a=c[b],a()||c[b]!==a||c.splice(b--,1);c.length||r.fx.stop(),ab=void 0},r.fx.timer=function(a){r.timers.push(a),r.fx.start()},r.fx.interval=13,r.fx.start=function(){bb||(bb=!0,eb())},r.fx.stop=function(){bb=null},r.fx.speeds={slow:600,fast:200,_default:400},r.fn.delay=function(b,c){return b=r.fx?r.fx.speeds[b]||b:b,c=c||"fx",this.queue(c,function(c,d){var e=a.setTimeout(c,b);d.stop=function(){a.clearTimeout(e)}})},function(){var a=d.createElement("input"),b=d.createElement("select"),c=b.appendChild(d.createElement("option"));a.type="checkbox",o.checkOn=""!==a.value,o.optSelected=c.selected,a=d.createElement("input"),a.value="t",a.type="radio",o.radioValue="t"===a.value}();var lb,mb=r.expr.attrHandle;r.fn.extend({attr:function(a,b){return T(this,r.attr,a,b,arguments.length>1)},removeAttr:function(a){return this.each(function(){r.removeAttr(this,a)})}}),r.extend({attr:function(a,b,c){var d,e,f=a.nodeType;if(3!==f&&8!==f&&2!==f)return"undefined"==typeof a.getAttribute?r.prop(a,b,c):(1===f&&r.isXMLDoc(a)||(e=r.attrHooks[b.toLowerCase()]||(r.expr.match.bool.test(b)?lb:void 0)),void 0!==c?null===c?void r.removeAttr(a,b):e&&"set"in e&&void 0!==(d=e.set(a,c,b))?d:(a.setAttribute(b,c+""),c):e&&"get"in e&&null!==(d=e.get(a,b))?d:(d=r.find.attr(a,b),
+null==d?void 0:d))},attrHooks:{type:{set:function(a,b){if(!o.radioValue&&"radio"===b&&B(a,"input")){var c=a.value;return a.setAttribute("type",b),c&&(a.value=c),b}}}},removeAttr:function(a,b){var c,d=0,e=b&&b.match(L);if(e&&1===a.nodeType)while(c=e[d++])a.removeAttribute(c)}}),lb={set:function(a,b,c){return b===!1?r.removeAttr(a,c):a.setAttribute(c,c),c}},r.each(r.expr.match.bool.source.match(/\w+/g),function(a,b){var c=mb[b]||r.find.attr;mb[b]=function(a,b,d){var e,f,g=b.toLowerCase();return d||(f=mb[g],mb[g]=e,e=null!=c(a,b,d)?g:null,mb[g]=f),e}});var nb=/^(?:input|select|textarea|button)$/i,ob=/^(?:a|area)$/i;r.fn.extend({prop:function(a,b){return T(this,r.prop,a,b,arguments.length>1)},removeProp:function(a){return this.each(function(){delete this[r.propFix[a]||a]})}}),r.extend({prop:function(a,b,c){var d,e,f=a.nodeType;if(3!==f&&8!==f&&2!==f)return 1===f&&r.isXMLDoc(a)||(b=r.propFix[b]||b,e=r.propHooks[b]),void 0!==c?e&&"set"in e&&void 0!==(d=e.set(a,c,b))?d:a[b]=c:e&&"get"in e&&null!==(d=e.get(a,b))?d:a[b]},propHooks:{tabIndex:{get:function(a){var b=r.find.attr(a,"tabindex");return b?parseInt(b,10):nb.test(a.nodeName)||ob.test(a.nodeName)&&a.href?0:-1}}},propFix:{"for":"htmlFor","class":"className"}}),o.optSelected||(r.propHooks.selected={get:function(a){var b=a.parentNode;return b&&b.parentNode&&b.parentNode.selectedIndex,null},set:function(a){var b=a.parentNode;b&&(b.selectedIndex,b.parentNode&&b.parentNode.selectedIndex)}}),r.each(["tabIndex","readOnly","maxLength","cellSpacing","cellPadding","rowSpan","colSpan","useMap","frameBorder","contentEditable"],function(){r.propFix[this.toLowerCase()]=this});function pb(a){var b=a.match(L)||[];return b.join(" ")}function qb(a){return a.getAttribute&&a.getAttribute("class")||""}r.fn.extend({addClass:function(a){var b,c,d,e,f,g,h,i=0;if(r.isFunction(a))return this.each(function(b){r(this).addClass(a.call(this,b,qb(this)))});if("string"==typeof a&&a){b=a.match(L)||[];while(c=this[i++])if(e=qb(c),d=1===c.nodeType&&" "+pb(e)+" "){g=0;while(f=b[g++])d.indexOf(" "+f+" ")<0&&(d+=f+" ");h=pb(d),e!==h&&c.setAttribute("class",h)}}return this},removeClass:function(a){var b,c,d,e,f,g,h,i=0;if(r.isFunction(a))return this.each(function(b){r(this).removeClass(a.call(this,b,qb(this)))});if(!arguments.length)return this.attr("class","");if("string"==typeof a&&a){b=a.match(L)||[];while(c=this[i++])if(e=qb(c),d=1===c.nodeType&&" "+pb(e)+" "){g=0;while(f=b[g++])while(d.indexOf(" "+f+" ")>-1)d=d.replace(" "+f+" "," ");h=pb(d),e!==h&&c.setAttribute("class",h)}}return this},toggleClass:function(a,b){var c=typeof a;return"boolean"==typeof b&&"string"===c?b?this.addClass(a):this.removeClass(a):r.isFunction(a)?this.each(function(c){r(this).toggleClass(a.call(this,c,qb(this),b),b)}):this.each(function(){var b,d,e,f;if("string"===c){d=0,e=r(this),f=a.match(L)||[];while(b=f[d++])e.hasClass(b)?e.removeClass(b):e.addClass(b)}else void 0!==a&&"boolean"!==c||(b=qb(this),b&&W.set(this,"__className__",b),this.setAttribute&&this.setAttribute("class",b||a===!1?"":W.get(this,"__className__")||""))})},hasClass:function(a){var b,c,d=0;b=" "+a+" ";while(c=this[d++])if(1===c.nodeType&&(" "+pb(qb(c))+" ").indexOf(b)>-1)return!0;return!1}});var rb=/\r/g;r.fn.extend({val:function(a){var b,c,d,e=this[0];{if(arguments.length)return d=r.isFunction(a),this.each(function(c){var e;1===this.nodeType&&(e=d?a.call(this,c,r(this).val()):a,null==e?e="":"number"==typeof e?e+="":Array.isArray(e)&&(e=r.map(e,function(a){return null==a?"":a+""})),b=r.valHooks[this.type]||r.valHooks[this.nodeName.toLowerCase()],b&&"set"in b&&void 0!==b.set(this,e,"value")||(this.value=e))});if(e)return b=r.valHooks[e.type]||r.valHooks[e.nodeName.toLowerCase()],b&&"get"in b&&void 0!==(c=b.get(e,"value"))?c:(c=e.value,"string"==typeof c?c.replace(rb,""):null==c?"":c)}}}),r.extend({valHooks:{option:{get:function(a){var b=r.find.attr(a,"value");return null!=b?b:pb(r.text(a))}},select:{get:function(a){var b,c,d,e=a.options,f=a.selectedIndex,g="select-one"===a.type,h=g?null:[],i=g?f+1:e.length;for(d=f<0?i:g?f:0;d<i;d++)if(c=e[d],(c.selected||d===f)&&!c.disabled&&(!c.parentNode.disabled||!B(c.parentNode,"optgroup"))){if(b=r(c).val(),g)return b;h.push(b)}return h},set:function(a,b){var c,d,e=a.options,f=r.makeArray(b),g=e.length;while(g--)d=e[g],(d.selected=r.inArray(r.valHooks.option.get(d),f)>-1)&&(c=!0);return c||(a.selectedIndex=-1),f}}}}),r.each(["radio","checkbox"],function(){r.valHooks[this]={set:function(a,b){if(Array.isArray(b))return a.checked=r.inArray(r(a).val(),b)>-1}},o.checkOn||(r.valHooks[this].get=function(a){return null===a.getAttribute("value")?"on":a.value})});var sb=/^(?:focusinfocus|focusoutblur)$/;r.extend(r.event,{trigger:function(b,c,e,f){var g,h,i,j,k,m,n,o=[e||d],p=l.call(b,"type")?b.type:b,q=l.call(b,"namespace")?b.namespace.split("."):[];if(h=i=e=e||d,3!==e.nodeType&&8!==e.nodeType&&!sb.test(p+r.event.triggered)&&(p.indexOf(".")>-1&&(q=p.split("."),p=q.shift(),q.sort()),k=p.indexOf(":")<0&&"on"+p,b=b[r.expando]?b:new r.Event(p,"object"==typeof b&&b),b.isTrigger=f?2:3,b.namespace=q.join("."),b.rnamespace=b.namespace?new RegExp("(^|\\.)"+q.join("\\.(?:.*\\.|)")+"(\\.|$)"):null,b.result=void 0,b.target||(b.target=e),c=null==c?[b]:r.makeArray(c,[b]),n=r.event.special[p]||{},f||!n.trigger||n.trigger.apply(e,c)!==!1)){if(!f&&!n.noBubble&&!r.isWindow(e)){for(j=n.delegateType||p,sb.test(j+p)||(h=h.parentNode);h;h=h.parentNode)o.push(h),i=h;i===(e.ownerDocument||d)&&o.push(i.defaultView||i.parentWindow||a)}g=0;while((h=o[g++])&&!b.isPropagationStopped())b.type=g>1?j:n.bindType||p,m=(W.get(h,"events")||{})[b.type]&&W.get(h,"handle"),m&&m.apply(h,c),m=k&&h[k],m&&m.apply&&U(h)&&(b.result=m.apply(h,c),b.result===!1&&b.preventDefault());return b.type=p,f||b.isDefaultPrevented()||n._default&&n._default.apply(o.pop(),c)!==!1||!U(e)||k&&r.isFunction(e[p])&&!r.isWindow(e)&&(i=e[k],i&&(e[k]=null),r.event.triggered=p,e[p](),r.event.triggered=void 0,i&&(e[k]=i)),b.result}},simulate:function(a,b,c){var d=r.extend(new r.Event,c,{type:a,isSimulated:!0});r.event.trigger(d,null,b)}}),r.fn.extend({trigger:function(a,b){return this.each(function(){r.event.trigger(a,b,this)})},triggerHandler:function(a,b){var c=this[0];if(c)return r.event.trigger(a,b,c,!0)}}),r.each("blur focus focusin focusout resize scroll click dblclick mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave change select submit keydown keypress keyup contextmenu".split(" "),function(a,b){r.fn[b]=function(a,c){return arguments.length>0?this.on(b,null,a,c):this.trigger(b)}}),r.fn.extend({hover:function(a,b){return this.mouseenter(a).mouseleave(b||a)}}),o.focusin="onfocusin"in a,o.focusin||r.each({focus:"focusin",blur:"focusout"},function(a,b){var c=function(a){r.event.simulate(b,a.target,r.event.fix(a))};r.event.special[b]={setup:function(){var d=this.ownerDocument||this,e=W.access(d,b);e||d.addEventListener(a,c,!0),W.access(d,b,(e||0)+1)},teardown:function(){var d=this.ownerDocument||this,e=W.access(d,b)-1;e?W.access(d,b,e):(d.removeEventListener(a,c,!0),W.remove(d,b))}}});var tb=a.location,ub=r.now(),vb=/\?/;r.parseXML=function(b){var c;if(!b||"string"!=typeof b)return null;try{c=(new a.DOMParser).parseFromString(b,"text/xml")}catch(d){c=void 0}return c&&!c.getElementsByTagName("parsererror").length||r.error("Invalid XML: "+b),c};var wb=/\[\]$/,xb=/\r?\n/g,yb=/^(?:submit|button|image|reset|file)$/i,zb=/^(?:input|select|textarea|keygen)/i;function Ab(a,b,c,d){var e;if(Array.isArray(b))r.each(b,function(b,e){c||wb.test(a)?d(a,e):Ab(a+"["+("object"==typeof e&&null!=e?b:"")+"]",e,c,d)});else if(c||"object"!==r.type(b))d(a,b);else for(e in b)Ab(a+"["+e+"]",b[e],c,d)}r.param=function(a,b){var c,d=[],e=function(a,b){var c=r.isFunction(b)?b():b;d[d.length]=encodeURIComponent(a)+"="+encodeURIComponent(null==c?"":c)};if(Array.isArray(a)||a.jquery&&!r.isPlainObject(a))r.each(a,function(){e(this.name,this.value)});else for(c in a)Ab(c,a[c],b,e);return d.join("&")},r.fn.extend({serialize:function(){return r.param(this.serializeArray())},serializeArray:function(){return this.map(function(){var a=r.prop(this,"elements");return a?r.makeArray(a):this}).filter(function(){var a=this.type;return this.name&&!r(this).is(":disabled")&&zb.test(this.nodeName)&&!yb.test(a)&&(this.checked||!ja.test(a))}).map(function(a,b){var c=r(this).val();return null==c?null:Array.isArray(c)?r.map(c,function(a){return{name:b.name,value:a.replace(xb,"\r\n")}}):{name:b.name,value:c.replace(xb,"\r\n")}}).get()}});var Bb=/%20/g,Cb=/#.*$/,Db=/([?&])_=[^&]*/,Eb=/^(.*?):[ \t]*([^\r\n]*)$/gm,Fb=/^(?:about|app|app-storage|.+-extension|file|res|widget):$/,Gb=/^(?:GET|HEAD)$/,Hb=/^\/\//,Ib={},Jb={},Kb="*/".concat("*"),Lb=d.createElement("a");Lb.href=tb.href;function Mb(a){return function(b,c){"string"!=typeof b&&(c=b,b="*");var d,e=0,f=b.toLowerCase().match(L)||[];if(r.isFunction(c))while(d=f[e++])"+"===d[0]?(d=d.slice(1)||"*",(a[d]=a[d]||[]).unshift(c)):(a[d]=a[d]||[]).push(c)}}function Nb(a,b,c,d){var e={},f=a===Jb;function g(h){var i;return e[h]=!0,r.each(a[h]||[],function(a,h){var j=h(b,c,d);return"string"!=typeof j||f||e[j]?f?!(i=j):void 0:(b.dataTypes.unshift(j),g(j),!1)}),i}return g(b.dataTypes[0])||!e["*"]&&g("*")}function Ob(a,b){var c,d,e=r.ajaxSettings.flatOptions||{};for(c in b)void 0!==b[c]&&((e[c]?a:d||(d={}))[c]=b[c]);return d&&r.extend(!0,a,d),a}function Pb(a,b,c){var d,e,f,g,h=a.contents,i=a.dataTypes;while("*"===i[0])i.shift(),void 0===d&&(d=a.mimeType||b.getResponseHeader("Content-Type"));if(d)for(e in h)if(h[e]&&h[e].test(d)){i.unshift(e);break}if(i[0]in c)f=i[0];else{for(e in c){if(!i[0]||a.converters[e+" "+i[0]]){f=e;break}g||(g=e)}f=f||g}if(f)return f!==i[0]&&i.unshift(f),c[f]}function Qb(a,b,c,d){var e,f,g,h,i,j={},k=a.dataTypes.slice();if(k[1])for(g in a.converters)j[g.toLowerCase()]=a.converters[g];f=k.shift();while(f)if(a.responseFields[f]&&(c[a.responseFields[f]]=b),!i&&d&&a.dataFilter&&(b=a.dataFilter(b,a.dataType)),i=f,f=k.shift())if("*"===f)f=i;else if("*"!==i&&i!==f){if(g=j[i+" "+f]||j["* "+f],!g)for(e in j)if(h=e.split(" "),h[1]===f&&(g=j[i+" "+h[0]]||j["* "+h[0]])){g===!0?g=j[e]:j[e]!==!0&&(f=h[0],k.unshift(h[1]));break}if(g!==!0)if(g&&a["throws"])b=g(b);else try{b=g(b)}catch(l){return{state:"parsererror",error:g?l:"No conversion from "+i+" to "+f}}}return{state:"success",data:b}}r.extend({active:0,lastModified:{},etag:{},ajaxSettings:{url:tb.href,type:"GET",isLocal:Fb.test(tb.protocol),global:!0,processData:!0,async:!0,contentType:"application/x-www-form-urlencoded; charset=UTF-8",accepts:{"*":Kb,text:"text/plain",html:"text/html",xml:"application/xml, text/xml",json:"application/json, text/javascript"},contents:{xml:/\bxml\b/,html:/\bhtml/,json:/\bjson\b/},responseFields:{xml:"responseXML",text:"responseText",json:"responseJSON"},converters:{"* text":String,"text html":!0,"text json":JSON.parse,"text xml":r.parseXML},flatOptions:{url:!0,context:!0}},ajaxSetup:function(a,b){return b?Ob(Ob(a,r.ajaxSettings),b):Ob(r.ajaxSettings,a)},ajaxPrefilter:Mb(Ib),ajaxTransport:Mb(Jb),ajax:function(b,c){"object"==typeof b&&(c=b,b=void 0),c=c||{};var e,f,g,h,i,j,k,l,m,n,o=r.ajaxSetup({},c),p=o.context||o,q=o.context&&(p.nodeType||p.jquery)?r(p):r.event,s=r.Deferred(),t=r.Callbacks("once memory"),u=o.statusCode||{},v={},w={},x="canceled",y={readyState:0,getResponseHeader:function(a){var b;if(k){if(!h){h={};while(b=Eb.exec(g))h[b[1].toLowerCase()]=b[2]}b=h[a.toLowerCase()]}return null==b?null:b},getAllResponseHeaders:function(){return k?g:null},setRequestHeader:function(a,b){return null==k&&(a=w[a.toLowerCase()]=w[a.toLowerCase()]||a,v[a]=b),this},overrideMimeType:function(a){return null==k&&(o.mimeType=a),this},statusCode:function(a){var b;if(a)if(k)y.always(a[y.status]);else for(b in a)u[b]=[u[b],a[b]];return this},abort:function(a){var b=a||x;return e&&e.abort(b),A(0,b),this}};if(s.promise(y),o.url=((b||o.url||tb.href)+"").replace(Hb,tb.protocol+"//"),o.type=c.method||c.type||o.method||o.type,o.dataTypes=(o.dataType||"*").toLowerCase().match(L)||[""],null==o.crossDomain){j=d.createElement("a");try{j.href=o.url,j.href=j.href,o.crossDomain=Lb.protocol+"//"+Lb.host!=j.protocol+"//"+j.host}catch(z){o.crossDomain=!0}}if(o.data&&o.processData&&"string"!=typeof o.data&&(o.data=r.param(o.data,o.traditional)),Nb(Ib,o,c,y),k)return y;l=r.event&&o.global,l&&0===r.active++&&r.event.trigger("ajaxStart"),o.type=o.type.toUpperCase(),o.hasContent=!Gb.test(o.type),f=o.url.replace(Cb,""),o.hasContent?o.data&&o.processData&&0===(o.contentType||"").indexOf("application/x-www-form-urlencoded")&&(o.data=o.data.replace(Bb,"+")):(n=o.url.slice(f.length),o.data&&(f+=(vb.test(f)?"&":"?")+o.data,delete o.data),o.cache===!1&&(f=f.replace(Db,"$1"),n=(vb.test(f)?"&":"?")+"_="+ub++ +n),o.url=f+n),o.ifModified&&(r.lastModified[f]&&y.setRequestHeader("If-Modified-Since",r.lastModified[f]),r.etag[f]&&y.setRequestHeader("If-None-Match",r.etag[f])),(o.data&&o.hasContent&&o.contentType!==!1||c.contentType)&&y.setRequestHeader("Content-Type",o.contentType),y.setRequestHeader("Accept",o.dataTypes[0]&&o.accepts[o.dataTypes[0]]?o.accepts[o.dataTypes[0]]+("*"!==o.dataTypes[0]?", "+Kb+"; q=0.01":""):o.accepts["*"]);for(m in o.headers)y.setRequestHeader(m,o.headers[m]);if(o.beforeSend&&(o.beforeSend.call(p,y,o)===!1||k))return y.abort();if(x="abort",t.add(o.complete),y.done(o.success),y.fail(o.error),e=Nb(Jb,o,c,y)){if(y.readyState=1,l&&q.trigger("ajaxSend",[y,o]),k)return y;o.async&&o.timeout>0&&(i=a.setTimeout(function(){y.abort("timeout")},o.timeout));try{k=!1,e.send(v,A)}catch(z){if(k)throw z;A(-1,z)}}else A(-1,"No Transport");function A(b,c,d,h){var j,m,n,v,w,x=c;k||(k=!0,i&&a.clearTimeout(i),e=void 0,g=h||"",y.readyState=b>0?4:0,j=b>=200&&b<300||304===b,d&&(v=Pb(o,y,d)),v=Qb(o,v,y,j),j?(o.ifModified&&(w=y.getResponseHeader("Last-Modified"),w&&(r.lastModified[f]=w),w=y.getResponseHeader("etag"),w&&(r.etag[f]=w)),204===b||"HEAD"===o.type?x="nocontent":304===b?x="notmodified":(x=v.state,m=v.data,n=v.error,j=!n)):(n=x,!b&&x||(x="error",b<0&&(b=0))),y.status=b,y.statusText=(c||x)+"",j?s.resolveWith(p,[m,x,y]):s.rejectWith(p,[y,x,n]),y.statusCode(u),u=void 0,l&&q.trigger(j?"ajaxSuccess":"ajaxError",[y,o,j?m:n]),t.fireWith(p,[y,x]),l&&(q.trigger("ajaxComplete",[y,o]),--r.active||r.event.trigger("ajaxStop")))}return y},getJSON:function(a,b,c){return r.get(a,b,c,"json")},getScript:function(a,b){return r.get(a,void 0,b,"script")}}),r.each(["get","post"],function(a,b){r[b]=function(a,c,d,e){return r.isFunction(c)&&(e=e||d,d=c,c=void 0),r.ajax(r.extend({url:a,type:b,dataType:e,data:c,success:d},r.isPlainObject(a)&&a))}}),r._evalUrl=function(a){return r.ajax({url:a,type:"GET",dataType:"script",cache:!0,async:!1,global:!1,"throws":!0})},r.fn.extend({wrapAll:function(a){var b;return this[0]&&(r.isFunction(a)&&(a=a.call(this[0])),b=r(a,this[0].ownerDocument).eq(0).clone(!0),this[0].parentNode&&b.insertBefore(this[0]),b.map(function(){var a=this;while(a.firstElementChild)a=a.firstElementChild;return a}).append(this)),this},wrapInner:function(a){return r.isFunction(a)?this.each(function(b){r(this).wrapInner(a.call(this,b))}):this.each(function(){var b=r(this),c=b.contents();c.length?c.wrapAll(a):b.append(a)})},wrap:function(a){var b=r.isFunction(a);return this.each(function(c){r(this).wrapAll(b?a.call(this,c):a)})},unwrap:function(a){return this.parent(a).not("body").each(function(){r(this).replaceWith(this.childNodes)}),this}}),r.expr.pseudos.hidden=function(a){return!r.expr.pseudos.visible(a)},r.expr.pseudos.visible=function(a){return!!(a.offsetWidth||a.offsetHeight||a.getClientRects().length)},r.ajaxSettings.xhr=function(){try{return new a.XMLHttpRequest}catch(b){}};var Rb={0:200,1223:204},Sb=r.ajaxSettings.xhr();o.cors=!!Sb&&"withCredentials"in Sb,o.ajax=Sb=!!Sb,r.ajaxTransport(function(b){var c,d;if(o.cors||Sb&&!b.crossDomain)return{send:function(e,f){var g,h=b.xhr();if(h.open(b.type,b.url,b.async,b.username,b.password),b.xhrFields)for(g in b.xhrFields)h[g]=b.xhrFields[g];b.mimeType&&h.overrideMimeType&&h.overrideMimeType(b.mimeType),b.crossDomain||e["X-Requested-With"]||(e["X-Requested-With"]="XMLHttpRequest");for(g in e)h.setRequestHeader(g,e[g]);c=function(a){return function(){c&&(c=d=h.onload=h.onerror=h.onabort=h.onreadystatechange=null,"abort"===a?h.abort():"error"===a?"number"!=typeof h.status?f(0,"error"):f(h.status,h.statusText):f(Rb[h.status]||h.status,h.statusText,"text"!==(h.responseType||"text")||"string"!=typeof h.responseText?{binary:h.response}:{text:h.responseText},h.getAllResponseHeaders()))}},h.onload=c(),d=h.onerror=c("error"),void 0!==h.onabort?h.onabort=d:h.onreadystatechange=function(){4===h.readyState&&a.setTimeout(function(){c&&d()})},c=c("abort");try{h.send(b.hasContent&&b.data||null)}catch(i){if(c)throw i}},abort:function(){c&&c()}}}),r.ajaxPrefilter(function(a){a.crossDomain&&(a.contents.script=!1)}),r.ajaxSetup({accepts:{script:"text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"},contents:{script:/\b(?:java|ecma)script\b/},converters:{"text script":function(a){return r.globalEval(a),a}}}),r.ajaxPrefilter("script",function(a){void 0===a.cache&&(a.cache=!1),a.crossDomain&&(a.type="GET")}),r.ajaxTransport("script",function(a){if(a.crossDomain){var b,c;return{send:function(e,f){b=r("<script>").prop({charset:a.scriptCharset,src:a.url}).on("load error",c=function(a){b.remove(),c=null,a&&f("error"===a.type?404:200,a.type)}),d.head.appendChild(b[0])},abort:function(){c&&c()}}}});var Tb=[],Ub=/(=)\?(?=&|$)|\?\?/;r.ajaxSetup({jsonp:"callback",jsonpCallback:function(){var a=Tb.pop()||r.expando+"_"+ub++;return this[a]=!0,a}}),r.ajaxPrefilter("json jsonp",function(b,c,d){var e,f,g,h=b.jsonp!==!1&&(Ub.test(b.url)?"url":"string"==typeof b.data&&0===(b.contentType||"").indexOf("application/x-www-form-urlencoded")&&Ub.test(b.data)&&"data");if(h||"jsonp"===b.dataTypes[0])return e=b.jsonpCallback=r.isFunction(b.jsonpCallback)?b.jsonpCallback():b.jsonpCallback,h?b[h]=b[h].replace(Ub,"$1"+e):b.jsonp!==!1&&(b.url+=(vb.test(b.url)?"&":"?")+b.jsonp+"="+e),b.converters["script json"]=function(){return g||r.error(e+" was not called"),g[0]},b.dataTypes[0]="json",f=a[e],a[e]=function(){g=arguments},d.always(function(){void 0===f?r(a).removeProp(e):a[e]=f,b[e]&&(b.jsonpCallback=c.jsonpCallback,Tb.push(e)),g&&r.isFunction(f)&&f(g[0]),g=f=void 0}),"script"}),o.createHTMLDocument=function(){var a=d.implementation.createHTMLDocument("").body;return a.innerHTML="<form></form><form></form>",2===a.childNodes.length}(),r.parseHTML=function(a,b,c){if("string"!=typeof a)return[];"boolean"==typeof b&&(c=b,b=!1);var e,f,g;return b||(o.createHTMLDocument?(b=d.implementation.createHTMLDocument(""),e=b.createElement("base"),e.href=d.location.href,b.head.appendChild(e)):b=d),f=C.exec(a),g=!c&&[],f?[b.createElement(f[1])]:(f=qa([a],b,g),g&&g.length&&r(g).remove(),r.merge([],f.childNodes))},r.fn.load=function(a,b,c){var d,e,f,g=this,h=a.indexOf(" ");return h>-1&&(d=pb(a.slice(h)),a=a.slice(0,h)),r.isFunction(b)?(c=b,b=void 0):b&&"object"==typeof b&&(e="POST"),g.length>0&&r.ajax({url:a,type:e||"GET",dataType:"html",data:b}).done(function(a){f=arguments,g.html(d?r("<div>").append(r.parseHTML(a)).find(d):a)}).always(c&&function(a,b){g.each(function(){c.apply(this,f||[a.responseText,b,a])})}),this},r.each(["ajaxStart","ajaxStop","ajaxComplete","ajaxError","ajaxSuccess","ajaxSend"],function(a,b){r.fn[b]=function(a){return this.on(b,a)}}),r.expr.pseudos.animated=function(a){return r.grep(r.timers,function(b){return a===b.elem}).length},r.offset={setOffset:function(a,b,c){var d,e,f,g,h,i,j,k=r.css(a,"position"),l=r(a),m={};"static"===k&&(a.style.position="relative"),h=l.offset(),f=r.css(a,"top"),i=r.css(a,"left"),j=("absolute"===k||"fixed"===k)&&(f+i).indexOf("auto")>-1,j?(d=l.position(),g=d.top,e=d.left):(g=parseFloat(f)||0,e=parseFloat(i)||0),r.isFunction(b)&&(b=b.call(a,c,r.extend({},h))),null!=b.top&&(m.top=b.top-h.top+g),null!=b.left&&(m.left=b.left-h.left+e),"using"in b?b.using.call(a,m):l.css(m)}},r.fn.extend({offset:function(a){if(arguments.length)return void 0===a?this:this.each(function(b){r.offset.setOffset(this,a,b)});var b,c,d,e,f=this[0];if(f)return f.getClientRects().length?(d=f.getBoundingClientRect(),b=f.ownerDocument,c=b.documentElement,e=b.defaultView,{top:d.top+e.pageYOffset-c.clientTop,left:d.left+e.pageXOffset-c.clientLeft}):{top:0,left:0}},position:function(){if(this[0]){var a,b,c=this[0],d={top:0,left:0};return"fixed"===r.css(c,"position")?b=c.getBoundingClientRect():(a=this.offsetParent(),b=this.offset(),B(a[0],"html")||(d=a.offset()),d={top:d.top+r.css(a[0],"borderTopWidth",!0),left:d.left+r.css(a[0],"borderLeftWidth",!0)}),{top:b.top-d.top-r.css(c,"marginTop",!0),left:b.left-d.left-r.css(c,"marginLeft",!0)}}},offsetParent:function(){return this.map(function(){var a=this.offsetParent;while(a&&"static"===r.css(a,"position"))a=a.offsetParent;return a||ra})}}),r.each({scrollLeft:"pageXOffset",scrollTop:"pageYOffset"},function(a,b){var c="pageYOffset"===b;r.fn[a]=function(d){return T(this,function(a,d,e){var f;return r.isWindow(a)?f=a:9===a.nodeType&&(f=a.defaultView),void 0===e?f?f[b]:a[d]:void(f?f.scrollTo(c?f.pageXOffset:e,c?e:f.pageYOffset):a[d]=e)},a,d,arguments.length)}}),r.each(["top","left"],function(a,b){r.cssHooks[b]=Pa(o.pixelPosition,function(a,c){if(c)return c=Oa(a,b),Ma.test(c)?r(a).position()[b]+"px":c})}),r.each({Height:"height",Width:"width"},function(a,b){r.each({padding:"inner"+a,content:b,"":"outer"+a},function(c,d){r.fn[d]=function(e,f){var g=arguments.length&&(c||"boolean"!=typeof e),h=c||(e===!0||f===!0?"margin":"border");return T(this,function(b,c,e){var f;return r.isWindow(b)?0===d.indexOf("outer")?b["inner"+a]:b.document.documentElement["client"+a]:9===b.nodeType?(f=b.documentElement,Math.max(b.body["scroll"+a],f["scroll"+a],b.body["offset"+a],f["offset"+a],f["client"+a])):void 0===e?r.css(b,c,h):r.style(b,c,e,h)},b,g?e:void 0,g)}})}),r.fn.extend({bind:function(a,b,c){return this.on(a,null,b,c)},unbind:function(a,b){return this.off(a,null,b)},delegate:function(a,b,c,d){return this.on(b,a,c,d)},undelegate:function(a,b,c){return 1===arguments.length?this.off(a,"**"):this.off(b,a||"**",c)}}),r.holdReady=function(a){a?r.readyWait++:r.ready(!0)},r.isArray=Array.isArray,r.parseJSON=JSON.parse,r.nodeName=B,"function"==typeof define&&define.amd&&define("jquery",[],function(){return r});var Vb=a.jQuery,Wb=a.$;return r.noConflict=function(b){return a.$===r&&(a.$=Wb),b&&a.jQuery===r&&(a.jQuery=Vb),r},b||(a.jQuery=a.$=r),r});
diff --git a/doc/html/_static/language_data.js b/doc/html/_static/language_data.js
new file mode 100644
index 0000000000000000000000000000000000000000..5266fb19ecb24d085a338bdace79a063326b1cff
--- /dev/null
+++ b/doc/html/_static/language_data.js
@@ -0,0 +1,297 @@
+/*
+ * language_data.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+
+
+/* Non-minified version JS is _stemmer.js if file is provided */
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+ var step2list = {
+ ational: 'ate',
+ tional: 'tion',
+ enci: 'ence',
+ anci: 'ance',
+ izer: 'ize',
+ bli: 'ble',
+ alli: 'al',
+ entli: 'ent',
+ eli: 'e',
+ ousli: 'ous',
+ ization: 'ize',
+ ation: 'ate',
+ ator: 'ate',
+ alism: 'al',
+ iveness: 'ive',
+ fulness: 'ful',
+ ousness: 'ous',
+ aliti: 'al',
+ iviti: 'ive',
+ biliti: 'ble',
+ logi: 'log'
+ };
+
+ var step3list = {
+ icate: 'ic',
+ ative: '',
+ alize: 'al',
+ iciti: 'ic',
+ ical: 'ic',
+ ful: '',
+ ness: ''
+ };
+
+ var c = "[^aeiou]"; // consonant
+ var v = "[aeiouy]"; // vowel
+ var C = c + "[^aeiouy]*"; // consonant sequence
+ var V = v + "[aeiou]*"; // vowel sequence
+
+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
+ var s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ this.stemWord = function (w) {
+ var stem;
+ var suffix;
+ var firstch;
+ var origword = w;
+
+ if (w.length < 3)
+ return w;
+
+ var re;
+ var re2;
+ var re3;
+ var re4;
+
+ firstch = w.substr(0,1);
+ if (firstch == "y")
+ w = firstch.toUpperCase() + w.substr(1);
+
+ // Step 1a
+ re = /^(.+?)(ss|i)es$/;
+ re2 = /^(.+?)([^s])s$/;
+
+ if (re.test(w))
+ w = w.replace(re,"$1$2");
+ else if (re2.test(w))
+ w = w.replace(re2,"$1$2");
+
+ // Step 1b
+ re = /^(.+?)eed$/;
+ re2 = /^(.+?)(ed|ing)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = new RegExp(mgr0);
+ if (re.test(fp[1])) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = new RegExp(s_v);
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = /(at|bl|iz)$/;
+ re3 = new RegExp("([^aeiouylsz])\\1$");
+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re2.test(w))
+ w = w + "e";
+ else if (re3.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ else if (re4.test(w))
+ w = w + "e";
+ }
+ }
+
+ // Step 1c
+ re = /^(.+?)y$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(s_v);
+ if (re.test(stem))
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step2list[suffix];
+ }
+
+ // Step 3
+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step3list[suffix];
+ }
+
+ // Step 4
+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ re2 = /^(.+?)(s|t)(ion)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ if (re.test(stem))
+ w = stem;
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = new RegExp(mgr1);
+ if (re2.test(stem))
+ w = stem;
+ }
+
+ // Step 5
+ re = /^(.+?)e$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ re2 = new RegExp(meq1);
+ re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+ w = stem;
+ }
+ re = /ll$/;
+ re2 = new RegExp(mgr1);
+ if (re.test(w) && re2.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+ if (firstch == "y")
+ w = firstch.toLowerCase() + w.substr(1);
+ return w;
+ }
+}
+
+
+
+
+
+var splitChars = (function() {
+ var result = {};
+ var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
+ 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
+ 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
+ 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
+ 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
+ 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
+ 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
+ 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
+ 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
+ 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
+ var i, j, start, end;
+ for (i = 0; i < singles.length; i++) {
+ result[singles[i]] = true;
+ }
+ var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
+ [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
+ [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
+ [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
+ [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
+ [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
+ [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
+ [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
+ [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
+ [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
+ [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
+ [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
+ [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
+ [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
+ [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
+ [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
+ [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
+ [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
+ [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
+ [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
+ [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
+ [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
+ [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
+ [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
+ [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
+ [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
+ [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
+ [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
+ [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
+ [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
+ [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
+ [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
+ [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
+ [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
+ [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
+ [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
+ [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
+ [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
+ [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
+ [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
+ [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
+ [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
+ [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
+ [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
+ [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
+ [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
+ [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
+ [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
+ [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
+ for (i = 0; i < ranges.length; i++) {
+ start = ranges[i][0];
+ end = ranges[i][1];
+ for (j = start; j <= end; j++) {
+ result[j] = true;
+ }
+ }
+ return result;
+})();
+
+function splitQuery(query) {
+ var result = [];
+ var start = -1;
+ for (var i = 0; i < query.length; i++) {
+ if (splitChars[query.charCodeAt(i)]) {
+ if (start !== -1) {
+ result.push(query.slice(start, i));
+ start = -1;
+ }
+ } else if (start === -1) {
+ start = i;
+ }
+ }
+ if (start !== -1) {
+ result.push(query.slice(start));
+ }
+ return result;
+}
+
+
diff --git a/doc/html/_static/minus.png b/doc/html/_static/minus.png
index 0f22b16b038f9578a40314ff2b5acb88402a1496..d96755fdaf8bb2214971e0db9c1fd3077d7c419d 100644
Binary files a/doc/html/_static/minus.png and b/doc/html/_static/minus.png differ
diff --git a/doc/html/_static/plus.png b/doc/html/_static/plus.png
index 0cfe084cfc8d10d7151a0f00faee3667afe0b24b..7107cec93a979b9a5f64843235a16651d563ce2d 100644
Binary files a/doc/html/_static/plus.png and b/doc/html/_static/plus.png differ
diff --git a/doc/html/_static/searchtools.js b/doc/html/_static/searchtools.js
index ba82ad4877ca5803883434a08f1aea6afb43f3b6..6031f991319e4a258c6aba6ad0512fd7b91fe5cb 100644
--- a/doc/html/_static/searchtools.js
+++ b/doc/html/_static/searchtools.js
@@ -1,331 +1,54 @@
/*
- * searchtools.js_t
+ * searchtools.js
* ~~~~~~~~~~~~~~~~
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
-
-/* Non-minified version JS is _stemmer.js if file is provided */
-/**
- * Porter Stemmer
- */
-var Stemmer = function() {
-
- var step2list = {
- ational: 'ate',
- tional: 'tion',
- enci: 'ence',
- anci: 'ance',
- izer: 'ize',
- bli: 'ble',
- alli: 'al',
- entli: 'ent',
- eli: 'e',
- ousli: 'ous',
- ization: 'ize',
- ation: 'ate',
- ator: 'ate',
- alism: 'al',
- iveness: 'ive',
- fulness: 'ful',
- ousness: 'ous',
- aliti: 'al',
- iviti: 'ive',
- biliti: 'ble',
- logi: 'log'
- };
-
- var step3list = {
- icate: 'ic',
- ative: '',
- alize: 'al',
- iciti: 'ic',
- ical: 'ic',
- ful: '',
- ness: ''
+if (!Scorer) {
+ /**
+ * Simple result scoring code.
+ */
+ var Scorer = {
+ // Implement the following function to further tweak the score for each result
+ // The function takes a result array [filename, title, anchor, descr, score]
+ // and returns the new score.
+ /*
+ score: function(result) {
+ return result[4];
+ },
+ */
+
+ // query matches the full name of an object
+ objNameMatch: 11,
+ // or matches in the last dotted part of the object name
+ objPartialMatch: 6,
+ // Additive scores depending on the priority of the object
+ objPrio: {0: 15, // used to be importantResults
+ 1: 5, // used to be objectResults
+ 2: -5}, // used to be unimportantResults
+ // Used when the priority is not in the mapping.
+ objPrioDefault: 0,
+
+ // query found in title
+ title: 15,
+ partialTitle: 7,
+ // query found in terms
+ term: 5,
+ partialTerm: 2
};
-
- var c = "[^aeiou]"; // consonant
- var v = "[aeiouy]"; // vowel
- var C = c + "[^aeiouy]*"; // consonant sequence
- var V = v + "[aeiou]*"; // vowel sequence
-
- var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
- var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
- var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
- var s_v = "^(" + C + ")?" + v; // vowel in stem
-
- this.stemWord = function (w) {
- var stem;
- var suffix;
- var firstch;
- var origword = w;
-
- if (w.length < 3)
- return w;
-
- var re;
- var re2;
- var re3;
- var re4;
-
- firstch = w.substr(0,1);
- if (firstch == "y")
- w = firstch.toUpperCase() + w.substr(1);
-
- // Step 1a
- re = /^(.+?)(ss|i)es$/;
- re2 = /^(.+?)([^s])s$/;
-
- if (re.test(w))
- w = w.replace(re,"$1$2");
- else if (re2.test(w))
- w = w.replace(re2,"$1$2");
-
- // Step 1b
- re = /^(.+?)eed$/;
- re2 = /^(.+?)(ed|ing)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- re = new RegExp(mgr0);
- if (re.test(fp[1])) {
- re = /.$/;
- w = w.replace(re,"");
- }
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1];
- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
}
-
-
-/**
- * Simple result scoring code.
- */
-var Scorer = {
- // Implement the following function to further tweak the score for each result
- // The function takes a result array [filename, title, anchor, descr, score]
- // and returns the new score.
- /*
- score: function(result) {
- return result[4];
- },
- */
-
- // query matches the full name of an object
- objNameMatch: 11,
- // or matches in the last dotted part of the object name
- objPartialMatch: 6,
- // Additive scores depending on the priority of the object
- objPrio: {0: 15, // used to be importantResults
- 1: 5, // used to be objectResults
- 2: -5}, // used to be unimportantResults
- // Used when the priority is not in the mapping.
- objPrioDefault: 0,
-
- // query found in title
- title: 15,
- // query found in terms
- term: 5
-};
-
-
-
-
-
-var splitChars = (function() {
- var result = {};
- var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
- 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
- 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
- 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
- 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
- 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
- 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
- 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
- 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
- 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
- var i, j, start, end;
- for (i = 0; i < singles.length; i++) {
- result[singles[i]] = true;
- }
- var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
- [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
- [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
- [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
- [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
- [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
- [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
- [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
- [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
- [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
- [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
- [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
- [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
- [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
- [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
- [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
- [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
- [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
- [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
- [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
- [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
- [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
- [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
- [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
- [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
- [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
- [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
- [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
- [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
- [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
- [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
- [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
- [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
- [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
- [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
- [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
- [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
- [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
- [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
- [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
- [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
- [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
- [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
- [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
- [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
- [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
- [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
- [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
- [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
- for (i = 0; i < ranges.length; i++) {
- start = ranges[i][0];
- end = ranges[i][1];
- for (j = start; j <= end; j++) {
- result[j] = true;
- }
- }
- return result;
-})();
-
-function splitQuery(query) {
- var result = [];
- var start = -1;
- for (var i = 0; i < query.length; i++) {
- if (splitChars[query.charCodeAt(i)]) {
- if (start !== -1) {
- result.push(query.slice(start, i));
- start = -1;
- }
- } else if (start === -1) {
- start = i;
- }
- }
- if (start !== -1) {
- result.push(query.slice(start));
- }
- return result;
+if (!splitQuery) {
+ function splitQuery(query) {
+ return query.split(/\s+/);
+ }
}
-
-
-
/**
* Search Module
*/
@@ -335,6 +58,14 @@ var Search = {
_queued_query : null,
_pulse_status : -1,
+ htmlToText : function(htmlString) {
+ var htmlElement = document.createElement('span');
+ htmlElement.innerHTML = htmlString;
+ $(htmlElement).find('.headerlink').remove();
+ docContent = $(htmlElement).find('[role=main]')[0];
+ return docContent.textContent || docContent.innerText;
+ },
+
init : function() {
var params = $.getQueryParameters();
if (params.q) {
@@ -399,7 +130,7 @@ var Search = {
this.out = $('#search-results');
this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
+ this.status = $('<p class="search-summary"> </p>').appendTo(this.out);
this.output = $('<ul class="search"/>').appendTo(this.out);
$('#search-progress').text(_('Preparing search...'));
@@ -417,7 +148,6 @@ var Search = {
*/
query : function(query) {
var i;
- var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
// stem the searchterms and add them to the correct list
var stemmer = new Stemmer();
@@ -438,6 +168,10 @@ var Search = {
}
// stem the word
var word = stemmer.stemWord(tmp[i].toLowerCase());
+ // prevent stemmer from cutting word smaller than two chars
+ if(word.length < 3 && tmp[i].length >= 3) {
+ word = tmp[i];
+ }
var toAppend;
// select the correct list
if (word[0] == '-') {
@@ -535,7 +269,7 @@ var Search = {
displayNextItem();
});
} else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
+ $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX,
dataType: "text",
complete: function(jqxhr, textstatus) {
var data = jqxhr.responseText;
@@ -574,6 +308,7 @@ var Search = {
*/
performObjectSearch : function(object, otherterms) {
var filenames = this._index.filenames;
+ var docnames = this._index.docnames;
var objects = this._index.objects;
var objnames = this._index.objnames;
var titles = this._index.titles;
@@ -584,12 +319,13 @@ var Search = {
for (var prefix in objects) {
for (var name in objects[prefix]) {
var fullname = (prefix ? prefix + '.' : '') + name;
- if (fullname.toLowerCase().indexOf(object) > -1) {
+ var fullnameLower = fullname.toLowerCase()
+ if (fullnameLower.indexOf(object) > -1) {
var score = 0;
- var parts = fullname.split('.');
+ var parts = fullnameLower.split('.');
// check for different match types: exact matches of full name or
// "last name" (i.e. last dotted part)
- if (fullname == object || parts[parts.length - 1] == object) {
+ if (fullnameLower == object || parts[parts.length - 1] == object) {
score += Scorer.objNameMatch;
// matches in last name
} else if (parts[parts.length - 1].indexOf(object) > -1) {
@@ -627,7 +363,7 @@ var Search = {
} else {
score += Scorer.objPrioDefault;
}
- results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
+ results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
}
}
}
@@ -639,6 +375,7 @@ var Search = {
* search for full-text terms in the index
*/
performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+ var docnames = this._index.docnames;
var filenames = this._index.filenames;
var titles = this._index.titles;
@@ -655,6 +392,19 @@ var Search = {
{files: terms[word], score: Scorer.term},
{files: titleterms[word], score: Scorer.title}
];
+ // add support for partial matches
+ if (word.length > 2) {
+ for (var w in terms) {
+ if (w.match(word) && !terms[word]) {
+ _o.push({files: terms[w], score: Scorer.partialTerm})
+ }
+ }
+ for (var w in titleterms) {
+ if (w.match(word) && !titleterms[word]) {
+ _o.push({files: titleterms[w], score: Scorer.partialTitle})
+ }
+ }
+ }
// no match but word was a required one
if ($u.every(_o, function(o){return o.files === undefined;})) {
@@ -694,8 +444,12 @@ var Search = {
var valid = true;
// check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
+ var filteredTermCount = // as search terms with length < 3 are discarded: ignore
+ searchterms.filter(function(term){return term.length > 2}).length
+ if (
+ fileMap[file].length != searchterms.length &&
+ fileMap[file].length != filteredTermCount
+ ) continue;
// ensure that none of the excluded terms is in the search result
for (i = 0; i < excluded.length; i++) {
@@ -713,7 +467,7 @@ var Search = {
// select one (max) score for the file.
// for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
- results.push([filenames[file], titles[file], '', null, score]);
+ results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
}
}
return results;
@@ -726,7 +480,8 @@ var Search = {
* words. the first one is used to find the occurrence, the
* latter for highlighting it.
*/
- makeSearchSummary : function(text, keywords, hlwords) {
+ makeSearchSummary : function(htmlText, keywords, hlwords) {
+ var text = Search.htmlToText(htmlText);
var textLower = text.toLowerCase();
var start = 0;
$.each(keywords, function() {
@@ -748,4 +503,4 @@ var Search = {
$(document).ready(function() {
Search.init();
-});
\ No newline at end of file
+});
diff --git a/doc/html/_static/up-pressed.png b/doc/html/_static/up-pressed.png
deleted file mode 100644
index 99e7210962b0667e47408b40fdb5dd14749a156e..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/up-pressed.png and /dev/null differ
diff --git a/doc/html/_static/up.png b/doc/html/_static/up.png
deleted file mode 100644
index 26de002e85d3f5df53163e80b61af59bc4a6389b..0000000000000000000000000000000000000000
Binary files a/doc/html/_static/up.png and /dev/null differ
diff --git a/doc/html/_static/websupport.js b/doc/html/_static/websupport.js
deleted file mode 100644
index 98e7f40b6327e673e382068cdfb3bf3674a06cca..0000000000000000000000000000000000000000
--- a/doc/html/_static/websupport.js
+++ /dev/null
@@ -1,808 +0,0 @@
-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilities for all documentation.
- *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-(function($) {
- $.fn.autogrow = function() {
- return this.each(function() {
- var textarea = this;
-
- $.fn.autogrow.resize(textarea);
-
- $(textarea)
- .focus(function() {
- textarea.interval = setInterval(function() {
- $.fn.autogrow.resize(textarea);
- }, 500);
- })
- .blur(function() {
- clearInterval(textarea.interval);
- });
- });
- };
-
- $.fn.autogrow.resize = function(textarea) {
- var lineHeight = parseInt($(textarea).css('line-height'), 10);
- var lines = textarea.value.split('\n');
- var columns = textarea.cols;
- var lineCount = 0;
- $.each(lines, function() {
- lineCount += Math.ceil(this.length / columns) || 1;
- });
- var height = lineHeight * (lineCount + 1);
- $(textarea).css('height', height);
- };
-})(jQuery);
-
-(function($) {
- var comp, by;
-
- function init() {
- initEvents();
- initComparator();
- }
-
- function initEvents() {
- $(document).on("click", 'a.comment-close', function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.vote', function(event) {
- event.preventDefault();
- handleVote($(this));
- });
- $(document).on("click", 'a.reply', function(event) {
- event.preventDefault();
- openReply($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.close-reply', function(event) {
- event.preventDefault();
- closeReply($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.sort-option', function(event) {
- event.preventDefault();
- handleReSort($(this));
- });
- $(document).on("click", 'a.show-proposal', function(event) {
- event.preventDefault();
- showProposal($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.hide-proposal', function(event) {
- event.preventDefault();
- hideProposal($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.show-propose-change', function(event) {
- event.preventDefault();
- showProposeChange($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.hide-propose-change', function(event) {
- event.preventDefault();
- hideProposeChange($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.accept-comment', function(event) {
- event.preventDefault();
- acceptComment($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.delete-comment', function(event) {
- event.preventDefault();
- deleteComment($(this).attr('id').substring(2));
- });
- $(document).on("click", 'a.comment-markup', function(event) {
- event.preventDefault();
- toggleCommentMarkupBox($(this).attr('id').substring(2));
- });
- }
-
- /**
- * Set comp, which is a comparator function used for sorting and
- * inserting comments into the list.
- */
- function setComparator() {
- // If the first three letters are "asc", sort in ascending order
- // and remove the prefix.
- if (by.substring(0,3) == 'asc') {
- var i = by.substring(3);
- comp = function(a, b) { return a[i] - b[i]; };
- } else {
- // Otherwise sort in descending order.
- comp = function(a, b) { return b[by] - a[by]; };
- }
-
- // Reset link styles and format the selected sort option.
- $('a.sel').attr('href', '#').removeClass('sel');
- $('a.by' + by).removeAttr('href').addClass('sel');
- }
-
- /**
- * Create a comp function. If the user has preferences stored in
- * the sortBy cookie, use those, otherwise use the default.
- */
- function initComparator() {
- by = 'rating'; // Default to sort by rating.
- // If the sortBy cookie is set, use that instead.
- if (document.cookie.length > 0) {
- var start = document.cookie.indexOf('sortBy=');
- if (start != -1) {
- start = start + 7;
- var end = document.cookie.indexOf(";", start);
- if (end == -1) {
- end = document.cookie.length;
- by = unescape(document.cookie.substring(start, end));
- }
- }
- }
- setComparator();
- }
-
- /**
- * Show a comment div.
- */
- function show(id) {
- $('#ao' + id).hide();
- $('#ah' + id).show();
- var context = $.extend({id: id}, opts);
- var popup = $(renderTemplate(popupTemplate, context)).hide();
- popup.find('textarea[name="proposal"]').hide();
- popup.find('a.by' + by).addClass('sel');
- var form = popup.find('#cf' + id);
- form.submit(function(event) {
- event.preventDefault();
- addComment(form);
- });
- $('#s' + id).after(popup);
- popup.slideDown('fast', function() {
- getComments(id);
- });
- }
-
- /**
- * Hide a comment div.
- */
- function hide(id) {
- $('#ah' + id).hide();
- $('#ao' + id).show();
- var div = $('#sc' + id);
- div.slideUp('fast', function() {
- div.remove();
- });
- }
-
- /**
- * Perform an ajax request to get comments for a node
- * and insert the comments into the comments tree.
- */
- function getComments(id) {
- $.ajax({
- type: 'GET',
- url: opts.getCommentsURL,
- data: {node: id},
- success: function(data, textStatus, request) {
- var ul = $('#cl' + id);
- var speed = 100;
- $('#cf' + id)
- .find('textarea[name="proposal"]')
- .data('source', data.source);
-
- if (data.comments.length === 0) {
- ul.html('<li>No comments yet.</li>');
- ul.data('empty', true);
- } else {
- // If there are comments, sort them and put them in the list.
- var comments = sortComments(data.comments);
- speed = data.comments.length * 100;
- appendComments(comments, ul);
- ul.data('empty', false);
- }
- $('#cn' + id).slideUp(speed + 200);
- ul.slideDown(speed);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem retrieving the comments.');
- },
- dataType: 'json'
- });
- }
-
- /**
- * Add a comment via ajax and insert the comment into the comment tree.
- */
- function addComment(form) {
- var node_id = form.find('input[name="node"]').val();
- var parent_id = form.find('input[name="parent"]').val();
- var text = form.find('textarea[name="comment"]').val();
- var proposal = form.find('textarea[name="proposal"]').val();
-
- if (text == '') {
- showError('Please enter a comment.');
- return;
- }
-
- // Disable the form that is being submitted.
- form.find('textarea,input').attr('disabled', 'disabled');
-
- // Send the comment to the server.
- $.ajax({
- type: "POST",
- url: opts.addCommentURL,
- dataType: 'json',
- data: {
- node: node_id,
- parent: parent_id,
- text: text,
- proposal: proposal
- },
- success: function(data, textStatus, error) {
- // Reset the form.
- if (node_id) {
- hideProposeChange(node_id);
- }
- form.find('textarea')
- .val('')
- .add(form.find('input'))
- .removeAttr('disabled');
- var ul = $('#cl' + (node_id || parent_id));
- if (ul.data('empty')) {
- $(ul).empty();
- ul.data('empty', false);
- }
- insertComment(data.comment);
- var ao = $('#ao' + node_id);
- ao.find('img').attr({'src': opts.commentBrightImage});
- if (node_id) {
- // if this was a "root" comment, remove the commenting box
- // (the user can get it back by reopening the comment popup)
- $('#ca' + node_id).slideUp();
- }
- },
- error: function(request, textStatus, error) {
- form.find('textarea,input').removeAttr('disabled');
- showError('Oops, there was a problem adding the comment.');
- }
- });
- }
-
- /**
- * Recursively append comments to the main comment list and children
- * lists, creating the comment tree.
- */
- function appendComments(comments, ul) {
- $.each(comments, function() {
- var div = createCommentDiv(this);
- ul.append($(document.createElement('li')).html(div));
- appendComments(this.children, div.find('ul.comment-children'));
- // To avoid stagnating data, don't store the comments children in data.
- this.children = null;
- div.data('comment', this);
- });
- }
-
- /**
- * After adding a new comment, it must be inserted in the correct
- * location in the comment tree.
- */
- function insertComment(comment) {
- var div = createCommentDiv(comment);
-
- // To avoid stagnating data, don't store the comments children in data.
- comment.children = null;
- div.data('comment', comment);
-
- var ul = $('#cl' + (comment.node || comment.parent));
- var siblings = getChildren(ul);
-
- var li = $(document.createElement('li'));
- li.hide();
-
- // Determine where in the parents children list to insert this comment.
- for(i=0; i < siblings.length; i++) {
- if (comp(comment, siblings[i]) <= 0) {
- $('#cd' + siblings[i].id)
- .parent()
- .before(li.html(div));
- li.slideDown('fast');
- return;
- }
- }
-
- // If we get here, this comment rates lower than all the others,
- // or it is the only comment in the list.
- ul.append(li.html(div));
- li.slideDown('fast');
- }
-
- function acceptComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.acceptCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- $('#cm' + id).fadeOut('fast');
- $('#cd' + id).removeClass('moderate');
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem accepting the comment.');
- }
- });
- }
-
- function deleteComment(id) {
- $.ajax({
- type: 'POST',
- url: opts.deleteCommentURL,
- data: {id: id},
- success: function(data, textStatus, request) {
- var div = $('#cd' + id);
- if (data == 'delete') {
- // Moderator mode: remove the comment and all children immediately
- div.slideUp('fast', function() {
- div.remove();
- });
- return;
- }
- // User mode: only mark the comment as deleted
- div
- .find('span.user-id:first')
- .text('[deleted]').end()
- .find('div.comment-text:first')
- .text('[deleted]').end()
- .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
- ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
- .remove();
- var comment = div.data('comment');
- comment.username = '[deleted]';
- comment.text = '[deleted]';
- div.data('comment', comment);
- },
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem deleting the comment.');
- }
- });
- }
-
- function showProposal(id) {
- $('#sp' + id).hide();
- $('#hp' + id).show();
- $('#pr' + id).slideDown('fast');
- }
-
- function hideProposal(id) {
- $('#hp' + id).hide();
- $('#sp' + id).show();
- $('#pr' + id).slideUp('fast');
- }
-
- function showProposeChange(id) {
- $('#pc' + id).hide();
- $('#hc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val(textarea.data('source'));
- $.fn.autogrow.resize(textarea[0]);
- textarea.slideDown('fast');
- }
-
- function hideProposeChange(id) {
- $('#hc' + id).hide();
- $('#pc' + id).show();
- var textarea = $('#pt' + id);
- textarea.val('').removeAttr('disabled');
- textarea.slideUp('fast');
- }
-
- function toggleCommentMarkupBox(id) {
- $('#mb' + id).toggle();
- }
-
- /** Handle when the user clicks on a sort by link. */
- function handleReSort(link) {
- var classes = link.attr('class').split(/\s+/);
- for (var i=0; i<classes.length; i++) {
- if (classes[i] != 'sort-option') {
- by = classes[i].substring(2);
- }
- }
- setComparator();
- // Save/update the sortBy cookie.
- var expiration = new Date();
- expiration.setDate(expiration.getDate() + 365);
- document.cookie= 'sortBy=' + escape(by) +
- ';expires=' + expiration.toUTCString();
- $('ul.comment-ul').each(function(index, ul) {
- var comments = getChildren($(ul), true);
- comments = sortComments(comments);
- appendComments(comments, $(ul).empty());
- });
- }
-
- /**
- * Function to process a vote when a user clicks an arrow.
- */
- function handleVote(link) {
- if (!opts.voting) {
- showError("You'll need to login to vote.");
- return;
- }
-
- var id = link.attr('id');
- if (!id) {
- // Didn't click on one of the voting arrows.
- return;
- }
- // If it is an unvote, the new vote value is 0,
- // Otherwise it's 1 for an upvote, or -1 for a downvote.
- var value = 0;
- if (id.charAt(1) != 'u') {
- value = id.charAt(0) == 'u' ? 1 : -1;
- }
- // The data to be sent to the server.
- var d = {
- comment_id: id.substring(2),
- value: value
- };
-
- // Swap the vote and unvote links.
- link.hide();
- $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
- .show();
-
- // The div the comment is displayed in.
- var div = $('div#cd' + d.comment_id);
- var data = div.data('comment');
-
- // If this is not an unvote, and the other vote arrow has
- // already been pressed, unpress it.
- if ((d.value !== 0) && (data.vote === d.value * -1)) {
- $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
- $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
- }
-
- // Update the comments rating in the local data.
- data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
- data.vote = d.value;
- div.data('comment', data);
-
- // Change the rating text.
- div.find('.rating:first')
- .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
- // Send the vote information to the server.
- $.ajax({
- type: "POST",
- url: opts.processVoteURL,
- data: d,
- error: function(request, textStatus, error) {
- showError('Oops, there was a problem casting that vote.');
- }
- });
- }
-
- /**
- * Open a reply form used to reply to an existing comment.
- */
- function openReply(id) {
- // Swap out the reply link for the hide link
- $('#rl' + id).hide();
- $('#cr' + id).show();
-
- // Add the reply li to the children ul.
- var div = $(renderTemplate(replyTemplate, {id: id})).hide();
- $('#cl' + id)
- .prepend(div)
- // Setup the submit handler for the reply form.
- .find('#rf' + id)
- .submit(function(event) {
- event.preventDefault();
- addComment($('#rf' + id));
- closeReply(id);
- })
- .find('input[type=button]')
- .click(function() {
- closeReply(id);
- });
- div.slideDown('fast', function() {
- $('#rf' + id).find('textarea').focus();
- });
- }
-
- /**
- * Close the reply form opened with openReply.
- */
- function closeReply(id) {
- // Remove the reply div from the DOM.
- $('#rd' + id).slideUp('fast', function() {
- $(this).remove();
- });
-
- // Swap out the hide link for the reply link
- $('#cr' + id).hide();
- $('#rl' + id).show();
- }
-
- /**
- * Recursively sort a tree of comments using the comp comparator.
- */
- function sortComments(comments) {
- comments.sort(comp);
- $.each(comments, function() {
- this.children = sortComments(this.children);
- });
- return comments;
- }
-
- /**
- * Get the children comments from a ul. If recursive is true,
- * recursively include childrens' children.
- */
- function getChildren(ul, recursive) {
- var children = [];
- ul.children().children("[id^='cd']")
- .each(function() {
- var comment = $(this).data('comment');
- if (recursive)
- comment.children = getChildren($(this).find('#cl' + comment.id), true);
- children.push(comment);
- });
- return children;
- }
-
- /** Create a div to display a comment in. */
- function createCommentDiv(comment) {
- if (!comment.displayed && !opts.moderator) {
- return $('<div class="moderate">Thank you! Your comment will show up '
- + 'once it is has been approved by a moderator.</div>');
- }
- // Prettify the comment rating.
- comment.pretty_rating = comment.rating + ' point' +
- (comment.rating == 1 ? '' : 's');
- // Make a class (for displaying not yet moderated comments differently)
- comment.css_class = comment.displayed ? '' : ' moderate';
- // Create a div for this comment.
- var context = $.extend({}, opts, comment);
- var div = $(renderTemplate(commentTemplate, context));
-
- // If the user has voted on this comment, highlight the correct arrow.
- if (comment.vote) {
- var direction = (comment.vote == 1) ? 'u' : 'd';
- div.find('#' + direction + 'v' + comment.id).hide();
- div.find('#' + direction + 'u' + comment.id).show();
- }
-
- if (opts.moderator || comment.text != '[deleted]') {
- div.find('a.reply').show();
- if (comment.proposal_diff)
- div.find('#sp' + comment.id).show();
- if (opts.moderator && !comment.displayed)
- div.find('#cm' + comment.id).show();
- if (opts.moderator || (opts.username == comment.username))
- div.find('#dc' + comment.id).show();
- }
- return div;
- }
-
- /**
- * A simple template renderer. Placeholders such as <%id%> are replaced
- * by context['id'] with items being escaped. Placeholders such as <#id#>
- * are not escaped.
- */
- function renderTemplate(template, context) {
- var esc = $(document.createElement('div'));
-
- function handle(ph, escape) {
- var cur = context;
- $.each(ph.split('.'), function() {
- cur = cur[this];
- });
- return escape ? esc.text(cur || "").html() : cur;
- }
-
- return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
- return handle(arguments[2], arguments[1] == '%' ? true : false);
- });
- }
-
- /** Flash an error message briefly. */
- function showError(message) {
- $(document.createElement('div')).attr({'class': 'popup-error'})
- .append($(document.createElement('div'))
- .attr({'class': 'error-message'}).text(message))
- .appendTo('body')
- .fadeIn("slow")
- .delay(2000)
- .fadeOut("slow");
- }
-
- /** Add a link the user uses to open the comments popup. */
- $.fn.comment = function() {
- return this.each(function() {
- var id = $(this).attr('id').substring(1);
- var count = COMMENT_METADATA[id];
- var title = count + ' comment' + (count == 1 ? '' : 's');
- var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
- var addcls = count == 0 ? ' nocomment' : '';
- $(this)
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-open' + addcls,
- id: 'ao' + id
- })
- .append($(document.createElement('img')).attr({
- src: image,
- alt: 'comment',
- title: title
- }))
- .click(function(event) {
- event.preventDefault();
- show($(this).attr('id').substring(2));
- })
- )
- .append(
- $(document.createElement('a')).attr({
- href: '#',
- 'class': 'sphinx-comment-close hidden',
- id: 'ah' + id
- })
- .append($(document.createElement('img')).attr({
- src: opts.closeCommentImage,
- alt: 'close',
- title: 'close'
- }))
- .click(function(event) {
- event.preventDefault();
- hide($(this).attr('id').substring(2));
- })
- );
- });
- };
-
- var opts = {
- processVoteURL: '/_process_vote',
- addCommentURL: '/_add_comment',
- getCommentsURL: '/_get_comments',
- acceptCommentURL: '/_accept_comment',
- deleteCommentURL: '/_delete_comment',
- commentImage: '/static/_static/comment.png',
- closeCommentImage: '/static/_static/comment-close.png',
- loadingImage: '/static/_static/ajax-loader.gif',
- commentBrightImage: '/static/_static/comment-bright.png',
- upArrow: '/static/_static/up.png',
- downArrow: '/static/_static/down.png',
- upArrowPressed: '/static/_static/up-pressed.png',
- downArrowPressed: '/static/_static/down-pressed.png',
- voting: false,
- moderator: false
- };
-
- if (typeof COMMENT_OPTIONS != "undefined") {
- opts = jQuery.extend(opts, COMMENT_OPTIONS);
- }
-
- var popupTemplate = '\
- <div class="sphinx-comments" id="sc<%id%>">\
- <p class="sort-options">\
- Sort by:\
- <a href="#" class="sort-option byrating">best rated</a>\
- <a href="#" class="sort-option byascage">newest</a>\
- <a href="#" class="sort-option byage">oldest</a>\
- </p>\
- <div class="comment-header">Comments</div>\
- <div class="comment-loading" id="cn<%id%>">\
- loading comments... <img src="<%loadingImage%>" alt="" /></div>\
- <ul id="cl<%id%>" class="comment-ul"></ul>\
- <div id="ca<%id%>">\
- <p class="add-a-comment">Add a comment\
- (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
- <div class="comment-markup-box" id="mb<%id%>">\
- reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
- <code>``code``</code>, \
- code blocks: <code>::</code> and an indented block after blank line</div>\
- <form method="post" id="cf<%id%>" class="comment-form" action="">\
- <textarea name="comment" cols="80"></textarea>\
- <p class="propose-button">\
- <a href="#" id="pc<%id%>" class="show-propose-change">\
- Propose a change ▹\
- </a>\
- <a href="#" id="hc<%id%>" class="hide-propose-change">\
- Propose a change ▿\
- </a>\
- </p>\
- <textarea name="proposal" id="pt<%id%>" cols="80"\
- spellcheck="false"></textarea>\
- <input type="submit" value="Add comment" />\
- <input type="hidden" name="node" value="<%id%>" />\
- <input type="hidden" name="parent" value="" />\
- </form>\
- </div>\
- </div>';
-
- var commentTemplate = '\
- <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
- <div class="vote">\
- <div class="arrow">\
- <a href="#" id="uv<%id%>" class="vote" title="vote up">\
- <img src="<%upArrow%>" />\
- </a>\
- <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
- <img src="<%upArrowPressed%>" />\
- </a>\
- </div>\
- <div class="arrow">\
- <a href="#" id="dv<%id%>" class="vote" title="vote down">\
- <img src="<%downArrow%>" id="da<%id%>" />\
- </a>\
- <a href="#" id="du<%id%>" class="un vote" title="vote down">\
- <img src="<%downArrowPressed%>" />\
- </a>\
- </div>\
- </div>\
- <div class="comment-content">\
- <p class="tagline comment">\
- <span class="user-id"><%username%></span>\
- <span class="rating"><%pretty_rating%></span>\
- <span class="delta"><%time.delta%></span>\
- </p>\
- <div class="comment-text comment"><#text#></div>\
- <p class="comment-opts comment">\
- <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
- <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
- <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
- <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
- <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
- <span id="cm<%id%>" class="moderation hidden">\
- <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
- </span>\
- </p>\
- <pre class="proposal" id="pr<%id%>">\
-<#proposal_diff#>\
- </pre>\
- <ul class="comment-children" id="cl<%id%>"></ul>\
- </div>\
- <div class="clearleft"></div>\
- </div>\
- </div>';
-
- var replyTemplate = '\
- <li>\
- <div class="reply-div" id="rd<%id%>">\
- <form id="rf<%id%>">\
- <textarea name="comment" cols="80"></textarea>\
- <input type="submit" value="Add reply" />\
- <input type="button" value="Cancel" />\
- <input type="hidden" name="parent" value="<%id%>" />\
- <input type="hidden" name="node" value="" />\
- </form>\
- </div>\
- </li>';
-
- $(document).ready(function() {
- init();
- });
-})(jQuery);
-
-$(document).ready(function() {
- // add comment anchors for all paragraphs that are commentable
- $('.sphinx-has-comment').comment();
-
- // highlight search words in search results
- $("div.context").each(function() {
- var params = $.getQueryParameters();
- var terms = (params.q) ? params.q[0].split(/\s+/) : [];
- var result = $(this);
- $.each(terms, function() {
- result.highlightText(this.toLowerCase(), 'highlighted');
- });
- });
-
- // directly open comment window if requested
- var anchor = document.location.hash;
- if (anchor.substring(0, 9) == '#comment-') {
- $('#ao' + anchor.substring(9)).click();
- document.location.hash = '#s' + anchor.substring(9);
- }
-});
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 5a1d1b275f86273cc4103e055379b5a42d74a62a..f8482376318926a09800444d23f50f62b8d18401 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>ProMod3 Actions — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>ProMod3 Actions — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Building ProMod3" href="../buildsystem.html" />
<link rel="prev" title="Getting Started" href="../gettingstarted.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -50,58 +36,56 @@
<div class="section" id="project-actions">
<span id="promod-actions"></span><h1>ProMod3 Actions<a class="headerlink" href="#project-actions" title="Permalink to this headline">¶</a></h1>
<p>A pure command line interface of ProMod3 is provided by actions.
-You can execute <code class="docutils literal"><span class="pre">pm</span> <span class="pre">help</span></code> for a list of possible actions and for every action,
-you can type <code class="docutils literal"><span class="pre">pm</span> <span class="pre"><ACTION></span> <span class="pre">-h</span></code> to get a description on its usage.</p>
+You can execute <code class="docutils literal notranslate"><span class="pre">pm</span> <span class="pre">help</span></code> for a list of possible actions and for every action,
+you can type <code class="docutils literal notranslate"><span class="pre">pm</span> <span class="pre"><ACTION></span> <span class="pre">-h</span></code> to get a description on its usage.</p>
<p>Here we list the most prominent actions with simple examples.</p>
<div class="section" id="building-models">
<span id="promod-build-model"></span><h2>Building models<a class="headerlink" href="#building-models" title="Permalink to this headline">¶</a></h2>
<p>You can run a full protein homology modelling pipeline from the command line
with</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-f <FILE> <span class="p">|</span> -c <FILE> <span class="p">|</span> -j <OBJECT><span class="p">|</span><FILE><span class="o">)</span>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-f <FILE> <span class="p">|</span> -c <FILE> <span class="p">|</span> -j <OBJECT><span class="p">|</span><FILE><span class="o">)</span>
<span class="go"> (-p <FILE> | -e <FILE>) [-s <FILE>] [-o <FILENAME>]</span>
<span class="go"> [-r] [-t]</span>
</pre></div>
</div>
<p>Example usage:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb
</pre></div>
</div>
-<p>This reads a target-template alignment from <code class="file docutils literal"><span class="pre">aln.fasta</span></code> and a matching
-structure from <code class="file docutils literal"><span class="pre">tpl.pdb</span></code> and produces a gap-less model which is stored as
-<code class="file docutils literal"><span class="pre">model.pdb</span></code>. The output filename can be controlled with the <code class="docutils literal"><span class="pre">-o</span></code> flag.</p>
-<p>Target-template alignments can be provided in FASTA (<code class="docutils literal"><span class="pre">-f</span></code>), CLUSTAL (<code class="docutils literal"><span class="pre">-c</span></code>)
-or as JSON files/objects (<code class="docutils literal"><span class="pre">-j</span></code>). Files can be plain or gzipped.
+<p>This reads a target-template alignment from <code class="file docutils literal notranslate"><span class="pre">aln.fasta</span></code> and a matching
+structure from <code class="file docutils literal notranslate"><span class="pre">tpl.pdb</span></code> and produces a gap-less model which is stored as
+<code class="file docutils literal notranslate"><span class="pre">model.pdb</span></code>. The output filename can be controlled with the <code class="docutils literal notranslate"><span class="pre">-o</span></code> flag.</p>
+<p>Target-template alignments can be provided in FASTA (<code class="docutils literal notranslate"><span class="pre">-f</span></code>), CLUSTAL (<code class="docutils literal notranslate"><span class="pre">-c</span></code>)
+or as JSON files/objects (<code class="docutils literal notranslate"><span class="pre">-j</span></code>). Files can be plain or gzipped.
At least one alignment must be given and you cannot mix file formats.
Multiple alignment files can be given and target chains will be appended in the
given order. The chains of the target model are named with default chain names
-(A, B, C, ..., see <a class="reference internal" href="../modelling/pipeline.html#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildRawModel()</span></code></a>).
+(A, B, C, …, see <a class="reference internal" href="../modelling/pipeline.html#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a>).
Notes on the input formats:</p>
<ul>
-<li><p class="first">Leading/trailing whitespaces of sequence names will always be deleted</p>
-</li>
-<li><p class="first">FASTA input example:</p>
-<div class="highlight-none"><div class="highlight"><pre><span></span>>target
+<li><p>Leading/trailing whitespaces of sequence names will always be deleted</p></li>
+<li><p>FASTA input example:</p>
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>>target
HGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLG
>2jlp-1.A|55
RAIHVHQFGDLSQGCESTGPHYNPLAVPH------PQHPG
</pre></div>
</div>
-<p>Target sequence is either named “trg” or “target” or the first sequence is
+<p>Target sequence is either named “trg” or “target” or the first sequence is
used. Template sequence names can encode an identifier for the chain to attach
to it and optionally an offset (here: 55, see below for details).
Leading whitespaces of fasta headers will be deleted</p>
</li>
-<li><p class="first">CLUSTAL input follows the same logic as FASTA input</p>
-</li>
-<li><p class="first">JSON input: filenames are not allowed to start with ‘{‘.
-JSON objects contain an entry with key ‘alignmentlist’.
-That in turn is an array of objects with keys ‘target’ and ‘template’.
+<li><p>CLUSTAL input follows the same logic as FASTA input</p></li>
+<li><p>JSON input: filenames are not allowed to start with ‘{‘.
+JSON objects contain an entry with key ‘alignmentlist’.
+That in turn is an array of objects with keys ‘target’ and ‘template’.
Those in turn are objects with keys
-‘name’ (string id. for sequence),
-‘seqres’ (string for aligned sequence) and optionally for templates
-‘offset’ (number of residues to skip in structure file attached to it).
+‘name’ (string id. for sequence),
+‘seqres’ (string for aligned sequence) and optionally for templates
+‘offset’ (number of residues to skip in structure file attached to it).
Example:</p>
-<div class="highlight-json"><div class="highlight"><pre><span></span><span class="p">{</span><span class="nt">"alignmentlist"</span><span class="p">:</span> <span class="p">[</span> <span class="p">{</span>
+<div class="highlight-json notranslate"><div class="highlight"><pre><span></span><span class="p">{</span><span class="nt">"alignmentlist"</span><span class="p">:</span> <span class="p">[</span> <span class="p">{</span>
<span class="nt">"target"</span><span class="p">:</span> <span class="p">{</span>
<span class="nt">"name"</span><span class="p">:</span> <span class="s2">"mytrg"</span><span class="p">,</span>
<span class="nt">"seqres"</span><span class="p">:</span> <span class="s2">"HGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLG"</span>
@@ -116,130 +100,130 @@ Example:</p>
</div>
</li>
</ul>
-<p>Structures can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
-chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
-<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>. At least one structure must be
+<p>Structures can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
+<code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>. At least one structure must be
given and you cannot mix file formats. Multiple structures can be given and each
structure may have multiple chains, but care must be taken to identify which
chain to attach to which template sequence. Chains for each sequence are
identified based on the sequence name of the templates in the alignments. Valid
sequence names are:</p>
<ul class="simple">
-<li>anything, if only one structure with one chain</li>
-<li>“<FILE>.<CHAIN>”, where <FILE> is the base file name of an imported structure
+<li><p>anything, if only one structure with one chain</p></li>
+<li><p>“<FILE>.<CHAIN>”, where <FILE> is the base file name of an imported structure
with no extensions and <CHAIN> is the identifier of the chain in the imported
-structure.</li>
-<li>“<FILE>” if only one chain in file</li>
-<li>“<CHAIN>” if only one file imported</li>
-<li>“<CHAINID>|<OFFSET>”, where <CHAINID> identifies the chain as above and
+structure.</p></li>
+<li><p>“<FILE>” if only one chain in file</p></li>
+<li><p>“<CHAIN>” if only one file imported</p></li>
+<li><p>“<CHAINID>|<OFFSET>”, where <CHAINID> identifies the chain as above and
<OFFSET> is the number of residues to skip for that chain to reach the first
residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID> and
-<OFFSET> are ignored.</li>
+<OFFSET> are ignored.</p></li>
</ul>
-<p>Example: <code class="docutils literal"><span class="pre">...</span> <span class="pre">-p</span> <span class="pre">data/2jlp.pdb.gz</span></code>, where the pdb file has chains <code class="docutils literal"><span class="pre">A</span></code>,
-<code class="docutils literal"><span class="pre">B</span></code>, <code class="docutils literal"><span class="pre">C</span></code> and the template sequence is named <code class="docutils literal"><span class="pre">2jlp.A|55</span></code>.</p>
-<p>You can optionally specify sequence profiles to be added (<code class="docutils literal"><span class="pre">-s</span></code>) and linked
+<p>Example: <code class="docutils literal notranslate"><span class="pre">...</span> <span class="pre">-p</span> <span class="pre">data/2jlp.pdb.gz</span></code>, where the pdb file has chains <code class="docutils literal notranslate"><span class="pre">A</span></code>,
+<code class="docutils literal notranslate"><span class="pre">B</span></code>, <code class="docutils literal notranslate"><span class="pre">C</span></code> and the template sequence is named <code class="docutils literal notranslate"><span class="pre">2jlp.A|55</span></code>.</p>
+<p>You can optionally specify sequence profiles to be added (<code class="docutils literal notranslate"><span class="pre">-s</span></code>) and linked
to the corresponding target sequences. This has an impact on loop scoring with
the database approach.
The profiles can be provided as plain files or gzipped. Following file
extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
-Consider to use <a class="reference external" href="https://www.openstructure.org/docs/2.0/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+Consider to use <a class="reference external" href="https://www.openstructure.org/docs/2.0/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
file in a3m format at hand.</p>
<ul class="simple">
-<li>The profiles are mapped based on exact matches towards the gapless
+<li><p>The profiles are mapped based on exact matches towards the gapless
target sequences from the provided alignment files,
-i.e. one profile is mapped to several chains in case of homo-oligomers</li>
-<li>Every profile must have a unique sequence to avoid ambiguities</li>
-<li>All or nothing - You cannot provide profiles for only a subset of
-target sequences</li>
+i.e. one profile is mapped to several chains in case of homo-oligomers</p></li>
+<li><p>Every profile must have a unique sequence to avoid ambiguities</p></li>
+<li><p>All or nothing - You cannot provide profiles for only a subset of
+target sequences</p></li>
</ul>
<p>Example usage:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
</pre></div>
</div>
<p>A fast torsion angle based sampling is performed in case of Monte Carlo
-sampling. You can enforce the usage of structural fragments with <code class="docutils literal"><span class="pre">-r</span></code>
+sampling. You can enforce the usage of structural fragments with <code class="docutils literal notranslate"><span class="pre">-r</span></code>
but this increases runtime due to searching the required fragments.
-Setup of the according <a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>
+Setup of the according <a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>
objects is performed in the
-<a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal"><span class="pre">PM3ArgumentParser</span></code></a> class as described in
-detail <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments" title="promod3.core.pm3argparse.PM3ArgumentParser.AddFragments"><code class="xref py py-meth docutils literal"><span class="pre">here</span></code></a>.</p>
+<a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal notranslate"><span class="pre">PM3ArgumentParser</span></code></a> class as described in
+detail <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments" title="promod3.core.pm3argparse.PM3ArgumentParser.AddFragments"><code class="xref py py-meth docutils literal notranslate"><span class="pre">here</span></code></a>.</p>
<p>The default modelling pipeline in ProMod3 is optimized to generate a gap-free
model of the region in the target sequence(s) that is covered with template
information. Terminal extensions without template coverage are negelected.
-You can enforce a model of the full target sequence(s) by adding <code class="docutils literal"><span class="pre">-t</span></code>.
+You can enforce a model of the full target sequence(s) by adding <code class="docutils literal notranslate"><span class="pre">-t</span></code>.
The terminal parts will be modelled with a crude Monte Carlo approach. Be aware
that the accuracy of those termini is likely to be limited. Termini of length 1
-won’t be modelled.</p>
+won’t be modelled.</p>
<p>Possible exit codes of the action:</p>
<ul class="simple">
-<li>0: all went well</li>
-<li>1: an unhandled exception was raised</li>
-<li>2: arguments cannot be parsed or required arguments are missing</li>
-<li>3: failed to perform modelling (internal error)</li>
-<li>4: failed to write results to file</li>
-<li>other non-zero: failure in argument checking
-(see <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.pm3argparse.PM3ArgumentParser</span></code></a>)</li>
+<li><p>0: all went well</p></li>
+<li><p>1: an unhandled exception was raised</p></li>
+<li><p>2: arguments cannot be parsed or required arguments are missing</p></li>
+<li><p>3: failed to perform modelling (internal error)</p></li>
+<li><p>4: failed to write results to file</p></li>
+<li><p>other non-zero: failure in argument checking
+(see <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.core.pm3argparse.PM3ArgumentParser</span></code></a>)</p></li>
</ul>
</div>
<div class="section" id="sidechain-modelling">
<h2>Sidechain Modelling<a class="headerlink" href="#sidechain-modelling" title="Permalink to this headline">¶</a></h2>
<p>You can (re-)construct the sidechains in a model from the command line.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> usage: build-sidechains <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-p <FILE> <span class="p">|</span> -e <FILE><span class="o">)</span> <span class="o">[</span>-o <FILENAME><span class="o">]</span> <span class="o">[</span>-k<span class="o">]</span> <span class="o">[</span>-n<span class="o">]</span>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> usage: build-sidechains <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-p <FILE> <span class="p">|</span> -e <FILE><span class="o">)</span> <span class="o">[</span>-o <FILENAME><span class="o">]</span> <span class="o">[</span>-k<span class="o">]</span> <span class="o">[</span>-n<span class="o">]</span>
<span class="go"> [-r] [-i] [-s]</span>
</pre></div>
</div>
<p>Example usage:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-sidechains -p input.pdb
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-sidechains -p input.pdb
</pre></div>
</div>
<p>This reads a structure stored in in.pdb, strips all sidechains,
detects and models disulfid bonds and reconstructs all sidechains with the
-flexible rotamer model. The result is stored as <code class="file docutils literal"><span class="pre">out.pdb</span></code>.
-The output filename can be controlled with the <code class="docutils literal"><span class="pre">-o</span></code> flag.</p>
-<p>A structure can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
-chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
-<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>.</p>
+flexible rotamer model. The result is stored as <code class="file docutils literal notranslate"><span class="pre">out.pdb</span></code>.
+The output filename can be controlled with the <code class="docutils literal notranslate"><span class="pre">-o</span></code> flag.</p>
+<p>A structure can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
+<code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>.</p>
<p>Several flags control the modelling behaviour:</p>
<dl class="option">
<dt id="cmdoption-k">
-<span id="cmdoption--keep-sidechains"></span><code class="descname">-k</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--keep-sidechains</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-k" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">-k</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--keep-sidechains</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-k" title="Permalink to this definition">¶</a></dt>
<dd><p>Keep existing sidechains.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-n">
-<span id="cmdoption--no-disulfids"></span><code class="descname">-n</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-disulfids</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-n" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">-n</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--no-disulfids</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-n" title="Permalink to this definition">¶</a></dt>
<dd><p>Do not build disulfid bonds before sidechain optimization</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-r">
-<span id="cmdoption--rigid-rotamers"></span><code class="descname">-r</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--rigid-rotamers</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-r" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">-r</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--rigid-rotamers</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-r" title="Permalink to this definition">¶</a></dt>
<dd><p>Do not use rotamers with subrotamers</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-i">
-<span id="cmdoption--backbone-independent"></span><code class="descname">-i</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--backbone-independent</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-i" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">-i</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--backbone-independent</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-i" title="Permalink to this definition">¶</a></dt>
<dd><p>Use backbone independent rotamer library
-(from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.LoadLib()</span></code></a>) instead of the default backbone
-dependent one (from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.LoadBBDepLib()</span></code></a>)</p>
+(from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.LoadLib()</span></code></a>) instead of the default backbone
+dependent one (from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.LoadBBDepLib()</span></code></a>)</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-s">
-<span id="cmdoption--no-subrotamer-optimization"></span><code class="descname">-s</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-subrotamer-optimization</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-s" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">-s</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--no-subrotamer-optimization</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-s" title="Permalink to this definition">¶</a></dt>
<dd><p>Dont do subrotamer optimization if flexible rotamer model is used</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-f">
-<span id="cmdoption--energy_function"></span><code class="descname">-f</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--energy_function</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-f" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">-f</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--energy_function</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-f" title="Permalink to this definition">¶</a></dt>
<dd><p>The energy function to be used. Default is SCWRL4, can be any function
-supported by <a class="reference internal" href="../modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-meth docutils literal"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>.</p>
+supported by <a class="reference internal" href="../modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>.</p>
</dd></dl>
</div>
@@ -252,14 +236,39 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">ProMod3 Actions</a><ul>
-<li><a class="reference internal" href="#building-models">Building models</a></li>
-<li><a class="reference internal" href="#sidechain-modelling">Sidechain Modelling</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -271,23 +280,24 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/actions/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -296,11 +306,11 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/actions/index.txt"
+ <a href="../_sources/actions/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 67a5965342612a3774545b48b53dc844be10c55a..63efba74b11ff525b6f2376e61bb5940f0f06106 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -1,34 +1,21 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>test_actions - Testing Actions — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>test_actions - Testing Actions — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developers" href="../developers.html" />
- <link rel="next" title="ProMod3‘s Share Of CMake" href="../cmake/index.html" />
+ <link rel="next" title="ProMod3’s Share Of CMake" href="../cmake/index.html" />
<link rel="prev" title="Contributing" href="../contributing.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,29 +34,29 @@
<div class="body" role="main">
<div class="section" id="module-test_actions">
-<span id="test-actions-testing-actions"></span><h1><a class="reference internal" href="#module-test_actions" title="test_actions: Testing Actions"><code class="xref py py-mod docutils literal"><span class="pre">test_actions</span></code></a> - Testing Actions<a class="headerlink" href="#module-test_actions" title="Permalink to this headline">¶</a></h1>
+<span id="test-actions-testing-actions"></span><h1><a class="reference internal" href="#module-test_actions" title="test_actions: Testing Actions"><code class="xref py py-mod docutils literal notranslate"><span class="pre">test_actions</span></code></a> - Testing Actions<a class="headerlink" href="#module-test_actions" title="Permalink to this headline">¶</a></h1>
<p>This module is <strong>not</strong> part of the ProMod3 binary distribution. That is the
productive bit running to produce models. It is only part of the source
distribution intended to help developing ProMod3. Basically it supports you
creating new actions along immediate tests, which will be stored as unit tests
and stay available to monitor later changes.</p>
<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">A couple of different paths will be mentioned in the following. To make
-things easier to tell apart, a prefix <code class="file docutils literal"><span class="pre"><SOURCE></span></code> refers to the code
-repository, <code class="file docutils literal"><span class="pre"><BUILD></span></code> to the build directory tree.</p>
+<p class="admonition-title">Note</p>
+<p>A couple of different paths will be mentioned in the following. To make
+things easier to tell apart, a prefix <code class="file docutils literal notranslate"><span class="pre"><SOURCE></span></code> refers to the code
+repository, <code class="file docutils literal notranslate"><span class="pre"><BUILD></span></code> to the build directory tree.</p>
</div>
<p>Inside the development environment, the module is only available to unit tests
-in the <code class="file docutils literal"><span class="pre"><SOURCE>/actions/tests</span></code> directory. There is one special thing
-about using it in your tests for an action, emerging from the way <code class="docutils literal"><span class="pre">make</span></code> runs
+in the <code class="file docutils literal notranslate"><span class="pre"><SOURCE>/actions/tests</span></code> directory. There is one special thing
+about using it in your tests for an action, emerging from the way <code class="docutils literal notranslate"><span class="pre">make</span></code> runs
unit tests as set up via CMake. Python modules are imported from the source
-directory, here this is <code class="file docutils literal"><span class="pre"><SOURCE>/actions/tests</span></code>, while the tests run
-inside <code class="file docutils literal"><span class="pre"><BUILD>/tests</span></code>, here this is <code class="file docutils literal"><span class="pre"><BUILD>/tests/actions</span></code>. When
+directory, here this is <code class="file docutils literal notranslate"><span class="pre"><SOURCE>/actions/tests</span></code>, while the tests run
+inside <code class="file docutils literal notranslate"><span class="pre"><BUILD>/tests</span></code>, here this is <code class="file docutils literal notranslate"><span class="pre"><BUILD>/tests/actions</span></code>. When
Python imports a module, its usually compiled into bytecode. This new file
would clutter up the source repository, it would always show up as untracked
-file on <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code>. To prevent this, tell Python to stop producing
+file on <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">status</span></code>. To prevent this, tell Python to stop producing
bytecode right at the beginning of your test-script:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
@@ -100,21 +86,21 @@ something, add new functionality, etc..</p>
<p>In the next couple of paragraphs, we will walk through setting up a new unit
test script for an imaginary action. We will continuously extend the file
started above, so keep an eye on line numbers. Lets just assume your action is
-called <code class="docutils literal"><span class="pre">do-awesome</span></code> for the rest of this section.</p>
+called <code class="docutils literal notranslate"><span class="pre">do-awesome</span></code> for the rest of this section.</p>
<div class="section" id="the-test-script">
<h3>The Test Script<a class="headerlink" href="#the-test-script" title="Permalink to this headline">¶</a></h3>
<p>The script to supervise your action needs to be placed in
-<code class="file docutils literal"><span class="pre"><SOURCE>/actions/tests</span></code> and follow the naming convention
-<code class="file docutils literal"><span class="pre">test_action_<NAME>.py</span></code>, where <code class="file docutils literal"><span class="pre"><NAME></span></code> is the name for your
-action. So here we create a file <code class="file docutils literal"><span class="pre">test_action_do_awesome.py</span></code> (recognise
-the underscore between <code class="docutils literal"><span class="pre">do</span></code> and <code class="docutils literal"><span class="pre">awesome</span></code> instead of a hyphen, that’s
+<code class="file docutils literal notranslate"><span class="pre"><SOURCE>/actions/tests</span></code> and follow the naming convention
+<code class="file docutils literal notranslate"><span class="pre">test_action_<NAME>.py</span></code>, where <code class="file docutils literal notranslate"><span class="pre"><NAME></span></code> is the name for your
+action. So here we create a file <code class="file docutils literal notranslate"><span class="pre">test_action_do_awesome.py</span></code> (recognise
+the underscore between <code class="docutils literal notranslate"><span class="pre">do</span></code> and <code class="docutils literal notranslate"><span class="pre">awesome</span></code> instead of a hyphen, that’s
<a class="reference external" href="https://www.python.org/dev/peps/pep-0008/">PEP 8</a>).</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch <SOURCE>/actions/tests/test_action_do_awesome.py
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> touch <SOURCE>/actions/tests/test_action_do_awesome.py
<span class="gp">$</span>
</pre></div>
</div>
<p>As a starter, we disable bytecode compilation in the script:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
@@ -130,9 +116,9 @@ the underscore between <code class="docutils literal"><span class="pre">do</span
<h3>CMake Integration<a class="headerlink" href="#cmake-integration" title="Permalink to this headline">¶</a></h3>
<p>As always, when introducing new material to ProMod3, it has to be announced
to the CMake build system. For action unit tests, fire up
-<code class="file docutils literal"><span class="pre"><SOURCE>/actions/tests/CMakeLists.txt</span></code> in your favourite text editor and
+<code class="file docutils literal notranslate"><span class="pre"><SOURCE>/actions/tests/CMakeLists.txt</span></code> in your favourite text editor and
add your new script:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
@@ -147,65 +133,65 @@ add your new script:</p>
<span class="nf">promod3_unittest(</span><span class="no">MODULE</span><span class="w"> </span><span class="nb">actions</span><span class="w"> </span><span class="no">SOURCES</span><span class="w"> </span><span class="s">"${ACTION_UNIT_TESTS}"</span><span class="w"> </span><span class="no">TARGET</span><span class="w"> </span><span class="nb">actions</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</td></tr></table></div>
-<p>The important thing is to leave <code class="file docutils literal"><span class="pre">test_actions.py</span></code> as last item in the
+<p>The important thing is to leave <code class="file docutils literal notranslate"><span class="pre">test_actions.py</span></code> as last item in the
list. This script contains the tests around the
-<a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> class, which is the foundation of the
+<a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal notranslate"><span class="pre">test_actions.ActionTestCase</span></code></a> class, which is the foundation of the
tests for your action. If this class is broken, we are lost. Putting it as the
last element in the list, CMake will execute this script first, before any
other action test script is run.</p>
</div>
<div class="section" id="creating-a-test-subclass">
<h3>Creating a Test Subclass<a class="headerlink" href="#creating-a-test-subclass" title="Permalink to this headline">¶</a></h3>
-<p><a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> is sort of a template class for your
+<p><a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal notranslate"><span class="pre">test_actions.ActionTestCase</span></code></a> is sort of a template class for your
tests. By spawning off from this you inherit a bunch of useful methods for your
testing. To make it work, the childclass needs to be set up properly. But
-first, <code class="file docutils literal"><span class="pre">test_actions.py</span></code> has to be loaded as a module:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>6</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">test_actions</span>
+first, <code class="file docutils literal notranslate"><span class="pre">test_actions.py</span></code> has to be loaded as a module:</p>
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>6</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">test_actions</span>
</pre></div>
</td></tr></table></div>
<p>To showcase, the test cases, we explain how one would (and does) test the
-<code class="docutils literal"><span class="pre">help</span></code> action of <code class="docutils literal"><span class="pre">pm</span></code>.
+<code class="docutils literal notranslate"><span class="pre">help</span></code> action of <code class="docutils literal notranslate"><span class="pre">pm</span></code>.
First, we create the childclass for the action.
-Go for <code class="xref py py-class docutils literal"><span class="pre"><NAME>ActionTests</span></code> as a naming scheme:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 7
+Go for <code class="xref py py-class docutils literal notranslate"><span class="pre"><NAME>ActionTests</span></code> as a naming scheme:</p>
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 7
8
9
10</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">HelpActionTests</span><span class="p">(</span><span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="p">):</span>
- <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span> <span class="o">=</span> <span class="s1">'help'</span>
</pre></div>
</td></tr></table></div>
-<p>Pay attention that in your own class, you must set <code class="xref py py-attr docutils literal"><span class="pre">pm_action</span></code> to make
-everything work. Also <code class="xref py py-meth docutils literal"><span class="pre">__init__()</span></code> needs certain parameters, as everything
-is derived from the <a class="reference external" href="https://docs.python.org/3.6/library/unittest.html#unittest.TestCase" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a> class.</p>
+<p>Pay attention that in your own class, you must set <code class="xref py py-attr docutils literal notranslate"><span class="pre">pm_action</span></code> to make
+everything work. Also <code class="xref py py-meth docutils literal notranslate"><span class="pre">__init__()</span></code> needs certain parameters, as everything
+is derived from the <a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a> class.</p>
</div>
<div class="section" id="must-have-tests">
<h3>Must Have Tests<a class="headerlink" href="#must-have-tests" title="Permalink to this headline">¶</a></h3>
<p>What needs testing without exclusion are the exit codes of actions. Those
states will be placed in the userlevel documentation. This topic is already
-covered in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> by <a class="reference internal" href="#test_actions.ActionTestCase.RunExitStatusTest" title="test_actions.ActionTestCase.RunExitStatusTest"><code class="xref py py-meth docutils literal"><span class="pre">RunExitStatusTest()</span></code></a>.
-As an example, testing for <code class="docutils literal"><span class="pre">$?=0</span></code> could work like this:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+covered in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal notranslate"><span class="pre">test_actions.ActionTestCase</span></code></a> by <a class="reference internal" href="#test_actions.ActionTestCase.RunExitStatusTest" title="test_actions.ActionTestCase.RunExitStatusTest"><code class="xref py py-meth docutils literal notranslate"><span class="pre">RunExitStatusTest()</span></code></a>.
+As an example, testing for <code class="docutils literal notranslate"><span class="pre">$?=0</span></code> could work like this:</p>
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
12</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">())</span>
</pre></div>
</td></tr></table></div>
-<p>That will call the action stored in <code class="xref py py-attr docutils literal"><span class="pre">pm_action</span></code> with the provided list of
-parameters and check that <code class="docutils literal"><span class="pre">0</span></code> is returned on the command line.</p>
+<p>That will call the action stored in <code class="xref py py-attr docutils literal notranslate"><span class="pre">pm_action</span></code> with the provided list of
+parameters and check that <code class="docutils literal notranslate"><span class="pre">0</span></code> is returned on the command line.</p>
<p>In a more general way, you need to test that your action is working as
intended. Do not forget some negative testing, with the idea in mind what
happens if a user throws dirty input data in.</p>
</div>
<div class="section" id="making-the-script-executable">
<h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="https://www.openstructure.org/docs/2.0/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
-<a class="reference external" href="https://docs.python.org/3.6/library/unittest.html#unittest.TestCase" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>’s <a class="reference external" href="https://www.openstructure.org/docs/2.0/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s
+<a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
as a script:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
14
15</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
- <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
+ <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">testutils</span>
<span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
</pre></div>
</td></tr></table></div>
@@ -213,40 +199,40 @@ as a script:</p>
</div>
<div class="section" id="running-the-test-script">
<h3>Running the Test Script<a class="headerlink" href="#running-the-test-script" title="Permalink to this headline">¶</a></h3>
-<p>Unit tests are executed via <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code> and so are ProMod3 action tests.
-But for every test script, we also provide a private <code class="docutils literal"><span class="pre">make</span></code> target, ending
-with <code class="file docutils literal"><span class="pre">_run</span></code>. To solely run the tests for the awesome action, hit</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
+<p>Unit tests are executed via <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> and so are ProMod3 action tests.
+But for every test script, we also provide a private <code class="docutils literal notranslate"><span class="pre">make</span></code> target, ending
+with <code class="file docutils literal notranslate"><span class="pre">_run</span></code>. To solely run the tests for the awesome action, hit</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
</pre></div>
</div>
</div>
<div class="section" id="output-of-test-actions-actiontestcase">
-<h3>Output Of <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a><a class="headerlink" href="#output-of-test-actions-actiontestcase" title="Permalink to this headline">¶</a></h3>
+<h3>Output Of <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal notranslate"><span class="pre">test_actions.ActionTestCase</span></code></a><a class="headerlink" href="#output-of-test-actions-actiontestcase" title="Permalink to this headline">¶</a></h3>
<p>When running the test script you will notice that its not really talkative.
-Basically you do not see output to <code class="file docutils literal"><span class="pre">stdout</span></code>/ <code class="file docutils literal"><span class="pre">stderr</span></code> of your
+Basically you do not see output to <code class="file docutils literal notranslate"><span class="pre">stdout</span></code>/ <code class="file docutils literal notranslate"><span class="pre">stderr</span></code> of your
action, while the test script fires it a couple of times. That is by design.
When running the full unit test suite, usually nobody wants to see the output
of <strong>everything</strong> tested and working. The interesting bits are where we fail.
But for developing a new application you certainly need all the output you can
-get. For this, some functions in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> have a
-parameter <code class="xref py py-attr docutils literal"><span class="pre">verbose</span></code>. That triggers specific functions to flush captured
+get. For this, some functions in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal notranslate"><span class="pre">test_actions.ActionTestCase</span></code></a> have a
+parameter <code class="xref py py-attr docutils literal notranslate"><span class="pre">verbose</span></code>. That triggers specific functions to flush captured
output onto the command line. The idea is to turn it on for development, but
once done, disable it to keep output of unit tests low.</p>
-<p>To get the test for exit code <code class="docutils literal"><span class="pre">0</span></code> talking to you, just do</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+<p>To get the test for exit code <code class="docutils literal notranslate"><span class="pre">0</span></code> talking to you, just do</p>
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
12</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">(),</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>
</td></tr></table></div>
<p>and</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
12</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">())</span>
</pre></div>
</td></tr></table></div>
-<p>keeps it silent (<code class="xref py py-attr docutils literal"><span class="pre">verbose</span></code> is set to <code class="docutils literal"><span class="pre">False</span></code> by default). If enabled,
-output will be separated into <code class="file docutils literal"><span class="pre">stdout</span></code> and <code class="file docutils literal"><span class="pre">stderr</span></code>:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
+<p>keeps it silent (<code class="xref py py-attr docutils literal notranslate"><span class="pre">verbose</span></code> is set to <code class="docutils literal notranslate"><span class="pre">False</span></code> by default). If enabled,
+output will be separated into <code class="file docutils literal notranslate"><span class="pre">stdout</span></code> and <code class="file docutils literal notranslate"><span class="pre">stderr</span></code>:</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
<span class="go"><Lots of output from the build process></span>
<span class="go">running checks test_action_do_awesome.py</span>
<span class="go">stdout of '<BUILD>/stage/bin/pm do-awesome'</span>
@@ -266,92 +252,78 @@ output will be separated into <code class="file docutils literal"><span class="p
<h2>Unit Test Actions API<a class="headerlink" href="#unit-test-actions-api" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="test_actions.ActionTestCase">
-<em class="property">class </em><code class="descclassname">test_actions.</code><code class="descname">ActionTestCase</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">test_actions.</code><code class="sig-name descname">ActionTestCase</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase" title="Permalink to this definition">¶</a></dt>
<dd><p>Class to help developing actions. Comes with a lot of convenience wrappers
-around what should be tested and serves as a recorder for test calls...
-just for in two years when you come back to rewrite the whole action...</p>
-<p>While inheriting this class, <a class="reference internal" href="#test_actions.ActionTestCase.pm_action" title="test_actions.ActionTestCase.pm_action"><code class="xref py py-attr docutils literal"><span class="pre">pm_action</span></code></a> needs to be defined.
+around what should be tested and serves as a recorder for test calls…
+just for in two years when you come back to rewrite the whole action…</p>
+<p>While inheriting this class, <a class="reference internal" href="#test_actions.ActionTestCase.pm_action" title="test_actions.ActionTestCase.pm_action"><code class="xref py py-attr docutils literal notranslate"><span class="pre">pm_action</span></code></a> needs to be defined.
Otherwise the whole idea does not work.</p>
<dl class="attribute">
<dt id="test_actions.ActionTestCase.pm_bin">
-<code class="descname">pm_bin</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_bin" title="Permalink to this definition">¶</a></dt>
-<dd><p>This is the path of the <code class="docutils literal"><span class="pre">pm</span></code> binary. Automatically set by calling
-<code class="xref py py-meth docutils literal"><span class="pre">__init__()</span></code> inside the initialisation of your class.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">pm_bin</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_bin" title="Permalink to this definition">¶</a></dt>
+<dd><p>This is the path of the <code class="docutils literal notranslate"><span class="pre">pm</span></code> binary. Automatically set by calling
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">__init__()</span></code> inside the initialisation of your class.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="test_actions.ActionTestCase.pm_action">
-<code class="descname">pm_action</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_action" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">pm_action</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_action" title="Permalink to this definition">¶</a></dt>
<dd><p>The action to be tested. Needs to be set by your initialisation routine,
-<strong>after</strong> calling <code class="xref py py-meth docutils literal"><span class="pre">__init__()</span></code> from here. Skip the
-“pm-” in front of the action name.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<strong>after</strong> calling <code class="xref py py-meth docutils literal notranslate"><span class="pre">__init__()</span></code> from here. Skip the
+“pm-” in front of the action name.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="test_actions.ActionTestCase.RunAction">
-<code class="descname">RunAction</code><span class="sig-paren">(</span><em>arguments</em>, <em>verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunAction" title="Permalink to this definition">¶</a></dt>
-<dd><p>Call an action, return the exit status (<code class="docutils literal"><span class="pre">$?</span></code> shell variable). May be
-set to <code class="docutils literal"><span class="pre">verbose</span></code> to print the actions terminal output. The action to
-be executed needs to be stored in <a class="reference internal" href="#test_actions.ActionTestCase.pm_action" title="test_actions.ActionTestCase.pm_action"><code class="xref py py-attr docutils literal"><span class="pre">pm_action</span></code></a> first.</p>
-<p>If in verbose mode, output to <code class="file docutils literal"><span class="pre">stdout</span></code> of the action will be
-printed first followed by <code class="file docutils literal"><span class="pre">stderr</span></code>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – A list of arguments for the call.</li>
-<li><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <code class="docutils literal"><span class="pre">True</span></code>, report output of the action.</li>
+<code class="sig-name descname">RunAction</code><span class="sig-paren">(</span><em class="sig-param">arguments</em>, <em class="sig-param">verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunAction" title="Permalink to this definition">¶</a></dt>
+<dd><p>Call an action, return the exit status (<code class="docutils literal notranslate"><span class="pre">$?</span></code> shell variable). May be
+set to <code class="docutils literal notranslate"><span class="pre">verbose</span></code> to print the actions terminal output. The action to
+be executed needs to be stored in <a class="reference internal" href="#test_actions.ActionTestCase.pm_action" title="test_actions.ActionTestCase.pm_action"><code class="xref py py-attr docutils literal notranslate"><span class="pre">pm_action</span></code></a> first.</p>
+<p>If in verbose mode, output to <code class="file docutils literal notranslate"><span class="pre">stdout</span></code> of the action will be
+printed first followed by <code class="file docutils literal notranslate"><span class="pre">stderr</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of arguments for the call.</p></li>
+<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code>, report output of the action.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The exit code of the action (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The exit code of the action (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="test_actions.ActionTestCase.RunExitStatusTest">
-<code class="descname">RunExitStatusTest</code><span class="sig-paren">(</span><em>exit_code</em>, <em>arguments</em>, <em>verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunExitStatusTest" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">RunExitStatusTest</code><span class="sig-paren">(</span><em class="sig-param">exit_code</em>, <em class="sig-param">arguments</em>, <em class="sig-param">verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunExitStatusTest" title="Permalink to this definition">¶</a></dt>
<dd><p>Run the action with given arguments and check the exit code.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>exit_code</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The expected return code, <code class="docutils literal"><span class="pre">$?</span></code> in a shell.</li>
-<li><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – A list of arguments for the call.</li>
-<li><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <code class="docutils literal"><span class="pre">True</span></code>, report output of the action.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>exit_code</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The expected return code, <code class="docutils literal notranslate"><span class="pre">$?</span></code> in a shell.</p></li>
+<li><p><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of arguments for the call.</p></li>
+<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code>, report output of the action.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="test_actions.ActionTestCase.testPMExists">
-<code class="descname">testPMExists</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.testPMExists" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">testPMExists</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.testPMExists" title="Permalink to this definition">¶</a></dt>
<dd><p>This is an internal test, executed when the source code of the test
-class is run as unit test. Verifies that <a class="reference internal" href="#test_actions.ActionTestCase.pm_bin" title="test_actions.ActionTestCase.pm_bin"><code class="xref py py-attr docutils literal"><span class="pre">pm_bin</span></code></a> is an existing
+class is run as unit test. Verifies that <a class="reference internal" href="#test_actions.ActionTestCase.pm_bin" title="test_actions.ActionTestCase.pm_bin"><code class="xref py py-attr docutils literal notranslate"><span class="pre">pm_bin</span></code></a> is an existing
file (also complains if a directory is found instead).</p>
</dd></dl>
@@ -367,51 +339,55 @@ file (also complains if a directory is found instead).</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">test_actions</span></code> - Testing Actions</a><ul>
-<li><a class="reference internal" href="#creating-an-action-unit-test-script">Creating an Action Unit Test Script</a><ul>
-<li><a class="reference internal" href="#the-test-script">The Test Script</a></li>
-<li><a class="reference internal" href="#cmake-integration">CMake Integration</a></li>
-<li><a class="reference internal" href="#creating-a-test-subclass">Creating a Test Subclass</a></li>
-<li><a class="reference internal" href="#must-have-tests">Must Have Tests</a></li>
-<li><a class="reference internal" href="#making-the-script-executable">Making the Script Executable</a></li>
-<li><a class="reference internal" href="#running-the-test-script">Running the Test Script</a></li>
-<li><a class="reference internal" href="#output-of-test-actions-actiontestcase">Output Of <code class="docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#unit-test-actions-api">Unit Test Actions API</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../users.html">Users</a></li>
</ul>
-</li>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../developers.html">Documentation For Developers</a><ul>
<li>Previous: <a href="../contributing.html" title="previous chapter">Contributing</a></li>
- <li>Next: <a href="../cmake/index.html" title="next chapter">ProMod3‘s Share Of CMake</a></li>
+ <li>Next: <a href="../cmake/index.html" title="next chapter">ProMod3’s Share Of CMake</a></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/actions/index_dev.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -420,11 +396,11 @@ file (also complains if a directory is found instead).</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/actions/index_dev.txt"
+ <a href="../_sources/actions/index_dev.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 50b1089f7036fe7bd2b6a25dda4c114845f2c1d0..21f67d724cc474aad4828460f8491ff47e2905e3 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Building ProMod3 — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Building ProMod3 — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="ProMod3 and Containers" href="container/index.html" />
<link rel="prev" title="ProMod3 Actions" href="actions/index.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -52,7 +38,7 @@
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-2.0.0. OST must be configured and compiled with <code class="docutils literal"><span class="pre">ENABLE_MM=1</span></code> to
+2.1.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
use <a class="reference external" href="http://openmm.org">OpenMM</a>. To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same
versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a> are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a>
we need at least version 3.3.0. To build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is
@@ -61,13 +47,13 @@ release supporting Python 2.7 is 2.1.0 which also requires OST to be
compiled with Python 2.7.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.0.0</li>
-<li><a class="reference external" href="http://openmm.org">OpenMM</a> 7.1.1</li>
-<li><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</li>
-<li><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</li>
-<li><a class="reference external" href="https://www.boost.org/">Boost</a> 1.68.0</li>
-<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.1</li>
-<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.3.1</li>
+<li><p><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.1.0</p></li>
+<li><p><a class="reference external" href="http://openmm.org">OpenMM</a> 7.1.1</p></li>
+<li><p><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</p></li>
+<li><p><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</p></li>
+<li><p><a class="reference external" href="https://www.boost.org/">Boost</a> 1.68.0</p></li>
+<li><p><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.1</p></li>
+<li><p><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.4.9</p></li>
</ul>
</div>
<div class="section" id="using-cmake">
@@ -75,46 +61,46 @@ compiled with Python 2.7.</p>
<p>CMake is used to configure the build system and in the end produces makefiles
and certain directories needed for building ProMod3. Basically it is called
right from a shell with the directory containing the top-level
-<code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> as an argument. The preferred approach is to generate a
+<code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code> as an argument. The preferred approach is to generate a
build folder and configure and compile in there:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">#</span> execute this in the ProMod3 root folder
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">#</span> execute this in the ProMod3 root folder
<span class="gp">$</span> mkdir build
<span class="gp">$</span> <span class="nb">cd</span> build
<span class="gp">$</span> cmake .. -DOST_ROOT<span class="o">=</span><PATH TO OST>
</pre></div>
</div>
<p>For us, at least pointer to the OST installation directory is needed,
-handed over to CMake by <code class="docutils literal"><span class="pre">-D</span></code> into the variable <code class="docutils literal"><span class="pre">OST_ROOT</span></code> (e.g. OST
-headers would be located in <code class="docutils literal"><span class="pre">OST_ROOT/include/ost</span></code>).</p>
+handed over to CMake by <code class="docutils literal notranslate"><span class="pre">-D</span></code> into the variable <code class="docutils literal notranslate"><span class="pre">OST_ROOT</span></code> (e.g. OST
+headers would be located in <code class="docutils literal notranslate"><span class="pre">OST_ROOT/include/ost</span></code>).</p>
<p>Similarly, one can specify folders for Boost, Python and Eigen 3
if multiple versions exist and/or they are not installed in a default location.
-These are set with the <code class="docutils literal"><span class="pre">BOOST_ROOT</span></code> (make sure that’s the same as for OST),
-<code class="docutils literal"><span class="pre">PYTHON_ROOT</span></code> and <code class="docutils literal"><span class="pre">EIGEN3_INCLUDE_DIR</span></code>.</p>
+These are set with the <code class="docutils literal notranslate"><span class="pre">BOOST_ROOT</span></code> (make sure that’s the same as for OST),
+<code class="docutils literal notranslate"><span class="pre">PYTHON_ROOT</span></code> and <code class="docutils literal notranslate"><span class="pre">EIGEN3_INCLUDE_DIR</span></code>.</p>
<p>Here is a list of more options used within ProMod3:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></code> Don’t build documentation, don’t search for Sphinx</li>
-<li><code class="docutils literal"><span class="pre">DISABLE_DOCTEST</span></code> Don’t run example code from documentation on
-<code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code> (implicit by <code class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</li>
-<li><code class="docutils literal"><span class="pre">DISABLE_LINKCHECK</span></code> Don’t test links from documentation on <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code>
-(implicit by <code class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</li>
-<li><code class="docutils literal"><span class="pre">ENABLE_SSE</span></code> Allow for more agressive optimization by adding -msse4 flag to
+<li><p><code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code> Don’t build documentation, don’t search for Sphinx</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">DISABLE_DOCTEST</span></code> Don’t run example code from documentation on
+<code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> (implicit by <code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">DISABLE_LINKCHECK</span></code> Don’t test links from documentation on <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code>
+(implicit by <code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">ENABLE_SSE</span></code> Allow for more agressive optimization by adding -msse4 flag to
the compiler. At some places within the code, we use SSE intrinsics explicitely.
This is only enabled if OST has been compiled with single precision.
-(<code class="docutils literal"><span class="pre">OST_DOUBLE_PRECISION</span></code> flag)</li>
+(<code class="docutils literal notranslate"><span class="pre">OST_DOUBLE_PRECISION</span></code> flag)</p></li>
</ul>
<p>Since we use OST in the background, some of its options for CMake are
also relevant, here. Basically they need to be set to exactly the same value.
Even if ProMod3 builds with different settings, it may start producing funny
results at an unexpected point. If you do not know the values, grep the option
-in the <code class="file docutils literal"><span class="pre">CMakeCache.txt</span></code> of OST:</p>
+in the <code class="file docutils literal notranslate"><span class="pre">CMakeCache.txt</span></code> of OST:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">OPTIMIZE</span></code></li>
-<li><code class="docutils literal"><span class="pre">OST_DOUBLE_PRECISION</span></code></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">OPTIMIZE</span></code></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">OST_DOUBLE_PRECISION</span></code></p></li>
</ul>
-<p>Instead of calling CMake by yourself, there is the <code class="file docutils literal"><span class="pre">conf-scripts</span></code>
+<p>Instead of calling CMake by yourself, there is the <code class="file docutils literal notranslate"><span class="pre">conf-scripts</span></code>
directory, providing smallish scripts to invoke CMake the right way for
various systems. Usually those scripts just need the OST path
-and the location of the top-level <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code>.</p>
+and the location of the top-level <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>.</p>
<p>As mentioned earlier, we highly recommend to use out-of-source builds.
This way, you can have several builds with different configurations. Also if
anything goes wrong, just remove the build directory to get to a clean state
@@ -124,39 +110,39 @@ really got rebuild and similar things required.</p>
<div class="section" id="running-make">
<h2>Running Make<a class="headerlink" href="#running-make" title="Permalink to this headline">¶</a></h2>
<p>After configuring, you want to build ProMod3 by</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> make
</pre></div>
</div>
-<p>to populate the <code class="file docutils literal"><span class="pre">stage</span></code> directory with a ready-to-go version of the
+<p>to populate the <code class="file docutils literal notranslate"><span class="pre">stage</span></code> directory with a ready-to-go version of the
latest code.</p>
-<p id="index-0">Beside the usual <code class="docutils literal"><span class="pre">make</span> <span class="pre">all</span></code> and other default targets, there are a few
+<p id="index-0">Beside the usual <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">all</span></code> and other default targets, there are a few
special targets:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">check</span></code> <span class="target" id="index-1"></span>make check Runs unit tests and if CMake was invoked in
-its standard configuration also documentation examples (<code class="docutils literal"><span class="pre">doctest</span></code>) and
-links in the doc. (<code class="docutils literal"><span class="pre">linkcheck</span></code>) are checked</li>
-<li><code class="docutils literal"><span class="pre">html</span></code> <span class="target" id="index-2"></span>make html Creates documentation as web page using the
-Sphinx <code class="docutils literal"><span class="pre">html</span></code> builder</li>
-<li><code class="docutils literal"><span class="pre">man</span></code> <span class="target" id="index-3"></span>make man Creates a manual page using the Sphinx <code class="docutils literal"><span class="pre">man</span></code>
-builder</li>
-<li><code class="docutils literal"><span class="pre">doc</span></code> <span class="target" id="index-4"></span>make doc Creates documentation using the <code class="docutils literal"><span class="pre">html</span></code> and
-<code class="docutils literal"><span class="pre">man</span></code> targets</li>
-<li><code class="docutils literal"><span class="pre">help</span></code> <span class="target" id="index-5"></span>make help Prints a list of targets available</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">check</span></code> <span class="target" id="index-1"></span>make check Runs unit tests and if CMake was invoked in
+its standard configuration also documentation examples (<code class="docutils literal notranslate"><span class="pre">doctest</span></code>) and
+links in the doc. (<code class="docutils literal notranslate"><span class="pre">linkcheck</span></code>) are checked</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">html</span></code> <span class="target" id="index-2"></span>make html Creates documentation as web page using the
+Sphinx <code class="docutils literal notranslate"><span class="pre">html</span></code> builder</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">man</span></code> <span class="target" id="index-3"></span>make man Creates a manual page using the Sphinx <code class="docutils literal notranslate"><span class="pre">man</span></code>
+builder</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">doc</span></code> <span class="target" id="index-4"></span>make doc Creates documentation using the <code class="docutils literal notranslate"><span class="pre">html</span></code> and
+<code class="docutils literal notranslate"><span class="pre">man</span></code> targets</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">help</span></code> <span class="target" id="index-5"></span>make help Prints a list of targets available</p></li>
</ul>
</div>
<div class="section" id="installing-project">
<h2>Installing ProMod3<a class="headerlink" href="#installing-project" title="Permalink to this headline">¶</a></h2>
<p>If you wish to install ProMod3 (note that you can also safely keep it all in
-the <code class="file docutils literal"><span class="pre">stage</span></code> directory), you can use</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make install
+the <code class="file docutils literal notranslate"><span class="pre">stage</span></code> directory), you can use</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> make install
</pre></div>
</div>
-<p>By default, this will copy the <code class="file docutils literal"><span class="pre">stage</span></code> directory to <code class="file docutils literal"><span class="pre">/usr/local</span></code>. To
-override this, you can add the <code class="docutils literal"><span class="pre">-DCMAKE_INSTALL_PREFIX=<INSTALL</span> <span class="pre">PATH></span></code> flag to
-your <code class="docutils literal"><span class="pre">cmake</span></code> call.</p>
+<p>By default, this will copy the <code class="file docutils literal notranslate"><span class="pre">stage</span></code> directory to <code class="file docutils literal notranslate"><span class="pre">/usr/local</span></code>. To
+override this, you can add the <code class="docutils literal notranslate"><span class="pre">-DCMAKE_INSTALL_PREFIX=<INSTALL</span> <span class="pre">PATH></span></code> flag to
+your <code class="docutils literal notranslate"><span class="pre">cmake</span></code> call.</p>
<p>After the installation, you should be able to delete the whole source folder. To
-ensure that everything works, you can use a set of automated “sanity checks”.
-Please follow the instructions in <code class="file docutils literal"><span class="pre">extras/sanity_checks/README</span></code> to setup
+ensure that everything works, you can use a set of automated “sanity checks”.
+Please follow the instructions in <code class="file docutils literal notranslate"><span class="pre">extras/sanity_checks/README</span></code> to setup
and run those tests after moving the source folder. If everything works, you can
safely delete the whole source folder.</p>
</div>
@@ -169,16 +155,39 @@ safely delete the whole source folder.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Building ProMod3</a><ul>
-<li><a class="reference internal" href="#dependencies">Dependencies</a></li>
-<li><a class="reference internal" href="#using-cmake">Using CMake</a></li>
-<li><a class="reference internal" href="#running-make">Running Make</a></li>
-<li><a class="reference internal" href="#installing-project">Installing ProMod3</a></li>
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -190,23 +199,24 @@ safely delete the whole source folder.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/buildsystem.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -215,11 +225,11 @@ safely delete the whole source folder.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/buildsystem.txt"
+ <a href="_sources/buildsystem.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index ab212521632947dc7b584fac966ae602c026e1d0..7218355aad831c79052b719d7821dae9832026fe 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -1,32 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Changelog — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Changelog — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
<link rel="prev" title="References" href="references.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -34,8 +22,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -47,124 +34,138 @@
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-3-1-1">
+<h2>Release 3.1.1<a class="headerlink" href="#release-3-1-1" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>Bugfix release: reintroduces backwards compatibility in BuildRawModel.
+See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details</p></li>
+</ul>
+</div>
+<div class="section" id="release-3-1-0">
+<h2>Release 3.1.0<a class="headerlink" href="#release-3-1-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>Introduce alignment processing steps in BuildRawModel</p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups.</p></li>
+</ul>
+</div>
<div class="section" id="release-3-0-0">
<h2>Release 3.0.0<a class="headerlink" href="#release-3-0-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li>First release supporting Python 3. Python 2 support has been dropped.</li>
-<li>Updated versions of dependencies.</li>
-<li>Reduced amount of warnings during compilation.</li>
-<li>Improved and simplified use of Docker and Singularity containers.</li>
-<li>Several minor bug fixes, improvements, and speed-ups.</li>
+<li><p>First release supporting Python 3. Python 2 support has been dropped.</p></li>
+<li><p>Updated versions of dependencies.</p></li>
+<li><p>Reduced amount of warnings during compilation.</p></li>
+<li><p>Improved and simplified use of Docker and Singularity containers.</p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups.</p></li>
</ul>
</div>
<div class="section" id="release-2-1-0">
<h2>Release 2.1.0<a class="headerlink" href="#release-2-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li>This is expected to be the last release supporting Python 2.</li>
-<li>This project now requires a C++11 compatible compiler.</li>
-<li>Introduced VINA scoring function in the sidechain module. A scoring function
+<li><p>This is expected to be the last release supporting Python 2.</p></li>
+<li><p>This project now requires a C++11 compatible compiler.</p></li>
+<li><p>Introduced VINA scoring function in the sidechain module. A scoring function
specific RotamerConstructor is provided that comes with extensive heuristics
-to parametrize arbitrary compounds.</li>
-<li>Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
-The algorithm is based on principles of geometric hashing.</li>
-<li>Several minor bug fixes, improvements, and speed-ups</li>
+to parametrize arbitrary compounds.</p></li>
+<li><p>Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+The algorithm is based on principles of geometric hashing.</p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
</ul>
</div>
<div class="section" id="release-2-0-0">
<h2>Release 2.0.0<a class="headerlink" href="#release-2-0-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li>Generalize particle scoring and rotamer construction in sidechain module.
+<li><p>Generalize particle scoring and rotamer construction in sidechain module.
This simplifies the addition of other scoring functions in the future.
Be aware of breaking changes introduced in the process!
(SCWRLRotamerConstructor -> SCWRL4RotamerConstructor, changed interface of
-Particle and RotamerConstructor classes).</li>
-<li>Enable possibility to use structural fragments in default modelling pipeline
-and build-model action</li>
-<li>Enable possibility to enforce full coverage models including termini without
-template coverage in default modelling pipeline and build-model action</li>
-<li>Modelling pipeline can track issues in the ModellingHandle object</li>
-<li>External example scripts can now be found in extras/external_scripts</li>
-<li>Improved support for recent compilers and libraries.</li>
-<li>Several minor bug fixes, improvements, and speed-ups</li>
+Particle and RotamerConstructor classes).</p></li>
+<li><p>Enable possibility to use structural fragments in default modelling pipeline
+and build-model action</p></li>
+<li><p>Enable possibility to enforce full coverage models including termini without
+template coverage in default modelling pipeline and build-model action</p></li>
+<li><p>Modelling pipeline can track issues in the ModellingHandle object</p></li>
+<li><p>External example scripts can now be found in extras/external_scripts</p></li>
+<li><p>Improved support for recent compilers and libraries.</p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
</ul>
</div>
<div class="section" id="release-1-3-0">
<h2>Release 1.3.0<a class="headerlink" href="#release-1-3-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li>Apply Apache Version 2.0 License to the project</li>
-<li>2010 Dunbrack rotamer library has been replaced by an own backbone dependent
+<li><p>Apply Apache Version 2.0 License to the project</p></li>
+<li><p>2010 Dunbrack rotamer library has been replaced by an own backbone dependent
rotamer library. All scripts required to reproduce the data are in
-extras/data_generation/rotamer_library</li>
-<li>Penultimate rotamer library has been replaced by an own backbone independent
+extras/data_generation/rotamer_library</p></li>
+<li><p>Penultimate rotamer library has been replaced by an own backbone independent
rotamer library. All scripts required to reproduce the data are in
-extras/data_generation/rotamer_library</li>
-<li>SampleMonteCarlo function moved to Python. This makes it possible to provide
-sampler/closer/scorer/cooler objects implemented in both, Python and C++</li>
-<li>Action script for sidechain modelling</li>
-<li>Allow sequence profiles as input for build-model action script.</li>
-<li>Recipe for Docker / Singularity container</li>
-<li>Check peptide bonds when building a RawModel. Treat as gap if bond is
-stereochemically problematic despite being in sequence.</li>
-<li>Several minor bug fixes, improvements, and speed-ups</li>
+extras/data_generation/rotamer_library</p></li>
+<li><p>SampleMonteCarlo function moved to Python. This makes it possible to provide
+sampler/closer/scorer/cooler objects implemented in both, Python and C++</p></li>
+<li><p>Action script for sidechain modelling</p></li>
+<li><p>Allow sequence profiles as input for build-model action script.</p></li>
+<li><p>Recipe for Docker / Singularity container</p></li>
+<li><p>Check peptide bonds when building a RawModel. Treat as gap if bond is
+stereochemically problematic despite being in sequence.</p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
</ul>
</div>
<div class="section" id="release-1-2-0">
<h2>Release 1.2.0<a class="headerlink" href="#release-1-2-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li>Graph optimizer has been separated from the sidechain module and can now be
+<li><p>Graph optimizer has been separated from the sidechain module and can now be
used for arbitrary optimization problems. Available optimization algorithms
-are TreePack, AStar and MonteCarlo.</li>
-<li>Make it possible to distinguish between the scores of a loop towards a constant
+are TreePack, AStar and MonteCarlo.</p></li>
+<li><p>Make it possible to distinguish between the scores of a loop towards a constant
environment (external scores) and the scores within the loop itself
-(internal scores).</li>
-<li>Most scores based on pairwise interactions are now pairwise decomposable.</li>
-<li>Disconnected loops at several locations can be scored at once.</li>
-<li>Avoid the usage of the DSSP executable and use the OpenStructure internal
-secondary structure assignment instead.</li>
-<li>Allow to decide whether the CB atom belongs to the actual rotamer or to the
+(internal scores).</p></li>
+<li><p>Most scores based on pairwise interactions are now pairwise decomposable.</p></li>
+<li><p>Disconnected loops at several locations can be scored at once.</p></li>
+<li><p>Avoid the usage of the DSSP executable and use the OpenStructure internal
+secondary structure assignment instead.</p></li>
+<li><p>Allow to decide whether the CB atom belongs to the actual rotamer or to the
constant frame in sidechain optimization. This can be useful in design
questions, where the identity of a rotamer is not given and you want to
-allow glycine or alanine.</li>
-<li>The naming of the entries in the StructureDB is not strictly limited to
-4 letter codes anymore, arbitrary strings can be used instead.</li>
-<li>Adding coordinates to the StructureDB does not require external tools anymore
-(msms, dssp etc.), internal implementations are used instead.</li>
-<li>The data that is stored in a StructureDB can be controlled at initialization,
-everything except the sequence and the actual coordinates is optional.</li>
-<li>Entries in the StructureDB can be removed again.</li>
-<li>Allow to search positions of arbitrary copies in DynamicSpatialOrganizer
-by providing RT operators.</li>
-<li>Several minor bug fixes, improvements, and speed-ups</li>
+allow glycine or alanine.</p></li>
+<li><p>The naming of the entries in the StructureDB is not strictly limited to
+4 letter codes anymore, arbitrary strings can be used instead.</p></li>
+<li><p>Adding coordinates to the StructureDB does not require external tools anymore
+(msms, dssp etc.), internal implementations are used instead.</p></li>
+<li><p>The data that is stored in a StructureDB can be controlled at initialization,
+everything except the sequence and the actual coordinates is optional.</p></li>
+<li><p>Entries in the StructureDB can be removed again.</p></li>
+<li><p>Allow to search positions of arbitrary copies in DynamicSpatialOrganizer
+by providing RT operators.</p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
</ul>
</div>
<div class="section" id="release-1-1-0">
<h2>Release 1.1.0<a class="headerlink" href="#release-1-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li>Updated dependencies: need Eigen 3.3.0 and OST 1.7</li>
-<li>Changes in modelling pipeline: remove clashing loop candidates early, new
+<li><p>Updated dependencies: need Eigen 3.3.0 and OST 1.7</p></li>
+<li><p>Changes in modelling pipeline: remove clashing loop candidates early, new
scores using sequence / structure profiles, new scoring weights, subrotamer
-optimization to reduce ring punches, and improved handling of ligands</li>
-<li>Improved build-model action to generate oligomeric models, input multiple
-files, and allow for residue offsets into structure files</li>
-<li>Improved computational runtime of relevant operations in pipeline (CCD,
+optimization to reduce ring punches, and improved handling of ligands</p></li>
+<li><p>Improved build-model action to generate oligomeric models, input multiple
+files, and allow for residue offsets into structure files</p></li>
+<li><p>Improved computational runtime of relevant operations in pipeline (CCD,
scorers, backbone list operations), superpositions and loop candidate
-clustering</li>
-<li>High-level functionality moved consistently to modelling module</li>
-<li>New modelling algorithms: rigid blocks to compare structures and improved
-fragment sampling for de novo modelling</li>
-<li>New rotamer graph solvers for sidechains: AStar and Monte Carlo</li>
-<li>Refactored backbone scoring to simplify extensions</li>
-<li>Added all atom scoring with possibilities to reconstruct sidechains for
-selected loops, reconstruct hydrogens and minimize energy with MM</li>
-<li>Refactored backbone list to speed it up</li>
-<li>Added runtime profiling for developers</li>
-<li>Several minor bug fixes, improvements, and speed-ups</li>
+clustering</p></li>
+<li><p>High-level functionality moved consistently to modelling module</p></li>
+<li><p>New modelling algorithms: rigid blocks to compare structures and improved
+fragment sampling for de novo modelling</p></li>
+<li><p>New rotamer graph solvers for sidechains: AStar and Monte Carlo</p></li>
+<li><p>Refactored backbone scoring to simplify extensions</p></li>
+<li><p>Added all atom scoring with possibilities to reconstruct sidechains for
+selected loops, reconstruct hydrogens and minimize energy with MM</p></li>
+<li><p>Refactored backbone list to speed it up</p></li>
+<li><p>Added runtime profiling for developers</p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
</ul>
</div>
<div class="section" id="release-1-0">
<h2>Release 1.0<a class="headerlink" href="#release-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li>Initial release of ProMod3 for use in productive instances of SMNG</li>
+<li><p>Initial release of ProMod3 for use in productive instances of SMNG</p></li>
</ul>
</div>
</div>
@@ -176,19 +177,26 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Changelog</a><ul>
-<li><a class="reference internal" href="#release-3-0-0">Release 3.0.0</a></li>
-<li><a class="reference internal" href="#release-2-1-0">Release 2.1.0</a></li>
-<li><a class="reference internal" href="#release-2-0-0">Release 2.0.0</a></li>
-<li><a class="reference internal" href="#release-1-3-0">Release 1.3.0</a></li>
-<li><a class="reference internal" href="#release-1-2-0">Release 1.2.0</a></li>
-<li><a class="reference internal" href="#release-1-1-0">Release 1.1.0</a></li>
-<li><a class="reference internal" href="#release-1-0">Release 1.0</a></li>
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
</ul>
-</li>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -197,23 +205,24 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/changelog.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -222,11 +231,11 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/changelog.txt"
+ <a href="_sources/changelog.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index a428cfebdfbcbaa6ae8fb92b90055a842119c8b5..6befa7a6af0daf22f5b8f958843e3dfbf236553f 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>ProMod3‘s Share Of CMake — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>ProMod3’s Share Of CMake — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
<link rel="prev" title="test_actions - Testing Actions" href="../actions/index_dev.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,40 +34,40 @@
<div class="body" role="main">
<div class="section" id="project-s-share-of-cmake">
-<span id="pm3-cmake-doc"></span><h1>ProMod3‘s Share Of CMake<a class="headerlink" href="#project-s-share-of-cmake" title="Permalink to this headline">¶</a></h1>
+<span id="pm3-cmake-doc"></span><h1>ProMod3’s Share Of CMake<a class="headerlink" href="#project-s-share-of-cmake" title="Permalink to this headline">¶</a></h1>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
-<p>This section describes the set of ProMod3‘s own set of CMake functions (or
-macros) fed from the <code class="file docutils literal"><span class="pre">cmake_support</span></code> directory. Those could be easily put
+<p>This section describes the set of ProMod3’s own set of CMake functions (or
+macros) fed from the <code class="file docutils literal notranslate"><span class="pre">cmake_support</span></code> directory. Those could be easily put
into three categories of varying relevance for you:</p>
<ol class="arabic simple">
-<li>Functions used to integrate your contribution into ProMod3. Its all about
+<li><p>Functions used to integrate your contribution into ProMod3. Its all about
adding files to the documentation, declaring unit tests and code management.
-Almost all of them have their home in the file <code class="file docutils literal"><span class="pre">PROMOD3.cmake</span></code>.</li>
-<li>Then there is a set of functions needed to set up CMake itself. Those are
+Almost all of them have their home in the file <code class="file docutils literal notranslate"><span class="pre">PROMOD3.cmake</span></code>.</p></li>
+<li><p>Then there is a set of functions needed to set up CMake itself. Those are
little helpers to find tools, external packages and such. These are found in
-<code class="file docutils literal"><span class="pre">Find<DEPENDENCY>.cmake</span></code> files.</li>
-<li>The last and probably least relevant category for you is also to be found in
-<code class="file docutils literal"><span class="pre">PROMOD3.cmake</span></code>. There is a set of functions used to define more
+<code class="file docutils literal notranslate"><span class="pre">Find<DEPENDENCY>.cmake</span></code> files.</p></li>
+<li><p>The last and probably least relevant category for you is also to be found in
+<code class="file docutils literal notranslate"><span class="pre">PROMOD3.cmake</span></code>. There is a set of functions used to define more
CMake functionality. You only need to consider those if you dare to extend
-this set up.</li>
+this set up.</p></li>
</ol>
<p>Best practices for using our home-brew CMake functions are found in the
-various <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> files in the project’s directory tree.</p>
+various <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code> files in the project’s directory tree.</p>
</div>
<div class="section" id="functions-for-module-action-maintenance">
<h2>Functions For Module/ Action Maintenance<a class="headerlink" href="#functions-for-module-action-maintenance" title="Permalink to this headline">¶</a></h2>
<div class="section" id="module-definition">
<h3>Module definition<a class="headerlink" href="#module-definition" title="Permalink to this headline">¶</a></h3>
-<p>Default dependencies in a module <code class="docutils literal"><span class="pre">NAME</span></code>:</p>
+<p>Default dependencies in a module <code class="docutils literal notranslate"><span class="pre">NAME</span></code>:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">_NAME</span></code> depends on <code class="docutils literal"><span class="pre">NAME_pymod</span></code> and <code class="docutils literal"><span class="pre">promod3_NAME</span></code> (if that exists)</li>
-<li><code class="docutils literal"><span class="pre">promod3_NAME</span></code> depends on <code class="docutils literal"><span class="pre">promod3_NAME_headers</span></code></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">_NAME</span></code> depends on <code class="docutils literal notranslate"><span class="pre">NAME_pymod</span></code> and <code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code> (if that exists)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code> depends on <code class="docutils literal notranslate"><span class="pre">promod3_NAME_headers</span></code></p></li>
</ul>
<dl class="command">
<dt id="command:module">
-<code class="descname">module</code><a class="headerlink" href="#command:module" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nf">module(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
+<code class="sig-name descname">module</code><a class="headerlink" href="#command:module" title="Permalink to this definition">¶</a></dt>
+<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">module(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">SOURCES</span><span class="w"> </span><span class="nb">source1</span><span class="w"> </span><span class="nb">source2</span><span class="w"></span>
<span class="w"> </span><span class="no">HEADERS</span><span class="w"> </span><span class="nb">header1</span><span class="w"> </span><span class="nb">header2</span><span class="w"> </span><span class="p">[</span><span class="no">IN_DIR</span><span class="w"> </span><span class="nb">dir</span><span class="p">]</span><span class="w"></span>
<span class="w"> </span><span class="p">[</span><span class="nb">header3</span><span class="w"> </span><span class="nb">header4</span><span class="w"> </span><span class="p">[</span><span class="no">IN_DIR</span><span class="w"> </span><span class="nb">dir</span><span class="p">]]</span><span class="w"></span>
@@ -91,38 +77,38 @@ various <code class="file docutils literal"><span class="pre">CMakeLists.txt</sp
</pre></div>
</div>
<p>Define a ProMod3 module from a set of C++ files. This will define the
-following make targets (where <code class="docutils literal"><span class="pre">NAME</span></code> is the provided module name):</p>
+following make targets (where <code class="docutils literal notranslate"><span class="pre">NAME</span></code> is the provided module name):</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">promod3_NAME</span></code>: builds library <code class="file docutils literal"><span class="pre">libpromod3_NAME</span></code></li>
-<li><code class="docutils literal"><span class="pre">promod3_NAME_headers</span></code>: copies all header files</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code>: builds library <code class="file docutils literal notranslate"><span class="pre">libpromod3_NAME</span></code></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">promod3_NAME_headers</span></code>: copies all header files</p></li>
</ul>
<p>The parameters are:</p>
-<dl class="docutils">
-<dt><code class="docutils literal"><span class="pre">NAME</span></code></dt>
-<dd>Specify the name of the module.</dd>
-<dt><code class="docutils literal"><span class="pre">SOURCES</span></code></dt>
-<dd>Set of C++ source files to be compiled.</dd>
-<dt><code class="docutils literal"><span class="pre">HEADERS</span></code></dt>
-<dd>Set of C++ header files to be copied. If the headers are located in
+<dl class="simple">
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify the name of the module.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">SOURCES</span></code></dt><dd><p>Set of C++ source files to be compiled.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">HEADERS</span></code></dt><dd><p>Set of C++ header files to be copied. If the headers are located in
a different directory than the current one, you must group them by directory
-and provide the directory name <code class="docutils literal"><span class="pre">dir</span></code> with <code class="docutils literal"><span class="pre">IN_DIR</span> <span class="pre">dir</span></code> after listing the
-header files in said directory.</dd>
-<dt><code class="docutils literal"><span class="pre">DEPENDS_ON</span></code></dt>
-<dd>Add dependencies on other targets (e.g. <code class="docutils literal"><span class="pre">promod3_MOD</span></code> for another
-ProMod3 module).</dd>
-<dt><code class="docutils literal"><span class="pre">HEADER_OUTPUT_DIR</span></code></dt>
-<dd>Define alternative folder to which to copy header files. Default is
-<code class="file docutils literal"><span class="pre">promod3/NAME</span></code>.</dd>
-<dt><code class="docutils literal"><span class="pre">LINK</span></code></dt>
-<dd>Add dependencies to external libraries. You may use some predefines set of
-libraries here, such as <code class="docutils literal"><span class="pre">${OST_LIBRARIES}</span></code> and <code class="docutils literal"><span class="pre">${BOOST_LIBRARIES}</span></code>.</dd>
+and provide the directory name <code class="docutils literal notranslate"><span class="pre">dir</span></code> with <code class="docutils literal notranslate"><span class="pre">IN_DIR</span> <span class="pre">dir</span></code> after listing the
+header files in said directory.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DEPENDS_ON</span></code></dt><dd><p>Add dependencies on other targets (e.g. <code class="docutils literal notranslate"><span class="pre">promod3_MOD</span></code> for another
+ProMod3 module).</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">HEADER_OUTPUT_DIR</span></code></dt><dd><p>Define alternative folder to which to copy header files. Default is
+<code class="file docutils literal notranslate"><span class="pre">promod3/NAME</span></code>.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">LINK</span></code></dt><dd><p>Add dependencies to external libraries. You may use some predefines set of
+libraries here, such as <code class="docutils literal notranslate"><span class="pre">${OST_LIBRARIES}</span></code> and <code class="docutils literal notranslate"><span class="pre">${BOOST_LIBRARIES}</span></code>.</p>
+</dd>
</dl>
</dd></dl>
<dl class="command">
<dt id="command:pymod">
-<code class="descname">pymod</code><a class="headerlink" href="#command:pymod" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nf">pymod(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
+<code class="sig-name descname">pymod</code><a class="headerlink" href="#command:pymod" title="Permalink to this definition">¶</a></dt>
+<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">pymod(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">CPP</span><span class="w"> </span><span class="nb">source1</span><span class="w"> </span><span class="nb">source2</span><span class="w"></span>
<span class="w"> </span><span class="no">PY</span><span class="w"> </span><span class="nb">source</span><span class="w"> </span><span class="nb">source2</span><span class="w"> </span><span class="p">[</span><span class="no">IN_DIR</span><span class="w"> </span><span class="nb">dir</span><span class="p">]</span><span class="w"></span>
<span class="w"> </span><span class="p">[</span><span class="nb">source3</span><span class="w"> </span><span class="nb">source4</span><span class="w"> </span><span class="p">[</span><span class="no">IN_DIR</span><span class="w"> </span><span class="nb">dir</span><span class="p">]]</span><span class="w"></span>
@@ -134,56 +120,55 @@ libraries here, such as <code class="docutils literal"><span class="pre">${OST_L
</div>
<p>Define the Python interface of a ProMod3 module from a set of C++
wrappers and/or Python files. This will define the following make targets
-(where <code class="docutils literal"><span class="pre">NAME</span></code> is the provided module name):</p>
+(where <code class="docutils literal notranslate"><span class="pre">NAME</span></code> is the provided module name):</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">_NAME</span></code>: builds library <code class="file docutils literal"><span class="pre">_NAME</span></code> for Python wrapper around C++</li>
-<li><code class="docutils literal"><span class="pre">NAME_pymod</span></code>: copies (and/or translates) all Python files</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">_NAME</span></code>: builds library <code class="file docutils literal notranslate"><span class="pre">_NAME</span></code> for Python wrapper around C++</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">NAME_pymod</span></code>: copies (and/or translates) all Python files</p></li>
</ul>
<p>The parameters are:</p>
-<dl class="docutils">
-<dt><code class="docutils literal"><span class="pre">NAME</span></code></dt>
-<dd>Specify the name of the module.</dd>
-<dt><code class="docutils literal"><span class="pre">CPP</span></code></dt>
-<dd>Set of C++ source files to be compiled.</dd>
-<dt><code class="docutils literal"><span class="pre">PY</span></code></dt>
-<dd><p class="first">Set of Python source files to be copied. If the files are located in
+<dl>
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify the name of the module.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">CPP</span></code></dt><dd><p>Set of C++ source files to be compiled.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">PY</span></code></dt><dd><p>Set of Python source files to be copied. If the files are located in
a different directory than the current one, you must group them by directory
-and provide the directory name <code class="docutils literal"><span class="pre">dir</span></code> with <code class="docutils literal"><span class="pre">IN_DIR</span> <span class="pre">dir</span></code> after listing the
+and provide the directory name <code class="docutils literal notranslate"><span class="pre">dir</span></code> with <code class="docutils literal notranslate"><span class="pre">IN_DIR</span> <span class="pre">dir</span></code> after listing the
header files in said directory.</p>
-<p class="last">If a Python source file needs to be translated by CMake, provide the
-dictionary after putting <code class="docutils literal"><span class="pre">TRANSLATE</span></code>. This assumes a <code class="docutils literal"><span class="pre"><FILE>.py.in</span></code> for
-<code class="docutils literal"><span class="pre"><FILE>.py</span></code>. <code class="docutils literal"><span class="pre">END_TRANSLATE</span></code> marks the end of the translation
+<p>If a Python source file needs to be translated by CMake, provide the
+dictionary after putting <code class="docutils literal notranslate"><span class="pre">TRANSLATE</span></code>. This assumes a <code class="docutils literal notranslate"><span class="pre"><FILE>.py.in</span></code> for
+<code class="docutils literal notranslate"><span class="pre"><FILE>.py</span></code>. <code class="docutils literal notranslate"><span class="pre">END_TRANSLATE</span></code> marks the end of the translation
dictionary.</p>
</dd>
-<dt><code class="docutils literal"><span class="pre">OUTPUT_DIR</span></code></dt>
-<dd>Define alternative folder (within Python tree) to place python files.
-Default is <code class="file docutils literal"><span class="pre">promod3/NAME</span></code>.</dd>
-<dt><code class="docutils literal"><span class="pre">DEPENDS_ON</span></code></dt>
-<dd>Add dependencies on other targets (e.g. <code class="docutils literal"><span class="pre">promod3_MOD</span></code> for another
-ProMod3 module).</dd>
-<dt><code class="docutils literal"><span class="pre">NEED_CONFIG_HEADER</span></code></dt>
-<dd>Makes the module depending on the config_header target, which provides the
-headers in the <code class="file docutils literal"><span class="pre">config</span></code> directory.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">OUTPUT_DIR</span></code></dt><dd><p>Define alternative folder (within Python tree) to place python files.
+Default is <code class="file docutils literal notranslate"><span class="pre">promod3/NAME</span></code>.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DEPENDS_ON</span></code></dt><dd><p>Add dependencies on other targets (e.g. <code class="docutils literal notranslate"><span class="pre">promod3_MOD</span></code> for another
+ProMod3 module).</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">NEED_CONFIG_HEADER</span></code></dt><dd><p>Makes the module depending on the config_header target, which provides the
+headers in the <code class="file docutils literal notranslate"><span class="pre">config</span></code> directory.</p>
+</dd>
</dl>
</dd></dl>
<dl class="command">
<dt id="command:convert_module_data">
-<code class="descname">convert_module_data</code><a class="headerlink" href="#command:convert_module_data" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nf">convert_module_data(</span><span class="no">MODULE</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
+<code class="sig-name descname">convert_module_data</code><a class="headerlink" href="#command:convert_module_data" title="Permalink to this definition">¶</a></dt>
+<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">convert_module_data(</span><span class="no">MODULE</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">FILE</span><span class="w"> </span><span class="nb">file</span><span class="w"></span>
<span class="w"> </span><span class="no">SCRIPT</span><span class="w"> </span><span class="nb">script</span><span class="w"></span>
<span class="w"> </span><span class="p">[</span><span class="no">ARGS</span><span class="w"> </span><span class="nb">args</span><span class="p">]</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</div>
<p>Use a Python script to convert a portable binary file to a non-portable one.
-Calls <code class="docutils literal"><span class="pre">python</span> <span class="pre">SCRIPT</span> <span class="pre">in_path</span> <span class="pre">out_path</span> <span class="pre">ARGS</span></code> (with access to OST and
+Calls <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">SCRIPT</span> <span class="pre">in_path</span> <span class="pre">out_path</span> <span class="pre">ARGS</span></code> (with access to OST and
ProMod3),
-where <code class="docutils literal"><span class="pre">in_path</span></code> = <code class="file docutils literal"><span class="pre">portable_FILE</span></code>
-(within path of current <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code>)
-and <code class="docutils literal"><span class="pre">out_path</span></code> = <code class="file docutils literal"><span class="pre">share/promod3/MODULE_data/FILE</span></code>
-(within the <code class="file docutils literal"><span class="pre">stage</span></code> directory).
-If given, <code class="docutils literal"><span class="pre">args</span></code> can also be multiple arguments (must be put in “” then).</p>
+where <code class="docutils literal notranslate"><span class="pre">in_path</span></code> = <code class="file docutils literal notranslate"><span class="pre">portable_FILE</span></code>
+(within path of current <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>)
+and <code class="docutils literal notranslate"><span class="pre">out_path</span></code> = <code class="file docutils literal notranslate"><span class="pre">share/promod3/MODULE_data/FILE</span></code>
+(within the <code class="file docutils literal notranslate"><span class="pre">stage</span></code> directory).
+If given, <code class="docutils literal notranslate"><span class="pre">args</span></code> can also be multiple arguments (must be put in “” then).</p>
</dd></dl>
</div>
@@ -191,8 +176,8 @@ If given, <code class="docutils literal"><span class="pre">args</span></code> ca
<h3>Unit Tests<a class="headerlink" href="#unit-tests" title="Permalink to this headline">¶</a></h3>
<dl class="command">
<dt id="command:promod3_unittest">
-<code class="descname">promod3_unittest</code><a class="headerlink" href="#command:promod3_unittest" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nf">promod3_unittest(</span><span class="no">MODULE</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
+<code class="sig-name descname">promod3_unittest</code><a class="headerlink" href="#command:promod3_unittest" title="Permalink to this definition">¶</a></dt>
+<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">promod3_unittest(</span><span class="no">MODULE</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">SOURCES</span><span class="w"> </span><span class="nb">source1</span><span class="w"> </span><span class="p">[</span><span class="nb">source2</span><span class="w"> </span><span class="p">...]</span><span class="w"></span>
<span class="w"> </span><span class="p">[</span><span class="no">LINK</span><span class="w"> </span><span class="na">library1/</span><span class="w"> </span><span class="nb">linker</span><span class="w"> </span><span class="nb">flag1</span><span class="w"> </span><span class="p">[</span><span class="na">library2/</span><span class="w"> </span><span class="nb">linker</span><span class="w"> </span><span class="nb">flag2</span><span class="w"> </span><span class="p">...]]</span><span class="w"></span>
<span class="w"> </span><span class="p">[</span><span class="no">DATA</span><span class="w"> </span><span class="nb">data1</span><span class="w"> </span><span class="p">[</span><span class="nb">data2</span><span class="w"> </span><span class="p">...]]</span><span class="w"></span>
@@ -202,43 +187,43 @@ If given, <code class="docutils literal"><span class="pre">args</span></code> ca
</div>
<p>Add unit tests to ProMod3. Unit tests should go in module-wise so all
source files containing test code go by a single call of
-<span class="target" id="index-0-command:promod3_unittest"></span><a class="reference internal" href="#command:promod3_unittest" title="promod3_unittest"><code class="xref cmake cmake-command docutils literal"><span class="pre">promod3_unittest()</span></code></a>. Test data also needs to be registered
+<span class="target" id="index-0-command:promod3_unittest"></span><a class="reference internal" href="#command:promod3_unittest" title="promod3_unittest"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">promod3_unittest()</span></code></a>. Test data also needs to be registered
here, since it will be copied to the build directory. That way, inside your
code you do not need to set a special path to your data. Additionally, since
it is out of the source tree, you may change test data as you like, without
-the Git repository noticing. Calling <span class="target" id="index-1-command:promod3_unittest"></span><a class="reference internal" href="#command:promod3_unittest" title="promod3_unittest"><code class="xref cmake cmake-command docutils literal"><span class="pre">promod3_unittest()</span></code></a> will
-create a set of certain <code class="docutils literal"><span class="pre">make</span></code> targets for you, beside feeding <code class="docutils literal"><span class="pre">codetest</span></code>.</p>
+the Git repository noticing. Calling <span class="target" id="index-1-command:promod3_unittest"></span><a class="reference internal" href="#command:promod3_unittest" title="promod3_unittest"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">promod3_unittest()</span></code></a> will
+create a set of certain <code class="docutils literal notranslate"><span class="pre">make</span></code> targets for you, beside feeding <code class="docutils literal notranslate"><span class="pre">codetest</span></code>.</p>
<p>The parameters are:</p>
-<dl class="docutils">
-<dt><code class="docutils literal"><span class="pre">MODULE</span></code></dt>
-<dd>Specify the name of the module these tests are made for. Needs to be set,
-needs to be a single word. Ends up in <code class="docutils literal"><span class="pre">make</span> <span class="pre">help</span></code> as a prefix, nothing
-will break if it does not match the name of any existing module.</dd>
-<dt><code class="docutils literal"><span class="pre">SOURCES</span></code></dt>
-<dd>Describe a set of files hosting unit test code here. If its a wild mix of
+<dl class="simple">
+<dt><code class="docutils literal notranslate"><span class="pre">MODULE</span></code></dt><dd><p>Specify the name of the module these tests are made for. Needs to be set,
+needs to be a single word. Ends up in <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">help</span></code> as a prefix, nothing
+will break if it does not match the name of any existing module.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">SOURCES</span></code></dt><dd><p>Describe a set of files hosting unit test code here. If its a wild mix of
C++ and Python files does not matter, CMake will sort this out for
-you. But the programming language makes a difference for the <code class="docutils literal"><span class="pre">make</span></code>
+you. But the programming language makes a difference for the <code class="docutils literal notranslate"><span class="pre">make</span></code>
targets produced. C++ files will all be gathered in a single
-<code class="docutils literal"><span class="pre">test_suite_<MODULE>_run</span></code> target (there is also a <code class="docutils literal"><span class="pre">_xml</span></code> target but
-this is for tools for automated testing). Python code works on a ‘one
-target per file’ basis. So <code class="file docutils literal"><span class="pre">test_foo.py</span></code> will have own target
-<code class="docutils literal"><span class="pre">test_foo.py_run</span></code>.</dd>
-<dt><code class="docutils literal"><span class="pre">LINK</span></code></dt>
-<dd>Add additional libraries and linker flags for C++ source files. Has no
-effect on Python tests.</dd>
-<dt><code class="docutils literal"><span class="pre">DATA</span></code></dt>
-<dd>Define test data. Instead of giving data directories its own
-<code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code>, those files are added here. Usually located
-somewhere in a dedicated <code class="file docutils literal"><span class="pre">data</span></code> subtree, files need to be given with
+<code class="docutils literal notranslate"><span class="pre">test_suite_<MODULE>_run</span></code> target (there is also a <code class="docutils literal notranslate"><span class="pre">_xml</span></code> target but
+this is for tools for automated testing). Python code works on a ‘one
+target per file’ basis. So <code class="file docutils literal notranslate"><span class="pre">test_foo.py</span></code> will have own target
+<code class="docutils literal notranslate"><span class="pre">test_foo.py_run</span></code>.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">LINK</span></code></dt><dd><p>Add additional libraries and linker flags for C++ source files. Has no
+effect on Python tests.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DATA</span></code></dt><dd><p>Define test data. Instead of giving data directories its own
+<code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>, those files are added here. Usually located
+somewhere in a dedicated <code class="file docutils literal notranslate"><span class="pre">data</span></code> subtree, files need to be given with
a path relative to this directory. That path will then be created in the
-build directory.</dd>
-<dt><code class="docutils literal"><span class="pre">TARGET</span></code></dt>
-<dd>This defines an additional dependency for the unit test. That is, before
-running this unit test, this target will be built.</dd>
-<dt><code class="docutils literal"><span class="pre">BASE_TARGET</span></code></dt>
-<dd>This defines an alternative base target to which to add this unit test.
+build directory.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">TARGET</span></code></dt><dd><p>This defines an additional dependency for the unit test. That is, before
+running this unit test, this target will be built.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">BASE_TARGET</span></code></dt><dd><p>This defines an alternative base target to which to add this unit test.
By default all unit tests are registered to be executed with the
-<code class="docutils literal"><span class="pre">codetest</span></code> target. This can be overridden by using this argument.</dd>
+<code class="docutils literal notranslate"><span class="pre">codetest</span></code> target. This can be overridden by using this argument.</p>
+</dd>
</dl>
</dd></dl>
@@ -247,50 +232,50 @@ By default all unit tests are registered to be executed with the
<h3>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h3>
<dl class="command">
<dt id="command:add_doc_source">
-<code class="descname">add_doc_source</code><a class="headerlink" href="#command:add_doc_source" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nf">add_doc_source(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
+<code class="sig-name descname">add_doc_source</code><a class="headerlink" href="#command:add_doc_source" title="Permalink to this definition">¶</a></dt>
+<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">add_doc_source(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">RST</span><span class="w"> </span><span class="nb">rst1</span><span class="w"> </span><span class="p">[</span><span class="nb">rst2...</span><span class="p">]</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</div>
<p>Add reStructuredText sources for the doc build system. This is most preferable
-used in <code class="file docutils literal"><span class="pre">doc</span></code> directories for keeping the documentation sorted per
-module. This does not create any <code class="docutils literal"><span class="pre">make</span></code> targets. Lists filled here will all
-be evaluated in the <code class="file docutils literal"><span class="pre">doc/CMakeLists.txt</span></code> of the repository root.</p>
+used in <code class="file docutils literal notranslate"><span class="pre">doc</span></code> directories for keeping the documentation sorted per
+module. This does not create any <code class="docutils literal notranslate"><span class="pre">make</span></code> targets. Lists filled here will all
+be evaluated in the <code class="file docutils literal notranslate"><span class="pre">doc/CMakeLists.txt</span></code> of the repository root.</p>
<p>The parameters are:</p>
-<dl class="docutils">
-<dt><code class="docutils literal"><span class="pre">NAME</span></code></dt>
-<dd>Specify the name of the module this branch of documentation belongs to.
+<dl class="simple">
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify the name of the module this branch of documentation belongs to.
Needs to be set, needs to be a single word. Using module names is best
practice, while nothing will break if it does not refer to an existing one.
-You will find a directory in <code class="file docutils literal"><span class="pre">doc/source</span></code> with that name in the build
-root.</dd>
-<dt><code class="docutils literal"><span class="pre">RST</span></code></dt>
-<dd>Describe a set of files containing the documentation. Feed it a single file
-name or a CMake list.</dd>
+You will find a directory in <code class="file docutils literal notranslate"><span class="pre">doc/source</span></code> with that name in the build
+root.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">RST</span></code></dt><dd><p>Describe a set of files containing the documentation. Feed it a single file
+name or a CMake list.</p>
+</dd>
</dl>
</dd></dl>
<dl class="command">
<dt id="command:add_doc_dependency">
-<code class="descname">add_doc_dependency</code><a class="headerlink" href="#command:add_doc_dependency" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nf">add_doc_dependency(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
+<code class="sig-name descname">add_doc_dependency</code><a class="headerlink" href="#command:add_doc_dependency" title="Permalink to this definition">¶</a></dt>
+<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">add_doc_dependency(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">DEP</span><span class="w"> </span><span class="nb">dependency1</span><span class="w"> </span><span class="p">[</span><span class="nb">dependency2...</span><span class="p">]</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</div>
<p>Add a dependency to the doc build system. For an existing name, add some
dependencies when it comes to building documentation. Mostly for internal use.</p>
<p>The parameters are:</p>
-<dl class="docutils">
-<dt><code class="docutils literal"><span class="pre">NAME</span></code></dt>
-<dd>Specify a name the dependencies belong to. This name needs to be already
+<dl class="simple">
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify a name the dependencies belong to. This name needs to be already
known in the doc build system. Names of Python modules are good, otherwise
-names introduced by <span class="target" id="index-0-command:add_doc_source"></span><a class="reference internal" href="#command:add_doc_source" title="add_doc_source"><code class="xref cmake cmake-command docutils literal"><span class="pre">add_doc_source()</span></code></a> work well. Dependencies
+names introduced by <span class="target" id="index-0-command:add_doc_source"></span><a class="reference internal" href="#command:add_doc_source" title="add_doc_source"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">add_doc_source()</span></code></a> work well. Dependencies
will be create for all reStructuredText files listed by
-<span class="target" id="index-1-command:add_doc_source"></span><a class="reference internal" href="#command:add_doc_source" title="add_doc_source"><code class="xref cmake cmake-command docutils literal"><span class="pre">add_doc_source()</span></code></a> under this name and for all <code class="docutils literal"><span class="pre">make</span></code>
-targets related to the documentation.</dd>
-<dt><code class="docutils literal"><span class="pre">DEP</span></code></dt>
-<dd>Hand over a dependency here or a CMake list. Files work, if given with
-absolute path.</dd>
+<span class="target" id="index-1-command:add_doc_source"></span><a class="reference internal" href="#command:add_doc_source" title="add_doc_source"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">add_doc_source()</span></code></a> under this name and for all <code class="docutils literal notranslate"><span class="pre">make</span></code>
+targets related to the documentation.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DEP</span></code></dt><dd><p>Hand over a dependency here or a CMake list. Files work, if given with
+absolute path.</p>
+</dd>
</dl>
</dd></dl>
@@ -299,25 +284,25 @@ absolute path.</dd>
<h3>Actions<a class="headerlink" href="#actions" title="Permalink to this headline">¶</a></h3>
<dl class="command">
<dt id="command:pm_action">
-<code class="descname">pm_action</code><a class="headerlink" href="#command:pm_action" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nf">pm_action(</span><span class="no">ACTION</span><span class="w"> </span><span class="nb">action-script</span><span class="w"></span>
+<code class="sig-name descname">pm_action</code><a class="headerlink" href="#command:pm_action" title="Permalink to this definition">¶</a></dt>
+<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">pm_action(</span><span class="no">ACTION</span><span class="w"> </span><span class="nb">action-script</span><span class="w"></span>
<span class="w"> </span><span class="no">TARGET</span><span class="w"> </span><span class="nb">target</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</div>
-<p>Add an action to ProMod3. Actions are scripts called by the <code class="docutils literal"><span class="pre">pm</span></code> launcher
-and should all live in the <code class="file docutils literal"><span class="pre">actions</span></code> directory as executable files.
+<p>Add an action to ProMod3. Actions are scripts called by the <code class="docutils literal notranslate"><span class="pre">pm</span></code> launcher
+and should all live in the <code class="file docutils literal notranslate"><span class="pre">actions</span></code> directory as executable files.
Adding an action means connecting its file with the given target to be copied
-to the <code class="file docutils literal"><span class="pre">libexec</span></code> directory. No dedicated <code class="docutils literal"><span class="pre">make</span></code> target will be
+to the <code class="file docutils literal notranslate"><span class="pre">libexec</span></code> directory. No dedicated <code class="docutils literal notranslate"><span class="pre">make</span></code> target will be
created.</p>
<p>The parameters are:</p>
-<dl class="docutils">
-<dt><code class="docutils literal"><span class="pre">ACTION</span></code></dt>
-<dd>Name of the action to be added. Should start with <code class="file docutils literal"><span class="pre">pm-</span></code>. Needs to be
+<dl class="simple">
+<dt><code class="docutils literal notranslate"><span class="pre">ACTION</span></code></dt><dd><p>Name of the action to be added. Should start with <code class="file docutils literal notranslate"><span class="pre">pm-</span></code>. Needs to be
an existing file in the same directory as the invoking
-<code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code>.</dd>
-<dt><code class="docutils literal"><span class="pre">TARGET</span></code></dt>
-<dd>Provide a <code class="docutils literal"><span class="pre">make</span></code> target to trigger copying the action’s script file. The
-target has to be created <strong>before</strong> any action may be attached to it.</dd>
+<code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>.</p>
+</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">TARGET</span></code></dt><dd><p>Provide a <code class="docutils literal notranslate"><span class="pre">make</span></code> target to trigger copying the action’s script file. The
+target has to be created <strong>before</strong> any action may be attached to it.</p>
+</dd>
</dl>
</dd></dl>
@@ -332,48 +317,55 @@ target has to be created <strong>before</strong> any action may be attached to i
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">ProMod3‘s Share Of CMake</a><ul>
-<li><a class="reference internal" href="#introduction">Introduction</a></li>
-<li><a class="reference internal" href="#functions-for-module-action-maintenance">Functions For Module/ Action Maintenance</a><ul>
-<li><a class="reference internal" href="#module-definition">Module definition</a></li>
-<li><a class="reference internal" href="#unit-tests">Unit Tests</a></li>
-<li><a class="reference internal" href="#documentation">Documentation</a></li>
-<li><a class="reference internal" href="#actions">Actions</a></li>
-</ul>
-</li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../users.html">Users</a></li>
</ul>
-</li>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../developers.html">Documentation For Developers</a><ul>
- <li>Previous: <a href="../actions/index_dev.html" title="previous chapter"><code class="docutils literal"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
+ <li>Previous: <a href="../actions/index_dev.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
<li>Next: <a href="../portableIO.html" title="next chapter">Using Binary Files In ProMod3</a></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/cmake/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -382,11 +374,11 @@ target has to be created <strong>before</strong> any action may be attached to i
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/cmake/index.txt"
+ <a href="../_sources/cmake/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index aaf0cd3df123050f0c7a2d1603464eedf3e9a566..366b0e48a631e7c0ffece72846b7bf4233b353c1 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Docker — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Docker — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="ProMod3 and Containers" href="index.html" />
<link rel="next" title="Singularity" href="singularity.html" />
<link rel="prev" title="ProMod3 and Containers" href="index.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -50,19 +36,19 @@
<div class="section" id="docker">
<h1>Docker<a class="headerlink" href="#docker" title="Permalink to this headline">¶</a></h1>
<div class="section" id="project-s-own-docker-registry">
-<h2>ProMod3‘s Own Docker Registry<a class="headerlink" href="#project-s-own-docker-registry" title="Permalink to this headline">¶</a></h2>
+<h2>ProMod3’s Own Docker Registry<a class="headerlink" href="#project-s-own-docker-registry" title="Permalink to this headline">¶</a></h2>
<p>For the current stable release of ProMod3, its
<a class="reference external" href="https://git.scicore.unibas.ch/schwede/ProMod3">GitLab project</a> is equipped with its own
<a class="reference external" href="https://git.scicore.unibas.ch/schwede/ProMod3/container_registry">registry for Docker images</a>. There you
can explore the current tag and simply pull a ready made built:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>docker pull registry.scicore.unibas.ch/schwede/promod3:<TAG>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker pull registry.scicore.unibas.ch/schwede/promod3:<TAG>
</pre></div>
</div>
</div>
<div class="section" id="build-docker-image">
<h2>Build Docker Image<a class="headerlink" href="#build-docker-image" title="Permalink to this headline">¶</a></h2>
<p>In order to build the image:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>docker build --tag <IMAGE_NAME> -f Dockerfile <PATH_TO_DOCKERFILE_DIR>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker build --tag <IMAGE_NAME> -f Dockerfile <PATH_TO_DOCKERFILE_DIR>
</pre></div>
</div>
<p>You can chose any image name (tag) eg. promod.</p>
@@ -75,23 +61,23 @@ path. Eg. assuming that we have a struc.pdb file in /home/<USER>/pdbs dire
a script.py in /home/<USER> we could mount the /home/<USER> to /home in docker as
above by specifying -v /home/<USER>:/home. To run the script we thus need to
provide the (relative) path to the script and (relative) path to the file eg:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>docker run --rm -v /home/<USER>:/home <IMAGE_NAME> script.py <span class="se">\</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker run --rm -v /home/<USER>:/home <IMAGE_NAME> script.py <span class="se">\</span>
pdbs/struct.pdb
</pre></div>
</div>
<p>or with absolute paths:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>docker run --rm -v /home/<USER>:/home <IMAGE_NAME> /home/script.py <span class="se">\</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker run --rm -v /home/<USER>:/home <IMAGE_NAME> /home/script.py <span class="se">\</span>
/home/pdbs/struct.pdb
</pre></div>
</div>
<p>An alternative is to mount the current working directory into the docker home:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home <IMAGE_NAME> script.py pdbs/struct.pdb
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home <IMAGE_NAME> script.py pdbs/struct.pdb
</pre></div>
</div>
</div>
<div class="section" id="the-compound-library">
<span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
-<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">CompoundLib</span></code></a> is generated.
Compound libraries contain information on chemical compounds, such as their
connectivity, chemical class and one-letter-code. The compound library has
several uses, but the most important one is to provide the connectivy
@@ -114,12 +100,12 @@ The files are rather large, it is therefore recommended to download the
gzipped version.</p>
<p>After downloading the file use <strong class="program">chemdict_tool</strong> in the container to
convert the mmCIF dictionary into our internal format:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home --entrypoint chemdict_tool <IMAGE_NAME> <span class="se">\</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home --entrypoint chemdict_tool <IMAGE_NAME> <span class="se">\</span>
create components.cif.gz compounds.chemlib
</pre></div>
</div>
<p>To run a script with the upated compound library, use the -v option for mounting/overriding:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>docker run --rm -v /home/<USER>:/home <span class="se">\</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker run --rm -v /home/<USER>:/home <span class="se">\</span>
-v <COMPLIB_DIR_LOCALHOST>/compounds.chemlib:<COMPLIB_DIR_CONTAINER>/compounds.chemlib <span class="se">\</span>
<IMAGE_NAME> script.py pdbs/struct.pdb
</pre></div>
@@ -131,10 +117,10 @@ If you didnt change anything in the Dockerfile, the latter should be
/usr/local/share/openstructure</p>
<p>You can check whether the default lib is successfully overriden by looking at the
output when running a Python script with following code in the container:</p>
-<div class="highlight-python"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">promod3</span> <span class="c1"># required to setup default lib</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">promod3</span> <span class="c1"># required to setup default lib</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
<span class="n">lib</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">()</span>
-<span class="nb">print</span><span class="p">(</span><span class="n">lib</span><span class="o">.</span><span class="n">GetCreationDate</span><span class="p">())</span>
+<span class="k">print</span><span class="p">(</span><span class="n">lib</span><span class="o">.</span><span class="n">GetCreationDate</span><span class="p">())</span>
</pre></div>
</div>
</div>
@@ -147,16 +133,39 @@ output when running a Python script with following code in the container:</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Docker</a><ul>
-<li><a class="reference internal" href="#project-s-own-docker-registry">ProMod3‘s Own Docker Registry</a></li>
-<li><a class="reference internal" href="#build-docker-image">Build Docker Image</a></li>
-<li><a class="reference internal" href="#run-scripts-and-actions-with-pm-executable">Run scripts and actions with pm executable</a></li>
-<li><a class="reference internal" href="#the-compound-library">The Compound Library</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -170,23 +179,24 @@ output when running a Python script with following code in the container:</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/container/docker.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -195,11 +205,11 @@ output when running a Python script with following code in the container:</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/container/docker.txt"
+ <a href="../_sources/container/docker.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index abc61252dde1b09dcbf12ba2382bd45be0cacfbb..05ee8d6ca11dbe12a90213b4fbdd0c9b964d5246 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>ProMod3 and Containers — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>ProMod3 and Containers — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Docker" href="docker.html" />
<link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,7 +34,7 @@
<div class="body" role="main">
<div class="section" id="project-and-containers">
-<h1>ProMod3 and Containers<a class="headerlink" href="#project-and-containers" title="Permalink to this headline">¶</a></h1>
+<span id="container"></span><h1>ProMod3 and Containers<a class="headerlink" href="#project-and-containers" title="Permalink to this headline">¶</a></h1>
<p>ProMod3 offers build recipes for Docker and Singularity in
<PATH_TO_PROMOD3_CHECKOUT>/container. To avoid code duplication,
the Singularity container bootstraps from the Docker one and adds
@@ -67,7 +53,41 @@ some sugar on top.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
@@ -78,23 +98,24 @@ some sugar on top.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/container/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -103,11 +124,11 @@ some sugar on top.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/container/index.txt"
+ <a href="../_sources/container/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index 196c7eaeb7f6d728fac372aed0dd5901e294c691..e1adf82aed4a1ee6aac3a6520e44753b37e7512d 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Singularity — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Singularity — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="ProMod3 and Containers" href="index.html" />
<link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
<link rel="prev" title="Docker" href="docker.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -49,60 +35,89 @@
<div class="section" id="singularity">
<h1>Singularity<a class="headerlink" href="#singularity" title="Permalink to this headline">¶</a></h1>
-<p>We do not provide a “standalone” Singularity image, but rather bootstrap from a
+<p>We do not provide a “standalone” Singularity image, but rather bootstrap from a
Docker image.</p>
-<p>Build the image with:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo singularity build promod.img Singularity
+<p>Change to the directory containing the Singularity file
+(<PROMOD3_CHECKOUT>/container) and build the image with:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo singularity build promod.img Singularity
</pre></div>
</div>
<div class="section" id="available-apps">
<h2>Available apps<a class="headerlink" href="#available-apps" title="Permalink to this headline">¶</a></h2>
-<dl class="docutils">
-<dt>This container includes the following apps:</dt>
-<dd><ul class="first last simple">
-<li><strong>OST</strong> - OpenStructure executable</li>
-<li><strong>PM</strong> - ProMod3 executable</li>
-<li><strong>IPython</strong> - OST/ProMod3-powered iPython shell</li>
-<li><strong>Notebook</strong> - A Jupyter notebook playground with OST, ProMod3 and nglview</li>
-<li><strong>lDDT</strong> - The Local Distance Difference Test</li>
-<li><strong>Molck</strong> - Molecular checker</li>
-<li><strong>ChemdictTool</strong> - Creating or update a compound library</li>
+<dl class="simple">
+<dt>This container includes the following apps:</dt><dd><ul class="simple">
+<li><p><strong>OST</strong> - OpenStructure executable</p></li>
+<li><p><strong>PM</strong> - ProMod3 executable</p></li>
+<li><p><strong>IPython</strong> - OST/ProMod3-powered iPython shell</p></li>
+<li><p><strong>Notebook</strong> - A Jupyter notebook playground with OST, ProMod3 and nglview</p></li>
+<li><p><strong>lDDT</strong> - The Local Distance Difference Test</p></li>
+<li><p><strong>Molck</strong> - Molecular checker</p></li>
+<li><p><strong>ChemdictTool</strong> - Creating or update a compound library</p></li>
</ul>
</dd>
</dl>
<p>To see the help for each individual app run:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run-help --app <APP NAME> <PATH TO PROMOD IMAGE>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run-help --app <APP NAME> <PATH TO PROMOD IMAGE>
</pre></div>
</div>
<p>Eg.:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run-help --app PM promod.img
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run-help --app PM promod.img
</pre></div>
</div>
<p>To list all available ProMod3 modelling actions:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run --app PM promod.img <span class="nb">help</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run --app PM promod.img <span class="nb">help</span>
+</pre></div>
+</div>
+<p>So you can either run an action with:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run --app PM promod.img build-model <span class="o">[</span>options<span class="o">]</span>
+</pre></div>
+</div>
+<p>or an arbitrary Python script using OpenStructure / ProMod3 with:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run --app PM promod.img my_script.py <span class="o">[</span>options<span class="o">]</span>
+</pre></div>
+</div>
+<p>The Notebook app provides a jupyter notebook playground with OST, ProMod3, and
+nglview available. You can fire it up with:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run --app Notebook promod.img
+</pre></div>
+</div>
+<p>connect to the notebook, start a new OST kernel and test it with the following
+code snippet:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<span class="kn">import</span> <span class="nn">nglview</span>
+
+<span class="c1"># generate backbone with dihedrals of a helix and store it</span>
+<span class="n">sequence</span> <span class="o">=</span> <span class="s2">"HELLYEAH"</span>
+<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"test.pdb"</span><span class="p">)</span>
+
+<span class="c1"># display stored file</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_file</span><span class="p">(</span><span class="s2">"test.pdb"</span><span class="p">)</span>
+<span class="n">view</span>
</pre></div>
</div>
</div>
<div class="section" id="the-compound-library">
<h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
-<p>You’ll have the exact same problem with outdated compound libraries as in the
+<p>You’ll have the exact same problem with outdated compound libraries as in the
raw Docker image. You can find more information on that matter in the Docker
section of the documentation: <a class="reference internal" href="docker.html#docker-compound-lib"><span class="std std-ref">The Compound Library</span></a>.</p>
<p>The same trick of mounting an up to date compound library from the local host into
the container applies. The two relevant commands for Singularity are building
a new library and mount it.</p>
<p>Build a new library:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run --app ChemdictTool <IMAGE> create components.cif.gz <span class="se">\</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run --app ChemdictTool <IMAGE> create components.cif.gz <span class="se">\</span>
compounds.chemlib
</pre></div>
</div>
<p>Run some script with an updated compound library from localhost:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run <span class="se">\</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run <span class="se">\</span>
-B <COMPLIB_DIR_LOCALHOST>/compounds.chemlib:<COMPLIB_DIR_CONTAINER>/compounds.chemlib <span class="se">\</span>
--app PM <IMAGE> my_script.py
</pre></div>
</div>
-<p>Same as for the Docker, if you didn’t meddle with the original Dockerfile,
+<p>Same as for the Docker, if you didn’t meddle with the original Dockerfile,
<COMPLIB_DIR_CONTAINER> should be /usr/local/share/openstructure.
<COMPLIB_DIR_LOCALHOST> is the directory that contains the compound lib with the
name compounds.chemlib that you created before. Make sure that everything works
@@ -118,14 +133,39 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Singularity</a><ul>
-<li><a class="reference internal" href="#available-apps">Available apps</a></li>
-<li><a class="reference internal" href="#the-compound-library">The Compound Library</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -133,29 +173,30 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html">ProMod3 and Containers</a><ul>
<li>Previous: <a href="docker.html" title="previous chapter">Docker</a></li>
- <li>Next: <a href="../modelling/index.html" title="next chapter"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+ <li>Next: <a href="../modelling/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/container/singularity.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -164,11 +205,11 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/container/singularity.txt"
+ <a href="../_sources/container/singularity.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 39048603718cb1826aaa45aab017d9b59709d956..d9f46848eb77534aaa0d7a766ba8f5d3244ebcce 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Contributing — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Contributing — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
<link rel="prev" title="ProMod3 Setup" href="dev_setup.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -59,8 +45,8 @@ as examples and to be consistent with what you already find here.</p>
<div class="section" id="how-to-share-your-own-script">
<h2>How To Share Your Own Script<a class="headerlink" href="#how-to-share-your-own-script" title="Permalink to this headline">¶</a></h2>
<p>If you have a useful script using ProMod3 that you want to share, it should go
-as a subfolder into the <code class="file docutils literal"><span class="pre">extras/external_scripts</span></code> folder. Make sure to
-describe the use and purpose of the script in a short <code class="file docutils literal"><span class="pre">README</span></code> including
+as a subfolder into the <code class="file docutils literal notranslate"><span class="pre">extras/external_scripts</span></code> folder. Make sure to
+describe the use and purpose of the script in a short <code class="file docutils literal notranslate"><span class="pre">README</span></code> including
working commands on how to use it.</p>
</div>
<div class="section" id="how-to-start-your-own-module">
@@ -68,69 +54,69 @@ working commands on how to use it.</p>
<p>This is just a walk-through how the topics from above work together when you
start your own module. For the entry point, lets assume that you already cloned
the repository into a directory and just changed into it.</p>
-<p>All new features should take off from the <code class="docutils literal"><span class="pre">develop</span></code> branch. That way, they
+<p>All new features should take off from the <code class="docutils literal notranslate"><span class="pre">develop</span></code> branch. That way, they
work fine with all the other new fellows waiting for release right from the
beginning. Therefore you need to switch branches as a first step. Git will
tell you for which branch you went, a story of failure otherwise.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
<span class="go">Switched to branch 'develop'</span>
</pre></div>
</div>
<p>Sitting on top of the right code basis, you should just spawn your own branch
-from it. As an example, your feature will go by the name of ‘sidechain’.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout -b sidechain
+from it. As an example, your feature will go by the name of ‘sidechain’.</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout -b sidechain
<span class="go">Switched to a new branch 'sidechain'</span>
</pre></div>
</div>
<p>This time, Git should tell you about going for <strong>a new</strong> branch.</p>
<p>Before starting to create anything for real, now is the perfect moment to
install our very own Git hook to check some coding rules on commit.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
</pre></div>
</div>
<p>With that in place, changes which break our coding standards will abort any
commit.</p>
<p>Now create the directory structure where your project will live. Here is the
list of directories which are likely to be used in every project.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir -p sidechain/doc
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir -p sidechain/doc
<span class="gp">$</span> mkdir -p sidechain/pymod
<span class="gp">$</span> mkdir -p sidechain/tests
</pre></div>
</div>
-<p>If you run <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code> at this point, you will see basically nothing. That
+<p>If you run <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">status</span></code> at this point, you will see basically nothing. That
is, Git does not admire empty directories. Before you bring your module under
version control, create a couple of files which are always needed.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/pymod/__init__.py
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/pymod/__init__.py
<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">":mod:\`~promod3.sidechain\` - ProMod3 side chain optimiser"</span> <span class="se">\</span>
>> sidechain/doc/index.rst
<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">"=========================================================="</span> <span class="se">\</span>
<span class="s2">"======================"</span> >> sidechain/doc/index.rst
</pre></div>
</div>
-<p>Having an empty <code class="file docutils literal"><span class="pre">__init__.py</span></code> is perfectly fine for Python, it just
-announces a directory as a module. But a blank <code class="file docutils literal"><span class="pre">index.rst</span></code> has the chance
+<p>Having an empty <code class="file docutils literal notranslate"><span class="pre">__init__.py</span></code> is perfectly fine for Python, it just
+announces a directory as a module. But a blank <code class="file docutils literal notranslate"><span class="pre">index.rst</span></code> has the chance
to give Sphinx quite a headache so you already fill it with a headline for
your documentation.</p>
<p>For integration with <strong class="command">make</strong>, the build system needs to now about the
new module and its members. This goes for setting up new CMake files and
extending some around the directory root.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/CMakeLists.txt
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/CMakeLists.txt
<span class="gp">$</span> touch sidechain/pymod/CMakeLists.txt
<span class="gp">$</span> touch sidechain/doc/CMakeLists.txt
</pre></div>
</div>
<p>Each of those files still needs a bit of content. The simplest one comes from
-the module’s root, <code class="file docutils literal"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+the module’s root, <code class="file docutils literal notranslate"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nf">add_subdirectory(</span><span class="nb">pymod</span><span class="nf">)</span><span class="w"></span>
<span class="nf">add_subdirectory(</span><span class="nb">doc</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</td></tr></table></div>
<p>Those two directives just tell CMake to go and look in directories
-<code class="file docutils literal"><span class="pre">pymod</span></code> and <code class="file docutils literal"><span class="pre">doc</span></code> below the current path for more CMake
-configurations. The next level in <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> magic comes for the
-<code class="file docutils literal"><span class="pre">doc</span></code> directory:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<code class="file docutils literal notranslate"><span class="pre">pymod</span></code> and <code class="file docutils literal notranslate"><span class="pre">doc</span></code> below the current path for more CMake
+configurations. The next level in <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code> magic comes for the
+<code class="file docutils literal notranslate"><span class="pre">doc</span></code> directory:</p>
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
@@ -141,21 +127,21 @@ configurations. The next level in <code class="file docutils literal"><span clas
<span class="nf">add_doc_source(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">sidechain</span><span class="w"> </span><span class="no">RST</span><span class="w"> </span><span class="o">${</span><span class="nt">SIDECHAIN_RST</span><span class="o">}</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</td></tr></table></div>
-<p><code class="docutils literal"><span class="pre">add_doc_source</span></code> is our custom CMake macro to register
+<p><code class="docutils literal notranslate"><span class="pre">add_doc_source</span></code> is our custom CMake macro to register
reST files for the documentation. On running
-<strong class="command">make</strong>, those files are placed in a <code class="file docutils literal"><span class="pre">doc/source</span></code> directory tree
+<strong class="command">make</strong>, those files are placed in a <code class="file docutils literal notranslate"><span class="pre">doc/source</span></code> directory tree
within the build directory. Each new submodule in your project should be
-covered by its own documentation entity, extending the list in <code class="docutils literal"><span class="pre">RST</span></code>.
+covered by its own documentation entity, extending the list in <code class="docutils literal notranslate"><span class="pre">RST</span></code>.
Maintaining readability, its good practice to store this list in a separate
-variable, called <code class="docutils literal"><span class="pre">SIDECHAIN_RST</span></code> here.</p>
+variable, called <code class="docutils literal notranslate"><span class="pre">SIDECHAIN_RST</span></code> here.</p>
<p>For the actual code, you should keep in mind that a Python module may be
rather complex. There is for sure Python code, there could be a bit of C++
and conditional compilation. In rare cases you also want to modify the
directory structure of the package. All this has to be declared in the
-<code class="file docutils literal"><span class="pre">pymod</span></code> subtree. We cannot enumerate all specialities but there should be
+<code class="file docutils literal notranslate"><span class="pre">pymod</span></code> subtree. We cannot enumerate all specialities but there should be
a couple of examples around in this repository. Here is the most basic
-<code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code>:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>:</p>
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
@@ -168,12 +154,12 @@ a couple of examples around in this repository. Here is the most basic
</td></tr></table></div>
<p>Source files should be again listed in a dedicated variable. Later, you
probably add some C++ code and settings diverging from the defaults via the
-<code class="docutils literal"><span class="pre">pymod</span></code> macro. This is where things clutter up quite quickly. As set up here,
-your project would be added as a module <code class="docutils literal"><span class="pre">sidechain</span></code> in the ProMod3
+<code class="docutils literal notranslate"><span class="pre">pymod</span></code> macro. This is where things clutter up quite quickly. As set up here,
+your project would be added as a module <code class="docutils literal notranslate"><span class="pre">sidechain</span></code> in the ProMod3
Python package tree.</p>
-<p>The final step towards CMake is to register your module’s directory in the
-top level <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code>:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+<p>The final step towards CMake is to register your module’s directory in the
+top level <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>:</p>
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
2
3
4
@@ -209,44 +195,44 @@ directory as shown in line 8.</p>
<p>This was the final step to set up the build system. Running CMake at this
point would create the build environment in place. But building software in
your code repository has several drawbacks. First of all, it puts all kind of
-new files in the directory tree and <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code> would show them all. Then
-its very likely, that manual intervention is needed after <code class="docutils literal"><span class="pre">make</span> <span class="pre">clean</span></code>. Plus,
+new files in the directory tree and <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">status</span></code> would show them all. Then
+its very likely, that manual intervention is needed after <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">clean</span></code>. Plus,
this would be very static. Imagine at one point you want to switch on all
debugging flags for your C++ code. So you either clean the whole repository
and rebuild or you go by two separated repositories copying code changes from A
-to B. The solution to this is instead of ‘in place’ you go ‘out of source’. You
+to B. The solution to this is instead of ‘in place’ you go ‘out of source’. You
still can stay in your repository while being out of the source tree by using
-sub-directories. ProMod3 comes with a dedicated prefix ‘build*’ in
-<code class="file docutils literal"><span class="pre">.gitignore</span></code>. Have a directory <code class="file docutils literal"><span class="pre">build</span></code> and <code class="file docutils literal"><span class="pre">build-dbg</span></code> and it
-will not show up in <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code>.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir build
+sub-directories. ProMod3 comes with a dedicated prefix ‘build*’ in
+<code class="file docutils literal notranslate"><span class="pre">.gitignore</span></code>. Have a directory <code class="file docutils literal notranslate"><span class="pre">build</span></code> and <code class="file docutils literal notranslate"><span class="pre">build-dbg</span></code> and it
+will not show up in <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">status</span></code>.</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir build
<span class="gp">$</span> <span class="nb">cd</span> build
</pre></div>
</div>
<p>To actually create all the makefiles and generated files, you may use one of
-the configuration scripts from the <code class="file docutils literal"><span class="pre">conf-scripts</span></code> directory. Usually
+the configuration scripts from the <code class="file docutils literal notranslate"><span class="pre">conf-scripts</span></code> directory. Usually
those scripts only need to be pointed to an OST staging tree. Even if you
are on a system not covered by available scripts, their code may help you at
the CMake command. Once you managed to conquer a new system, feel free to add
a new configuration script. The following example assumes Fedora 19.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> ../conf-scripts/fedora-19-conf ../../ost.git/stage
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> ../conf-scripts/fedora-19-conf ../../ost.git/stage
</pre></div>
</div>
<p>From this point, <strong class="command">make</strong> should work and you could start adding your
-files to the repository using <code class="docutils literal"><span class="pre">git</span> <span class="pre">add</span></code>.</p>
-<p>Up to now, we did not cover the <code class="file docutils literal"><span class="pre">tests</span></code> branch of a new module. But its
+files to the repository using <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">add</span></code>.</p>
+<p>Up to now, we did not cover the <code class="file docutils literal notranslate"><span class="pre">tests</span></code> branch of a new module. But its
good practice to develop new functionality along tests and that right from the
beginning. At some point, new code needs testing anyway to see if it does what
it should, so just do this by writing unit tests. Test sources are stored in
-files with a prefix <code class="file docutils literal"><span class="pre">test_</span></code> and usually come per submodule instead of
-sporting a single monolithic <code class="file docutils literal"><span class="pre">test_sidechain_reconstruction.py</span></code>.</p>
-<p>Python code is evaluated using its own <a class="reference external" href="https://docs.python.org/3.6/library/unittest.html">unit testing framework</a> with a little help from <a class="reference external" href="https://www.OpenStructure.org">OST</a> (C++ uses the
+files with a prefix <code class="file docutils literal notranslate"><span class="pre">test_</span></code> and usually come per submodule instead of
+sporting a single monolithic <code class="file docutils literal notranslate"><span class="pre">test_sidechain_reconstruction.py</span></code>.</p>
+<p>Python code is evaluated using its own <a class="reference external" href="https://docs.python.org/3.7/library/unittest.html">unit testing framework</a> with a little help from <a class="reference external" href="https://www.OpenStructure.org">OST</a> (C++ uses the
Boost <a class="reference external" href="https://www.boost.org/doc/libs/1_53_0/libs/test/doc/html/index.html">Test Library</a>). The
-basic scheme is to import your module, subclass <a class="reference external" href="https://docs.python.org/3.6/library/unittest.html#unittest.TestCase" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a> and
-make the whole file runnable as script using the most common <a class="reference external" href="https://docs.python.org/3.6/library/__main__.html"><a class="reference external" href="https://docs.python.org/3.6/reference/import.html#__name__" title="(in Python v3.6)"><code class="xref py py-attr docutils literal"><span class="pre">__name__</span></code></a></a>
+basic scheme is to import your module, subclass <a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a> and
+make the whole file runnable as script using the most common <a class="reference external" href="https://docs.python.org/3.7/library/__main__.html"><a class="reference external" href="https://docs.python.org/3.7/reference/import.html#__name__" title="(in Python v3.7)"><code class="xref py py-attr docutils literal notranslate"><span class="pre">__name__</span></code></a></a>
attribute. As an example we test the
-<a class="reference internal" href="modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a> function:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+<a class="reference internal" href="modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a> function:</p>
+<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
2
3
4
@@ -265,8 +251,8 @@ attribute. As an example we test the
17
18
19</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">unittest</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="k">class</span> <span class="nc">ReconstructTests</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
@@ -281,25 +267,25 @@ attribute. As an example we test the
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">GetAtomCount</span><span class="p">(),</span> <span class="n">prot_rec</span><span class="o">.</span><span class="n">GetAtomCount</span><span class="p">())</span>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
- <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
+ <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">testutils</span>
<span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
</pre></div>
</td></tr></table></div>
-<p>To hook up your tests with <code class="docutils literal"><span class="pre">make</span> <span class="pre">codetest</span></code> (and to create a
-<code class="docutils literal"><span class="pre">test_reconstruct_sidechains.py_run</span></code> target), everything has to be introduced to CMake.
-First, tell CMake to search <code class="file docutils literal"><span class="pre">tests</span></code> for a <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> file
-by extending the list of sub-directories in <code class="file docutils literal"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<p>To hook up your tests with <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">codetest</span></code> (and to create a
+<code class="docutils literal notranslate"><span class="pre">test_reconstruct_sidechains.py_run</span></code> target), everything has to be introduced to CMake.
+First, tell CMake to search <code class="file docutils literal notranslate"><span class="pre">tests</span></code> for a <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code> file
+by extending the list of sub-directories in <code class="file docutils literal notranslate"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="w"> </span><span class="nf">add_subdirectory(</span><span class="nb">pymod</span><span class="nf">)</span><span class="w"></span>
<span class="w"> </span><span class="nf">add_subdirectory(</span><span class="nb">doc</span><span class="nf">)</span><span class="w"></span>
<span class="w"> </span><span class="nf">add_subdirectory(</span><span class="nb">tests</span><span class="nf">)</span><span class="w"></span>
</pre></div>
</td></tr></table></div>
-<p>Then fill <code class="file docutils literal"><span class="pre">sidechain/tests/CMakeLists.txt</span></code> with your new test script and
-<code class="docutils literal"><span class="pre">make</span></code> will recognise the changes next time it is run and fix the rest for
+<p>Then fill <code class="file docutils literal notranslate"><span class="pre">sidechain/tests/CMakeLists.txt</span></code> with your new test script and
+<code class="docutils literal notranslate"><span class="pre">make</span></code> will recognise the changes next time it is run and fix the rest for
you.</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
2
3
4
@@ -325,17 +311,17 @@ you.</p>
</pre></div>
</td></tr></table></div>
<p>Note how we listed the test data that we require in the unit test by defining
-<code class="docutils literal"><span class="pre">SIDECHAIN_TEST_DATA</span></code>.</p>
-<p>Now tests should be available by <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code>, <code class="docutils literal"><span class="pre">make</span> <span class="pre">codetest</span></code> and
-<code class="docutils literal"><span class="pre">make</span> <span class="pre">test_reconstruct_sidechains.py_run</span></code>.</p>
+<code class="docutils literal notranslate"><span class="pre">SIDECHAIN_TEST_DATA</span></code>.</p>
+<p>Now tests should be available by <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code>, <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">codetest</span></code> and
+<code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">test_reconstruct_sidechains.py_run</span></code>.</p>
</div>
<div class="section" id="how-to-start-your-own-action">
<span id="id2"></span><h2>How To Start Your Own Action<a class="headerlink" href="#how-to-start-your-own-action" title="Permalink to this headline">¶</a></h2>
-<p>In ProMod3 we call scripts/ programs ‘actions’. They are started by a
-launcher found in your staging directory at <code class="file docutils literal"><span class="pre">stage/bin/pm</span></code>. This little
+<p>In ProMod3 we call scripts/ programs ‘actions’. They are started by a
+launcher found in your staging directory at <code class="file docutils literal notranslate"><span class="pre">stage/bin/pm</span></code>. This little
guy helps keeping the shell environment in the right mood to carry out your
job. So usually you will start an action by</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> stage/bin/pm <span class="nb">help</span>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> stage/bin/pm <span class="nb">help</span>
</pre></div>
</div>
<p>To start your own action, follow <a class="reference internal" href="#how-to-start-your-own-module"><span class="std std-ref">How To Start Your Own Module</span></a> until
@@ -345,19 +331,19 @@ other branches stay clean in case you have to do some work there which needs to
get public.</p>
<p>After preparing your repository its time to create a file for the action. That
is a bit different than for modules. Assuming we are sitting in the
-repository’s root:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch action/pm-awesome-action
+repository’s root:</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> touch action/pm-awesome-action
<span class="gp">$</span> chmod +x action/pm-awesome-action
</pre></div>
</div>
-<p>Two things are important here: actions are prefixed with <code class="file docutils literal"><span class="pre">pm-</span></code>, so they
-are recognised by the <code class="file docutils literal"><span class="pre">pm</span></code> launcher. Secondly, action files need to be
+<p>Two things are important here: actions are prefixed with <code class="file docutils literal notranslate"><span class="pre">pm-</span></code>, so they
+are recognised by the <code class="file docutils literal notranslate"><span class="pre">pm</span></code> launcher. Secondly, action files need to be
executable, which does not propagate if you do it <strong>after</strong> the first call to
-<code class="docutils literal"><span class="pre">make</span></code>.</p>
-<p>To get the new action recognised by <code class="docutils literal"><span class="pre">make</span></code> to be placed in
-<code class="file docutils literal"><span class="pre">stage/libexec/promod3</span></code>, it has to be registered with CMake in
-<code class="file docutils literal"><span class="pre">actions/CMakeLists.txt</span></code>:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<code class="docutils literal notranslate"><span class="pre">make</span></code>.</p>
+<p>To get the new action recognised by <code class="docutils literal notranslate"><span class="pre">make</span></code> to be placed in
+<code class="file docutils literal notranslate"><span class="pre">stage/libexec/promod3</span></code>, it has to be registered with CMake in
+<code class="file docutils literal notranslate"><span class="pre">actions/CMakeLists.txt</span></code>:</p>
+<div class="highlight-cmake notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
@@ -373,31 +359,30 @@ executable, which does not propagate if you do it <strong>after</strong> the fir
</pre></div>
</td></tr></table></div>
<p>Just add your action with its full filename with a call to
-<span class="target" id="index-0-command:pm_action"></span><a class="reference internal" href="cmake/index.html#command:pm_action" title="pm_action"><code class="xref cmake cmake-command docutils literal"><span class="pre">pm_action()</span></code></a> at the end of the file.</p>
+<span class="target" id="index-0-command:pm_action"></span><a class="reference internal" href="cmake/index.html#command:pm_action" title="pm_action"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">pm_action()</span></code></a> at the end of the file.</p>
<p>Before coding your action, lets set up unit tests for it. Usually when adding
features, you will immediately try them, check that everything works as
intended, etc.. ProMod3 helps you automatising those tests so its rather easy
to check later, if code changes break anything. For actions, we are using
-<a class="reference internal" href="actions/index_dev.html#module-test_actions" title="test_actions: Testing Actions"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> instead of
-<a class="reference external" href="https://docs.python.org/3.6/library/unittest.html#unittest.TestCase" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a>. Since testing has a lot in common for different
+<a class="reference internal" href="actions/index_dev.html#module-test_actions" title="test_actions: Testing Actions"><code class="xref py py-class docutils literal notranslate"><span class="pre">test_actions.ActionTestCase</span></code></a> instead of
+<a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a>. Since testing has a lot in common for different
actions, we decided to put up a little wrapper around this subject. See the
-documentation of <a class="reference internal" href="actions/index_dev.html#module-test_actions" title="test_actions: Testing Actions"><code class="xref py py-class docutils literal"><span class="pre">ActionTestCase</span></code></a> for more information.</p>
+documentation of <a class="reference internal" href="actions/index_dev.html#module-test_actions" title="test_actions: Testing Actions"><code class="xref py py-class docutils literal notranslate"><span class="pre">ActionTestCase</span></code></a> for more information.</p>
<p>Now its time to fill your action with code. Instead of reading a lot more of
-explanations, it should be easy to go by examples from the <code class="file docutils literal"><span class="pre">actions</span></code>
+explanations, it should be easy to go by examples from the <code class="file docutils literal notranslate"><span class="pre">actions</span></code>
directory. There are only two really important points:</p>
<ul>
-<li><p class="first">No shebang line (<code class="docutils literal"><span class="pre">#!</span> <span class="pre">/usr/bin/python</span></code>) in your action! Also no
-<code class="docutils literal"><span class="pre">#!</span> <span class="pre">/usr/bin/env</span> <span class="pre">python</span></code> or anything like this. This may lead to funny side
+<li><p>No shebang line (<code class="docutils literal notranslate"><span class="pre">#!</span> <span class="pre">/usr/bin/python</span></code>) in your action! Also no
+<code class="docutils literal notranslate"><span class="pre">#!</span> <span class="pre">/usr/bin/env</span> <span class="pre">python</span></code> or anything like this. This may lead to funny side
effects, like calling a Python interpreter from outside a virtual
environment or a different version OST. Basically it may mess up the
-environment your action is running in. Actions are called by <code class="file docutils literal"><span class="pre">pm</span></code>,
-that’s enough to get everything just right.</p>
-</li>
-<li><p class="first">The action of your action happens in the <a class="reference external" href="https://docs.python.org/3.6/library/__main__.html"><code class="xref py py-attr docutils literal"><span class="pre">__main__</span></code></a> branch of the script.
+environment your action is running in. Actions are called by <code class="file docutils literal notranslate"><span class="pre">pm</span></code>,
+that’s enough to get everything just right.</p></li>
+<li><p>The action of your action happens in the <a class="reference external" href="https://docs.python.org/3.7/library/__main__.html"><code class="xref py py-attr docutils literal notranslate"><span class="pre">__main__</span></code></a> branch of the script.
Your action will have own function definitions, variables and all the bells
-and whistles. Hiding behind <a class="reference external" href="https://docs.python.org/3.6/library/__main__.html"><code class="xref py py-attr docutils literal"><span class="pre">__main__</span></code></a> keeps everything separated and makes
+and whistles. Hiding behind <a class="reference external" href="https://docs.python.org/3.7/library/__main__.html"><code class="xref py py-attr docutils literal notranslate"><span class="pre">__main__</span></code></a> keeps everything separated and makes
things easier when it gets to debugging. So just after</p>
-<div class="highlight-python"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">alot</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">alot</span>
<span class="k">def</span> <span class="nf">functions_specific_to_your_action</span><span class="p">(</span><span class="o">...</span><span class="p">):</span>
@@ -411,11 +396,11 @@ things easier when it gets to debugging. So just after</p>
</div>
<div class="section" id="how-to-write-your-own-scorer">
<h2>How To Write Your Own Scorer<a class="headerlink" href="#how-to-write-your-own-scorer" title="Permalink to this headline">¶</a></h2>
-<p>The <a class="reference internal" href="scoring/index.html#module-promod3.scoring" title="promod3.scoring: Loop Scoring"><code class="xref py py-mod docutils literal"><span class="pre">scoring</span></code></a> module contains several classes to make it easy to
+<p>The <a class="reference internal" href="scoring/index.html#module-promod3.scoring" title="promod3.scoring: Loop Scoring"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code></a> module contains several classes to make it easy to
add new scorers. As usual, you can use existing bits and pieces as examples and
try to be consistent with it. Here, we quickly give an overview of the separation of concerns:</p>
<ul>
-<li><p class="first"><a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>:
+<li><p><a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>:
Defines the scorer with all its parameters and energies and the functionality
to compute scores. Scorers are setup by the user (or loaded from disk) if
necessary.</p>
@@ -423,16 +408,16 @@ necessary.</p>
pointers to env. data kept and updated by the score env.. Also, they may be
linked to a score env. listener to handle specially organized data.</p>
</li>
-<li><p class="first"><a class="reference internal" href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>:
+<li><p><a class="reference internal" href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>:
Handles all model-specific data used by the scorers. The user sets up the
environment and updates it whenever something changes.</p>
-<p>Residue-specific data is kept in arrays of fixed size (see <code class="xref py py-class docutils literal"><span class="pre">IdxHandler</span></code>
+<p>Residue-specific data is kept in arrays of fixed size (see <code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code>
for how the indexing is done). An array of bool-like integers can be accessed
-with “GetEnvSetData()” and used to determine whether env. data is available
+with “GetEnvSetData()” and used to determine whether env. data is available
for a certain residue. The list of sequences handled by the env. is fixed as
otherwise pointers into the data-storage would be invalidated.</p>
</li>
-<li><p class="first"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnvListener</span></code>:
+<li><p><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnvListener</span></code>:
Allows to have score-specific data to be extracted from the model-specific
data available in the score env. class. It is commonly used to define
spatially organized structures to quickly access other atoms within a given
@@ -440,59 +425,58 @@ radius.</p>
<p>All score env. listener are attached to a master score env. and they get
updated when the score env. gets updated. Multiple scorers can use the same
listener. Listeners are not accessible by anyone outside of the scorers and
-the score env. object responsible for it. Since the user doesn’t see them,
+the score env. object responsible for it. Since the user doesn’t see them,
there is no Python API for them.</p>
</li>
-<li><p class="first"><code class="xref py py-class docutils literal"><span class="pre">IdxHandler</span></code>:
+<li><p><code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code>:
This takes care of translating chain indices (range [0, GetNumChains()])
and residue numbers (range [1, GetChainSize(chain_idx)]) into the indexing
used internally by the score env. (range [0, GetNumResidues()]).
-The score env. takes care of this object and makes it accessible for scorers.</p>
-</li>
+The score env. takes care of this object and makes it accessible for scorers.</p></li>
</ul>
-<p>As an example, let’s look at the <a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">CBPackingScorer</span></code></a>:</p>
+<p>As an example, let’s look at the <a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a>:</p>
<ul class="simple">
-<li>it contains score-specific parameters and energies which can be either
-set manually or loaded from disk</li>
-<li>it is linked to a score env. listener of type <code class="xref py py-class docutils literal"><span class="pre">CBetaEnvListener</span></code>,
-which provides a <code class="xref py py-meth docutils literal"><span class="pre">FindWithin()</span></code> function to quickly access neighboring
+<li><p>it contains score-specific parameters and energies which can be either
+set manually or loaded from disk</p></li>
+<li><p>it is linked to a score env. listener of type <code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaEnvListener</span></code>,
+which provides a <code class="xref py py-meth docutils literal notranslate"><span class="pre">FindWithin()</span></code> function to quickly access neighboring
CB atoms (note that the same listener is also used by the
-<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal"><span class="pre">CBetaScorer</span></code></a>)</li>
-<li>a pointer to the <code class="xref py py-class docutils literal"><span class="pre">IdxHandler</span></code> object of the score env. is extracted
+<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a>)</p></li>
+<li><p>a pointer to the <code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code> object of the score env. is extracted
when the environment is attached and is used to get sequence-specific data
-when calculating the score</li>
+when calculating the score</p></li>
</ul>
-<p>As a second example, look at the <a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal"><span class="pre">PairwiseScorer</span></code></a>:</p>
+<p>As a second example, look at the <a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseScorer</span></code></a>:</p>
<ul class="simple">
-<li>it does not require any score-specific setup</li>
-<li>it is linked to residue-specific CA/CB positions and the pairwise functions
-defined in the score env.</li>
-<li>“GetEnvSetData()” of the score env. is used to determine if env. data is
-available for a given residue</li>
+<li><p>it does not require any score-specific setup</p></li>
+<li><p>it is linked to residue-specific CA/CB positions and the pairwise functions
+defined in the score env.</p></li>
+<li><p>“GetEnvSetData()” of the score env. is used to determine if env. data is
+available for a given residue</p></li>
</ul>
</div>
<div class="section" id="quick-testing-of-project-features">
<h2>Quick testing of ProMod3 features<a class="headerlink" href="#quick-testing-of-project-features" title="Permalink to this headline">¶</a></h2>
<p>High-level features of ProMod3, can be tested directly in an interactive
Python shell. First, you need to tell Python, where to find the modules by
-defining the <code class="docutils literal"><span class="pre">PYTHONPATH</span></code> env. variable in your shell to include the
-<code class="file docutils literal"><span class="pre">lib64/python3.6/site-packages</span></code> folders of the <code class="file docutils literal"><span class="pre">stage</span></code> folders of
+defining the <code class="docutils literal notranslate"><span class="pre">PYTHONPATH</span></code> env. variable in your shell to include the
+<code class="file docutils literal notranslate"><span class="pre">lib64/python3.6/site-packages</span></code> folders of the <code class="file docutils literal notranslate"><span class="pre">stage</span></code> folders of
ProMod3 and OST. For convenience, you can place the export-command in
-your <code class="file docutils literal"><span class="pre">.bashrc</span></code> (or so). Then, you can import modules from <code class="docutils literal"><span class="pre">promod3</span></code>
-and <code class="docutils literal"><span class="pre">ost</span></code> as in the example codes shown in this documentation.</p>
-<p>To test low-level C++ features, you can copy the <code class="file docutils literal"><span class="pre">extras/test_code</span></code>
+your <code class="file docutils literal notranslate"><span class="pre">.bashrc</span></code> (or so). Then, you can import modules from <code class="docutils literal notranslate"><span class="pre">promod3</span></code>
+and <code class="docutils literal notranslate"><span class="pre">ost</span></code> as in the example codes shown in this documentation.</p>
+<p>To test low-level C++ features, you can copy the <code class="file docutils literal notranslate"><span class="pre">extras/test_code</span></code>
folder and adapt it for your purposes. First, you will have to fix the paths
-to ProMod3 and OST in the <code class="file docutils literal"><span class="pre">Makefile</span></code> by changing the following
+to ProMod3 and OST in the <code class="file docutils literal notranslate"><span class="pre">Makefile</span></code> by changing the following
lines:</p>
-<div class="highlight-make"><div class="highlight"><pre><span></span><span class="c"># path to OST and ProMod3 stage</span>
+<div class="highlight-make notranslate"><div class="highlight"><pre><span></span><span class="c"># path to OST and ProMod3 stage</span>
<span class="nv">OST_ROOT</span> <span class="o">=</span> <DEFINEME>/ost/build/stage
<span class="nv">PROMOD3_ROOT</span> <span class="o">=</span> <DEFINEME>/ProMod3/build/stage
</pre></div>
</div>
<p>Afterwards, you should be able to compile and run small sample codes that use
-ProMod3 and OST as in the <code class="file docutils literal"><span class="pre">test.cc</span></code> example. You can compile your
-code by executing <code class="docutils literal"><span class="pre">make</span></code> and run it with <code class="docutils literal"><span class="pre">make</span> <span class="pre">run</span></code>. Also, remember to set
-the <code class="docutils literal"><span class="pre">PROMOD3_SHARED_DATA_PATH</span></code> variable if you moved the stage folder.</p>
+ProMod3 and OST as in the <code class="file docutils literal notranslate"><span class="pre">test.cc</span></code> example. You can compile your
+code by executing <code class="docutils literal notranslate"><span class="pre">make</span></code> and run it with <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">run</span></code>. Also, remember to set
+the <code class="docutils literal notranslate"><span class="pre">PROMOD3_SHARED_DATA_PATH</span></code> variable if you moved the stage folder.</p>
</div>
<div class="section" id="unit-tests">
<h2>Unit Tests<a class="headerlink" href="#unit-tests" title="Permalink to this headline">¶</a></h2>
@@ -501,28 +485,28 @@ tutorial on unit testing here. Again, have a look at how other modules treat
this topic and then there is quite a lot of educated material to be found on
the Internet. Nevertheless, here is a short list of most important advices:</p>
<ul class="simple">
-<li>Tests go into dedicated scripts/ source files in the <code class="file docutils literal"><span class="pre">tests</span></code> directory</li>
-<li>No external data dependencies, if tests need data, they find it in
-<code class="file docutils literal"><span class="pre">tests/data</span></code></li>
-<li>If ‘exotic’ Python modules are used, consider making the test aware of the
-possibility that the module is not available</li>
-<li>Tests do not fail on purpose</li>
-<li>No failing tests, that are considered ‘this does not affect anything’</li>
+<li><p>Tests go into dedicated scripts/ source files in the <code class="file docutils literal notranslate"><span class="pre">tests</span></code> directory</p></li>
+<li><p>No external data dependencies, if tests need data, they find it in
+<code class="file docutils literal notranslate"><span class="pre">tests/data</span></code></p></li>
+<li><p>If ‘exotic’ Python modules are used, consider making the test aware of the
+possibility that the module is not available</p></li>
+<li><p>Tests do not fail on purpose</p></li>
+<li><p>No failing tests, that are considered ‘this does not affect anything’</p></li>
</ul>
-<p>To run the whole test suite, <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code> is enough. This will also trigger
-the <code class="docutils literal"><span class="pre">doctest</span></code> and <code class="docutils literal"><span class="pre">linkcheck</span></code> targets. Alternatively you can run:</p>
+<p>To run the whole test suite, <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> is enough. This will also trigger
+the <code class="docutils literal notranslate"><span class="pre">doctest</span></code> and <code class="docutils literal notranslate"><span class="pre">linkcheck</span></code> targets. Alternatively you can run:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">make</span> <span class="pre">codetest</span></code> to run only unit tests from all modules in ProMod3.
-Note that <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code> does nothing more but invoking <code class="docutils literal"><span class="pre">doctest</span></code>,
-<code class="docutils literal"><span class="pre">linkcheck</span></code> and <code class="docutils literal"><span class="pre">codetest</span></code> as dependencies.</li>
-<li><code class="docutils literal"><span class="pre">make</span> <span class="pre">check_xml</span></code> to run tests without stopping after each failure.
+<li><p><code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">codetest</span></code> to run only unit tests from all modules in ProMod3.
+Note that <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> does nothing more but invoking <code class="docutils literal notranslate"><span class="pre">doctest</span></code>,
+<code class="docutils literal notranslate"><span class="pre">linkcheck</span></code> and <code class="docutils literal notranslate"><span class="pre">codetest</span></code> as dependencies.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check_xml</span></code> to run tests without stopping after each failure.
Failures are shortly reported to the command line and the result of each test
-is written in ‘PYTEST-<TestCaseName>.xml’ files in the ‘tests’ subfolders of
-your ‘build’ folder.</li>
-<li>Run single tests:
-assuming you have <code class="file docutils literal"><span class="pre">your_module/tests/test_awesome_feature.py</span></code>, CMake
-will provide you with a target <code class="docutils literal"><span class="pre">test_awesome_feature.py_run</span></code>. If your module
-has C++ tests, those will be available by <code class="docutils literal"><span class="pre">test_suite_your_module_run</span></code>.</li>
+is written in ‘PYTEST-<TestCaseName>.xml’ files in the ‘tests’ subfolders of
+your ‘build’ folder.</p></li>
+<li><p>Run single tests:
+assuming you have <code class="file docutils literal notranslate"><span class="pre">your_module/tests/test_awesome_feature.py</span></code>, CMake
+will provide you with a target <code class="docutils literal notranslate"><span class="pre">test_awesome_feature.py_run</span></code>. If your module
+has C++ tests, those will be available by <code class="docutils literal notranslate"><span class="pre">test_suite_your_module_run</span></code>.</p></li>
</ul>
</div>
<div class="section" id="writing-documentation">
@@ -534,47 +518,47 @@ or man pages.</p>
gives an idea of concepts and pulls in interfaces from source. Copying files to
the build directory, issuing the Sphinx call and everything else that is
needed to create the actual documentation is done by CMake and its makefiles.
-Hence, the <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> of the <code class="file docutils literal"><span class="pre">doc</span></code> directory of a module is
+Hence, the <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code> of the <code class="file docutils literal notranslate"><span class="pre">doc</span></code> directory of a module is
crucial. For documentation which does not relate to a particular module, the
-repository comes with a top-level <code class="file docutils literal"><span class="pre">doc</span></code> directory.</p>
+repository comes with a top-level <code class="file docutils literal notranslate"><span class="pre">doc</span></code> directory.</p>
<p>If you write new functionality for ProMod3, or fix bugs, feel free to extend
-the <code class="file docutils literal"><span class="pre">CHANGELOG</span></code> file. It will be automatically pulled into the
+the <code class="file docutils literal notranslate"><span class="pre">CHANGELOG</span></code> file. It will be automatically pulled into the
documentation.</p>
<p>It is highly recommended to add code examples with your documentation. For that
purpose, you should write a fully runnable script which is to be placed in the
-<code class="file docutils literal"><span class="pre">doc/tests/scripts</span></code> directory. The script is to be runnable from within
-the <code class="file docutils literal"><span class="pre">doc/tests</span></code> directory as <code class="docutils literal"><span class="pre">pm</span> <span class="pre">SCRIPTPATH</span></code> and may use data stored in
-the <code class="file docutils literal"><span class="pre">doc/tests/data</span></code> directory. The script and any data needed by it, must
-then be referenced in the <code class="file docutils literal"><span class="pre">doc/tests/CMakeLists.txt</span></code> file. Afterwards,
+<code class="file docutils literal notranslate"><span class="pre">doc/tests/scripts</span></code> directory. The script is to be runnable from within
+the <code class="file docutils literal notranslate"><span class="pre">doc/tests</span></code> directory as <code class="docutils literal notranslate"><span class="pre">pm</span> <span class="pre">SCRIPTPATH</span></code> and may use data stored in
+the <code class="file docutils literal notranslate"><span class="pre">doc/tests/data</span></code> directory. The script and any data needed by it, must
+then be referenced in the <code class="file docutils literal notranslate"><span class="pre">doc/tests/CMakeLists.txt</span></code> file. Afterwards,
they can be included in the documentation using the literalinclude
directive.
-For instance, if you add a new example code <code class="file docutils literal"><span class="pre">loop_main.py</span></code>,
+For instance, if you add a new example code <code class="file docutils literal notranslate"><span class="pre">loop_main.py</span></code>,
you would add it in your module documentation as follows:</p>
-<div class="highlight-rest"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../../tests/doc/scripts/loop_main.py
+<div class="highlight-rest notranslate"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../../tests/doc/scripts/loop_main.py
</pre></div>
</div>
<p>If your example does not relate to a specific module and the documentation is
-in the top-level <code class="file docutils literal"><span class="pre">doc</span></code> directory, you need to drop one of the <code class="docutils literal"><span class="pre">..</span></code> as
+in the top-level <code class="file docutils literal notranslate"><span class="pre">doc</span></code> directory, you need to drop one of the <code class="docutils literal notranslate"><span class="pre">..</span></code> as
follows:</p>
-<div class="highlight-rest"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../tests/doc/scripts/hello_world.py
+<div class="highlight-rest notranslate"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../tests/doc/scripts/hello_world.py
</pre></div>
</div>
<p>To ensure that the code examples keep on working, a unit test has to be defined
-in <code class="file docutils literal"><span class="pre">doc/tests/test_doctests.py</span></code>. Each example code is run by a dedicated
+in <code class="file docutils literal notranslate"><span class="pre">doc/tests/test_doctests.py</span></code>. Each example code is run by a dedicated
test function. Usually, the codes are run and the return code is checked.
Command-line output or resulting files can also be checked (see existing test
codes for examples). A few more guidelines for example codes:</p>
<ul class="simple">
-<li>If it generates files as output, please delete them after checking them.</li>
-<li>If it requires external modules or binaries, check for their availablity. If
+<li><p>If it generates files as output, please delete them after checking them.</p></li>
+<li><p>If it requires external modules or binaries, check for their availablity. If
the external dependencies are not available, output a warning and skip the
-test.</li>
+test.</p></li>
</ul>
-<p>A copy of the generated html documentation is kept in <code class="file docutils literal"><span class="pre">doc/html</span></code> so that
+<p>A copy of the generated html documentation is kept in <code class="file docutils literal notranslate"><span class="pre">doc/html</span></code> so that
there is no need to compile ProMod3 to read it. Our policy is to keep that
-folder in-sync with the latest documentation at least on the <code class="docutils literal"><span class="pre">master</span></code> branch
+folder in-sync with the latest documentation at least on the <code class="docutils literal notranslate"><span class="pre">master</span></code> branch
(i.e. for every release). You can use the following commands to do the update:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">cd</span> <PROMOD3_PATH>/build
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">cd</span> <PROMOD3_PATH>/build
<span class="gp">$</span> make html
<span class="gp">$</span> rsync -iv -az --exclude<span class="o">=</span><span class="s2">".*"</span> --delete <span class="se">\</span>
<span class="s2">"stage/share/promod3/html/"</span> <span class="s2">"../doc/html"</span>
@@ -586,23 +570,23 @@ folder in-sync with the latest documentation at least on the <code class="docuti
<p>For some tasks you may want to make use of third party contributions in your
module, for example</p>
<ul class="simple">
-<li>calling/ using the output of third party binaries</li>
-<li>external libraries</li>
-<li>smallish bits of source code included into the ProMod3 directory tree</li>
-<li>Python modules not distributed as part of the Python
-<a class="reference external" href="https://docs.python.org/3.6/library/">standard library</a></li>
+<li><p>calling/ using the output of third party binaries</p></li>
+<li><p>external libraries</p></li>
+<li><p>smallish bits of source code included into the ProMod3 directory tree</p></li>
+<li><p>Python modules not distributed as part of the Python
+<a class="reference external" href="https://docs.python.org/3.7/library/">standard library</a></p></li>
</ul>
<p>Modules from the Python standard library are covered by the Python
<a class="reference external" href="https://docs.python.org/3.6/license.html">license</a> and
licenses is what you have to watch out for with this subject. While the Python
license is safe to be used, in the past several projects went restrictive
-because of exclusive terms of use. Those issues often came from ‘academic
-licenses’, allowing use if free of charge but for commercial entities. To
+because of exclusive terms of use. Those issues often came from ‘academic
+licenses’, allowing use if free of charge but for commercial entities. To
prevent this is one reason for the existence of ProMod3. This means, before
utilising external code, third party libraries, basically anything not created
within this project (including pictures, test data, etc.), check licensing.
What cannot be used at all are items without any license. Those things are not
-‘free’ but more in a legally uncertain state. Also forbidden are licenses which
+‘free’ but more in a legally uncertain state. Also forbidden are licenses which
exclude commercial entities.</p>
<p>There are a lot of rather permissive licenses out there, very often asking for
acknowledgements. We definitively support this. Either go by example phrases
@@ -619,48 +603,55 @@ contributions to web pages using ProMod3.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Contributing</a><ul>
-<li><a class="reference internal" href="#how-to-share-your-own-script">How To Share Your Own Script</a></li>
-<li><a class="reference internal" href="#how-to-start-your-own-module">How To Start Your Own Module</a></li>
-<li><a class="reference internal" href="#how-to-start-your-own-action">How To Start Your Own Action</a></li>
-<li><a class="reference internal" href="#how-to-write-your-own-scorer">How To Write Your Own Scorer</a></li>
-<li><a class="reference internal" href="#quick-testing-of-project-features">Quick testing of ProMod3 features</a></li>
-<li><a class="reference internal" href="#unit-tests">Unit Tests</a></li>
-<li><a class="reference internal" href="#writing-documentation">Writing Documentation</a></li>
-<li><a class="reference internal" href="#third-party-contributions-license-issues">Third Party Contributions (License Issues)</a></li>
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
</ul>
-</li>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="developers.html">Documentation For Developers</a><ul>
<li>Previous: <a href="dev_setup.html" title="previous chapter">ProMod3 Setup</a></li>
- <li>Next: <a href="actions/index_dev.html" title="next chapter"><code class="docutils literal"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
+ <li>Next: <a href="actions/index_dev.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/contributing.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -669,11 +660,11 @@ contributions to web pages using ProMod3.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/contributing.txt"
+ <a href="_sources/contributing.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index e57421b6eeb86a7742ed20448ec9a4f9c424d902..3d3d48d0eded6e7120dd2612e133609454db8f92 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Geometry functions — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Geometry functions — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
<link rel="prev" title="helper - Shared Functionality For the Everything" href="helper.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -51,261 +37,219 @@
<h1>Geometry functions<a class="headerlink" href="#geometry-functions" title="Permalink to this headline">¶</a></h1>
<dl class="function">
<dt id="promod3.core.EvaluateGromacsPosRule">
-<code class="descclassname">promod3.core.</code><code class="descname">EvaluateGromacsPosRule</code><span class="sig-paren">(</span><em>rule</em>, <em>number</em>, <em>anchors</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.EvaluateGromacsPosRule" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">EvaluateGromacsPosRule</code><span class="sig-paren">(</span><em class="sig-param">rule</em>, <em class="sig-param">number</em>, <em class="sig-param">anchors</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.EvaluateGromacsPosRule" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs <em>number</em> positions with the given Gromacs rule and anchor positions
(see Gromacs manual for details).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Gromacs rule</li>
-<li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</li>
-<li><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Gromacs rule</p></li>
+<li><p><strong>number</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</p></li>
+<li><p><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Constructed <em>number</em> positions.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.core.ConstructCTerminalOxygens">
-<code class="descclassname">promod3.core.</code><code class="descname">ConstructCTerminalOxygens</code><span class="sig-paren">(</span><em>c_pos</em>, <em>ca_pos</em>, <em>n_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCTerminalOxygens" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">ConstructCTerminalOxygens</code><span class="sig-paren">(</span><em class="sig-param">c_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">n_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCTerminalOxygens" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs positions of O and OXT atoms for C terminal.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Positions of O and OXT atoms.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.core.ConstructAtomPos">
-<code class="descclassname">promod3.core.</code><code class="descname">ConstructAtomPos</code><span class="sig-paren">(</span><em>A</em>, <em>B</em>, <em>C</em>, <em>bond_length</em>, <em>angle</em>, <em>dihedral</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructAtomPos" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs position of atom “D” based on bond length (C-D), angle (B-C-D) and
+<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">ConstructAtomPos</code><span class="sig-paren">(</span><em class="sig-param">A</em>, <em class="sig-param">B</em>, <em class="sig-param">C</em>, <em class="sig-param">bond_length</em>, <em class="sig-param">angle</em>, <em class="sig-param">dihedral</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructAtomPos" title="Permalink to this definition">¶</a></dt>
+<dd><p>Constructs position of atom “D” based on bond length (C-D), angle (B-C-D) and
dihedral (A-B-C-D).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
-<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
-<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
-<li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Bond length (C-D)</li>
-<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (B-C-D)</li>
-<li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</p></li>
+<li><p><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</p></li>
+<li><p><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</p></li>
+<li><p><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bond length (C-D)</p></li>
+<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (B-C-D)</p></li>
+<li><p><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Position of atom D</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.core.ConstructCBetaPos">
-<code class="descclassname">promod3.core.</code><code class="descname">ConstructCBetaPos</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCBetaPos" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">ConstructCBetaPos</code><span class="sig-paren">(</span><em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">c_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCBetaPos" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs position of C-beta atom given the positions of the backbone nitrogen,
C-alpha and C atoms.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Position of C-beta atom</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.core.RotationAroundLine">
-<code class="descclassname">promod3.core.</code><code class="descname">RotationAroundLine</code><span class="sig-paren">(</span><em>axis</em>, <em>anchor</em>, <em>angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.RotationAroundLine" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">RotationAroundLine</code><span class="sig-paren">(</span><em class="sig-param">axis</em>, <em class="sig-param">anchor</em>, <em class="sig-param">angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.RotationAroundLine" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a geometric transform leading to a rotation with specified <cite>angle</cite>
around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
-<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
-<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
+<li><p><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</p></li>
+<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Transformation matrix</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt>
-<code class="descclassname">promod3.core.</code><code class="descname">RotationAroundLine</code><span class="sig-paren">(</span><em>axis</em>, <em>angle</em><span class="sig-paren">)</span></dt>
+<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">RotationAroundLine</code><span class="sig-paren">(</span><em class="sig-param">axis</em>, <em class="sig-param">angle</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a 3x3 matrix for a rotation by a specified <cite>angle</cite> around an <cite>axis</cite>
going through the origin.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
-<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
+<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Rotation matrix</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="class">
<dt id="promod3.core.StemCoords">
-<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemCoords</code><a class="headerlink" href="#promod3.core.StemCoords" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemCoords</code><a class="headerlink" href="#promod3.core.StemCoords" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemCoords</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemCoords</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span></dt>
<dd><p>Simple container class to store N, CA and C coordinates.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
-atoms.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
+atoms.</p>
+</dd>
+</dl>
<dl class="attribute">
<dt id="promod3.core.StemCoords.n_coord">
-<code class="descname">n_coord</code><a class="headerlink" href="#promod3.core.StemCoords.n_coord" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">n_coord</code><a class="headerlink" href="#promod3.core.StemCoords.n_coord" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemCoords.ca_coord">
-<code class="descname">ca_coord</code><a class="headerlink" href="#promod3.core.StemCoords.ca_coord" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ca_coord</code><a class="headerlink" href="#promod3.core.StemCoords.ca_coord" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemCoords.c_coord">
-<code class="descname">c_coord</code><a class="headerlink" href="#promod3.core.StemCoords.c_coord" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">c_coord</code><a class="headerlink" href="#promod3.core.StemCoords.c_coord" title="Permalink to this definition">¶</a></dt>
<dd><p>Position of nitrogen / alpha carbon / carbon atom.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.core.StemPairOrientation">
-<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemPairOrientation</code><a class="headerlink" href="#promod3.core.StemPairOrientation" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemPairOrientation</code><a class="headerlink" href="#promod3.core.StemPairOrientation" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemPairOrientation</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemPairOrientation</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span></dt>
<dd><p>Relative orientation of a pair of stems. Can be used to define gaps with four
angles and one distance and is used in the fragment database for fast lookups.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem A.</li>
-<li><strong>c_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem B.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal notranslate"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem A.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal notranslate"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem B.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="attribute">
<dt id="promod3.core.StemPairOrientation.distance">
-<code class="descname">distance</code><a class="headerlink" href="#promod3.core.StemPairOrientation.distance" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">distance</code><a class="headerlink" href="#promod3.core.StemPairOrientation.distance" title="Permalink to this definition">¶</a></dt>
<dd><p>Distance of C atom of stem A to N atom of stem B.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.core.StemPairOrientation.angle_one">
-<code class="descname">angle_one</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_one" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle_one</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_one" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemPairOrientation.angle_two">
-<code class="descname">angle_two</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_two" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle_two</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Angles defining relative orientation of stem B with respect to stem A.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.core.StemPairOrientation.angle_three">
-<code class="descname">angle_three</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_three" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle_three</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_three" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemPairOrientation.angle_four">
-<code class="descname">angle_four</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_four" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle_four</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_four" title="Permalink to this definition">¶</a></dt>
<dd><p>Angles defining relative orientation of stem A with respect to stem B.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -318,36 +262,71 @@ angles and one distance and is used in the fragment database for fast lookups.</
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
- <li>Previous: <a href="helper.html" title="previous chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="helper.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
<li>Next: <a href="runtime_profiling.html" title="next chapter">Runtime profiling</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/core/geometry.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -356,11 +335,11 @@ angles and one distance and is used in the fragment database for fast lookups.</
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/core/geometry.txt"
+ <a href="../_sources/core/geometry.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index adf8926ed535afe8424e99625273891a13433d23..7400bd5ea186025d8bc895f2dd18be80b6887142 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Graph Minimizer — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Graph Minimizer — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
<link rel="prev" title="Runtime profiling" href="runtime_profiling.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -50,155 +36,138 @@
<div class="section" id="graph-minimizer">
<h1>Graph Minimizer<a class="headerlink" href="#graph-minimizer" title="Permalink to this headline">¶</a></h1>
<p>The graph minimizer solves an energy minimization problem where we have n
-nodes <span class="math">\(N_i\)</span>, with each node having several possible solutions.
-Every solution has a self energy <span class="math">\(E_{self}\)</span> and pairwise energies in between nodes
+nodes <span class="math notranslate nohighlight">\(N_i\)</span>, with each node having several possible solutions.
+Every solution has a self energy <span class="math notranslate nohighlight">\(E_{self}\)</span> and pairwise energies in between nodes
are possible. The goal is to select exactly one solution per node to obtain
-a set <span class="math">\(X=[x_1, x_2, ..., x_n]\)</span> that minimizes:</p>
-<div class="math">
+a set <span class="math notranslate nohighlight">\(X=[x_1, x_2, ..., x_n]\)</span> that minimizes:</p>
+<div class="math notranslate nohighlight">
\[F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j>i}E_{pair}(N_i[x_i], N_j[x_j])\]</div>
<dl class="class">
<dt id="promod3.core.GraphMinimizer">
-<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">GraphMinimizer</code><a class="headerlink" href="#promod3.core.GraphMinimizer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">GraphMinimizer</code><a class="headerlink" href="#promod3.core.GraphMinimizer" title="Permalink to this definition">¶</a></dt>
<dd><dl class="method">
<dt id="promod3.core.GraphMinimizer.AddNode">
-<code class="descname">AddNode</code><span class="sig-paren">(</span><em>self_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddNode" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddNode</code><span class="sig-paren">(</span><em class="sig-param">self_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddNode" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds a node to the graph.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>self_energies</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Directly controls the number of possible solutions in that
-node and assigns the corresponding self energies</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The idx of the added node</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>self_energies</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Directly controls the number of possible solutions in that
+node and assigns the corresponding self energies</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The idx of the added node</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.AddEdge">
-<code class="descname">AddEdge</code><span class="sig-paren">(</span><em>node_idx_one</em>, <em>node_idx_two</em>, <em>pairwise_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddEdge" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddEdge</code><span class="sig-paren">(</span><em class="sig-param">node_idx_one</em>, <em class="sig-param">node_idx_two</em>, <em class="sig-param">pairwise_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddEdge" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds an edge between the specified nodes.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>node_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of the first node</li>
-<li><strong>node_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of the second node</li>
-<li><strong>pairwise_energies</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The pairwise energies that contribute to the
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>node_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the first node</p></li>
+<li><p><strong>node_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the second node</p></li>
+<li><p><strong>pairwise_energies</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The pairwise energies that contribute to the
overall energy function. There must be a list for
every possible solution in node one. All of those
lists must have exactly the length of possible
-solutions in node two.</li>
+solutions in node two.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The idx of the added edge</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>node_idx_one</em> or <em>node_idx_two</em>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The idx of the added edge</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>node_idx_one</em> or <em>node_idx_two</em>
specify non existent nodes or when <em>pairwise_energies</em> is
inconsistent with the number of solutions in the specified nodes.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.ApplyDEE">
-<code class="descname">ApplyDEE</code><span class="sig-paren">(</span><em>node_idx</em><span class="optional">[</span>, <em>e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyDEE" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyDEE</code><span class="sig-paren">(</span><em class="sig-param">node_idx</em><span class="optional">[</span>, <em class="sig-param">e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyDEE" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies dead end elimination on one particular node and potentially
deactivates certain solutions. The goldstein criterion is described in
-<a class="reference internal" href="../references.html#goldstein1994" id="id1">[goldstein1994]</a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Node to apply dead end elimination</li>
-<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If set to
+<a class="reference internal" href="../references.html#goldstein1994" id="id1"><span>[goldstein1994]</span></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Node to apply dead end elimination</p></li>
+<li><p><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If set to
0.0, the default goldstein criterion is applied =>
-a solution is removed if it’s dominated by all other
+a solution is removed if it’s dominated by all other
solutions in the same node. If you increase this value,
-a solution must be dominated by at least this <strong>e_cut</strong>.</li>
+a solution must be dominated by at least this <strong>e_cut</strong>.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether any solution has been deactivated.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> whether any solution has been deactivated.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.ApplyEdgeDecomposition">
-<code class="descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em>edge_idx</em>, <em>epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em class="sig-param">edge_idx</em>, <em class="sig-param">epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies edge decomposition on one particular edge and potentially
deactivates it. The exact decomposition procedure is described in
-<a class="reference internal" href="../references.html#krivov2009" id="id2">[krivov2009]</a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>edge_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Edge to decompose.</li>
-<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
+<a class="reference internal" href="../references.html#krivov2009" id="id2"><span>[krivov2009]</span></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>edge_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Edge to decompose.</p></li>
+<li><p><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the edge has been decomposed and
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> whether the edge has been decomposed and
deactivated</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.Prune">
-<code class="descname">Prune</code><span class="sig-paren">(</span><em>epsilon</em><span class="optional">[</span>, <em>e_cut=0.0</em>, <em>consider_all_nodes=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Prune" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Prune</code><span class="sig-paren">(</span><em class="sig-param">epsilon</em><span class="optional">[</span>, <em class="sig-param">e_cut=0.0</em>, <em class="sig-param">consider_all_nodes=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Prune" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs edge decomposition followed by dead end elimination in an
iterative manner until no changes can be observed anymore given
<strong>epsilon</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
-<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Parameter to control dead end elimination.</li>
-<li><strong>consider_all_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, wether the dead end elimination should be
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</p></li>
+<li><p><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Parameter to control dead end elimination.</p></li>
+<li><p><strong>consider_all_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, wether the dead end elimination should be
applied to all nodes, or only those who are
connected with an edge removed by edge
decomposition. This is useful if already a Prune
operation has been performed => only those nodes
connected to a removed edge have the chance for
-successful dead end elimination.</li>
+successful dead end elimination.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.Reset">
-<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Reset" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Reset" title="Permalink to this definition">¶</a></dt>
<dd><p>Resets the graph by undoing any pruning operation (DEE and edge decomposition)</p>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.TreeSolve">
-<code class="descname">TreeSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>max_complexity=inf</em>, <em>initial_epsilon=0.02</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.TreeSolve" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">TreeSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em class="sig-param">max_complexity=inf</em>, <em class="sig-param">initial_epsilon=0.02</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.TreeSolve" title="Permalink to this definition">¶</a></dt>
<dd><p>The method solves a graph using a minimal width tree decomposition
approach in an iterative manner. In every iteration, the algorithm performs
a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
@@ -208,73 +177,65 @@ particular connected component is is larger <strong>max_complexity</strong>,
this component is solved in a later iteration. The algorithm iterates until
all connected components are solved and steadily increases the epsilon value
resulting in a more and more agressive edge decomposition.
-Algorithm further descsribed in <a class="reference internal" href="../references.html#krivov2009" id="id3">[krivov2009]</a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of possible permutations, that have to
+Algorithm further descsribed in <a class="reference internal" href="../references.html#krivov2009" id="id3"><span>[krivov2009]</span></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max number of possible permutations, that have to
be enumerated in the resulting tree after tree
-decomposition.</li>
-<li><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The initial energy threshold to perform edge
-decomposition.</li>
+decomposition.</p></li>
+<li><p><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The initial energy threshold to perform edge
+decomposition.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of indices
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A tuple with the first element being a list of indices
representing the single solutions minimizing
the overall energy function.
The second element is the according energy value.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.AStarSolve">
-<code class="descname">AStarSolve</code><span class="sig-paren">(</span><em>e_thresh</em><span class="optional">[</span>, <em>max_n=100</em>, <em>max_visited_nodes=100000000</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AStarSolve" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AStarSolve</code><span class="sig-paren">(</span><em class="sig-param">e_thresh</em><span class="optional">[</span>, <em class="sig-param">max_n=100</em>, <em class="sig-param">max_visited_nodes=100000000</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AStarSolve" title="Permalink to this definition">¶</a></dt>
<dd><p>The method solves a graph using the A* algorithm. Besides creating the
minimal energy solution, the function produces a maximum of <strong>max_n</strong>
solutions sorted by energy. It aborts as soon as it sees the first solution
with an energy difference of <strong>e_thresh</strong> to the optimal solution or hits
-<strong>max_n</strong>. If you’re only interested in the optimal solution you should use
-the TreeSolve function since it’s much faster and uses less memory.
+<strong>max_n</strong>. If you’re only interested in the optimal solution you should use
+the TreeSolve function since it’s much faster and uses less memory.
There is no automatic pruning of the graph using DEE or edge decomposition,
-so you have to do it by yourself, otherwise you’ll have a looooooong
+so you have to do it by yourself, otherwise you’ll have a looooooong
runtime or even hit the <strong>max_visited_nodes</strong> parameter that caps the memory
usage.
To have a valid solution you have to take care that you set the <strong>e_cut</strong>
parameter in the pruning function to <strong>e_tresh</strong>.
-Algorithm is described in <a class="reference internal" href="../references.html#leach1998" id="id4">[leach1998]</a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal energy difference of a solution to the
-optimal solution to be considered.</li>
-<li><strong>max_n</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The maximum number of solutions that will be generated.</li>
-<li><strong>max_visited_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Caps the memory usage of the algorithm. Besides
+Algorithm is described in <a class="reference internal" href="../references.html#leach1998" id="id4"><span>[leach1998]</span></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal energy difference of a solution to the
+optimal solution to be considered.</p></li>
+<li><p><strong>max_n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The maximum number of solutions that will be generated.</p></li>
+<li><p><strong>max_visited_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Caps the memory usage of the algorithm. Besides
The memory used for pairwise energies and self
energies, the algorithm uses about
-<strong>max_visited_nodes</strong> * 20 bytes.</li>
+<strong>max_visited_nodes</strong> * 20 bytes.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A tuple with the first element being a list of
solutions. The second element is a list
of energies for the according solutions.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.MCSolve">
-<code class="descname">MCSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>n=100</em>, <em>mc_steps=100000</em>, <em>start_temperature=1000.0</em>, <em>change_frequency=1000</em>, <em>cooling_factor=0.9</em>, <em>seed=0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.MCSolve" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">MCSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em class="sig-param">n=100</em>, <em class="sig-param">mc_steps=100000</em>, <em class="sig-param">start_temperature=1000.0</em>, <em class="sig-param">change_frequency=1000</em>, <em class="sig-param">cooling_factor=0.9</em>, <em class="sig-param">seed=0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.MCSolve" title="Permalink to this definition">¶</a></dt>
<dd><p>Does a total of <strong>n</strong> Monte Carlo runs to find low energy solutions
of the graph. Each run starts with a random
configuration. At each of the <strong>mc_steps</strong> steps, a random node and
@@ -283,55 +244,48 @@ of that random selection relative to the current configuration is
estimated. If the difference in energy is negative, the step is
accepted. If not, the step is accepted with a probability given by
the temperature dependent Metropolis criterion
-<span class="math">\(exp^{\left(\frac{-e_{diff}}{T}\right)}\)</span>.
+<span class="math notranslate nohighlight">\(exp^{\left(\frac{-e_{diff}}{T}\right)}\)</span>.
The temperature for every run starts with <strong>start_temperature</strong>
and is multiplied every <strong>change_frequency</strong> steps with <strong>cooling_factor</strong>
to achieve a simulated annealing effect.
There is no automatic pruning of the graph using DEE or edge decomposition,
you have to do that by yourself.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo runs</li>
-<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo steps per run</li>
-<li><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Start temperature for the temperature dependent
-Metropolis criterion</li>
-<li><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of steps the temperature stays the same</li>
-<li><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Factor to multiply temperature each
-<strong>change_frequency</strong> steps</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Seed for random number generator</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo runs</p></li>
+<li><p><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo steps per run</p></li>
+<li><p><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Start temperature for the temperature dependent
+Metropolis criterion</p></li>
+<li><p><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of steps the temperature stays the same</p></li>
+<li><p><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor to multiply temperature each
+<strong>change_frequency</strong> steps</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Seed for random number generator</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A tuple with the first element being a list of
solutions. The second element is a list
of energies for the according solutions.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.NaiveSolve">
-<code class="descname">NaiveSolve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.NaiveSolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>Don’t even think of using this... This function only exists for debug
+<code class="sig-name descname">NaiveSolve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.NaiveSolve" title="Permalink to this definition">¶</a></dt>
+<dd><p>Don’t even think of using this… This function only exists for debug
purposes and does the full enumeration of the solution space.
It might become faster with the appropriate
<a class="reference external" href="https://www.youtube.com/watch?v=fQGbXmkSArs">techniques</a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A tuple with the first element being a list of indices
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>A tuple with the first element being a list of indices
representing the single solutions minimizing
the overall energy function.
-The second element is the according energy value.</td>
-</tr>
-</tbody>
-</table>
+The second element is the according energy value.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -344,36 +298,71 @@ The second element is the according energy value.</td>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
<li>Previous: <a href="runtime_profiling.html" title="previous chapter">Runtime profiling</a></li>
- <li>Next: <a href="setcompoundschemlib.html" title="next chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ <li>Next: <a href="setcompoundschemlib.html" title="next chapter"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/core/graph_minimizer.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -382,11 +371,11 @@ The second element is the according energy value.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/core/graph_minimizer.txt"
+ <a href="../_sources/core/graph_minimizer.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 8f3c424e4b05ba49071df41e1c570e813f9af2f9..bbbadede7dea5558dbbb5e04b972f70bebcaa347 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>helper - Shared Functionality For the Everything — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>helper - Shared Functionality For the Everything — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Geometry functions" href="geometry.html" />
<link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,7 +34,7 @@
<div class="body" role="main">
<div class="section" id="module-promod3.core.helper">
-<span id="helper-shared-functionality-for-the-everything"></span><h1><a class="reference internal" href="#module-promod3.core.helper" title="promod3.core.helper: Helper functions"><code class="xref py py-mod docutils literal"><span class="pre">helper</span></code></a> - Shared Functionality For the Everything<a class="headerlink" href="#module-promod3.core.helper" title="Permalink to this headline">¶</a></h1>
+<span id="helper-shared-functionality-for-the-everything"></span><h1><a class="reference internal" href="#module-promod3.core.helper" title="promod3.core.helper: Helper functions"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code></a> - Shared Functionality For the Everything<a class="headerlink" href="#module-promod3.core.helper" title="Permalink to this headline">¶</a></h1>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
<p>We collect functions here, which should be useful in many places but would make
@@ -56,42 +42,38 @@ rather empty modules left alone.</p>
</div>
<div class="section" id="messages">
<h2>Messages<a class="headerlink" href="#messages" title="Permalink to this headline">¶</a></h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">helper</span>
<span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Something failed!"</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</pre></div>
</div>
<dl class="function">
<dt id="promod3.core.helper.MsgErrorAndExit">
-<code class="descclassname">promod3.core.helper.</code><code class="descname">MsgErrorAndExit</code><span class="sig-paren">(</span><em>msg</em>, <em>exit_status</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.MsgErrorAndExit" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">MsgErrorAndExit</code><span class="sig-paren">(</span><em class="sig-param">msg</em>, <em class="sig-param">exit_status</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.MsgErrorAndExit" title="Permalink to this definition">¶</a></dt>
<dd><p>Send a messages to the OST <a class="reference external" href="https://www.openstructure.org/docs/base/logging/">error log</a> and
exit the Python interpreter.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>msg</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The message.</li>
-<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code, ends up in <code class="docutils literal"><span class="pre">$?</span></code> in the shell. <code class="docutils literal"><span class="pre">0</span></code> is
-traditionally reserved to successful commands.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>msg</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The message.</p></li>
+<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is
+traditionally reserved to successful commands.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">No return value, exits script with value <code class="docutils literal"><span class="pre">exit_status</span></code>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>No return value, exits script with value <code class="docutils literal notranslate"><span class="pre">exit_status</span></code>.</p>
+</dd>
+</dl>
</dd></dl>
</div>
<div class="section" id="file-tests">
<h2>File Tests<a class="headerlink" href="#file-tests" title="Permalink to this headline">¶</a></h2>
-<p>The following example parses an argument (call as <code class="docutils literal"><span class="pre">pm</span> <span class="pre">SCRIPTNAME</span> <span class="pre">FILENAME</span></code>) as
-a file name and checks whether it is a <code class="docutils literal"><span class="pre">pdb</span></code> or <code class="docutils literal"><span class="pre">mmcif</span></code> file.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="sd">"""Test for file reading."""</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
+<p>The following example parses an argument (call as <code class="docutils literal notranslate"><span class="pre">pm</span> <span class="pre">SCRIPTNAME</span> <span class="pre">FILENAME</span></code>) as
+a file name and checks whether it is a <code class="docutils literal notranslate"><span class="pre">pdb</span></code> or <code class="docutils literal notranslate"><span class="pre">mmcif</span></code> file.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="sd">"""Test for file reading."""</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">helper</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">pm3argparse</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">pm3argparse</span><span class="o">.</span><span class="n">PM3ArgumentParser</span><span class="p">(</span><span class="vm">__doc__</span><span class="p">)</span>
<span class="n">p</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'file'</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
@@ -107,96 +89,84 @@ a file name and checks whether it is a <code class="docutils literal"><span clas
</div>
<dl class="function">
<dt id="promod3.core.helper.FileExists">
-<code class="descclassname">promod3.core.helper.</code><code class="descname">FileExists</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExists" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">FileExists</code><span class="sig-paren">(</span><em class="sig-param">prefix</em>, <em class="sig-param">exit_status</em>, <em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExists" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks if a file exists, terminates if not. The error message displayed is
fixed and only needs a <em>prefix</em> describing the specimen of file.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
-“file does not exist: <code class="docutils literal"><span class="pre">file</span></code>”.</li>
-<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal"><span class="pre">$?</span></code> in the
-shell. <code class="docutils literal"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
-<li><strong>file</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
+“file does not exist: <code class="docutils literal notranslate"><span class="pre">file</span></code>”.</p></li>
+<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the
+shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to successful commands.</p></li>
+<li><p><strong>file</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">No return value, exits script with value <code class="docutils literal"><span class="pre">exit_status</span></code> if file
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>No return value, exits script with value <code class="docutils literal notranslate"><span class="pre">exit_status</span></code> if file
is missing.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.core.helper.FileExtension">
-<code class="descclassname">promod3.core.helper.</code><code class="descname">FileExtension</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em>, <em>extensions</em>, <em>gzip=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExtension" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">FileExtension</code><span class="sig-paren">(</span><em class="sig-param">prefix</em>, <em class="sig-param">exit_status</em>, <em class="sig-param">filename</em>, <em class="sig-param">extensions</em>, <em class="sig-param">gzip=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExtension" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks a file to carry a known extension given by a list of strings. Since
-files are very often compressed these days, an additional “gz” suffix can be
+files are very often compressed these days, an additional “gz” suffix can be
tracked automatically by this function. Thus, the list of <em>extensions</em> only
-needs to contain what you are really looking for, e.g. (“pdb”) instead of
-(“pdb”, “pdb.gz”). The <em>gzip</em> flag also determines the output of this
+needs to contain what you are really looking for, e.g. (“pdb”) instead of
+(“pdb”, “pdb.gz”). The <em>gzip</em> flag also determines the output of this
function. If enabled, a triple is returned: name of the file without
extension, its extension and a Boolean to tell whether the file carries the
gzip extension or not. If <em>gzip</em> detection is turned of, only a tuple is
returned: file name and extension. If the tested file name has an
unrecognised extension, this function terminates the script.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
-“file extension not supported: <code class="docutils literal"><span class="pre">filename</span></code>”.</li>
-<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal"><span class="pre">$?</span></code> in the
-shell. <code class="docutils literal"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
-<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
-<li><strong>extensions</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of strings without a leading ”.”.</li>
-<li><strong>gzip</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Indicates whether to check for an additional “gz” extension.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
+“file extension not supported: <code class="docutils literal notranslate"><span class="pre">filename</span></code>”.</p></li>
+<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the
+shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to successful commands.</p></li>
+<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</p></li>
+<li><p><strong>extensions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of strings without a leading “.”.</p></li>
+<li><p><strong>gzip</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Indicates whether to check for an additional “gz” extension.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(base name of <code class="docutils literal"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), extension of file
-without a ”.gz” (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), flag to indicate an additional
-”.gz” (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>)) <strong>if</strong> <code class="docutils literal"><span class="pre">gzip</span></code> is set, (base name of
-<code class="docutils literal"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), extension of file) <strong>if not</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>(base name of <code class="docutils literal notranslate"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>), extension of file
+without a “.gz” (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>), flag to indicate an additional
+“.gz” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>)) <strong>if</strong> <code class="docutils literal notranslate"><span class="pre">gzip</span></code> is set, (base name of
+<code class="docutils literal notranslate"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>), extension of file) <strong>if not</strong>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.core.helper.FileGzip">
-<code class="descclassname">promod3.core.helper.</code><code class="descname">FileGzip</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em>, <em>allowed=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileGzip" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">FileGzip</code><span class="sig-paren">(</span><em class="sig-param">prefix</em>, <em class="sig-param">exit_status</em>, <em class="sig-param">filename</em>, <em class="sig-param">allowed=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileGzip" title="Permalink to this definition">¶</a></dt>
<dd><p>See if a file is gzipped or not. This is basically done by checking for a
-“gz” suffix. May also be used to verify that a file is not compressed where
-it does not apply. That is where <em>allowed</em> comes in. If “gz” is not allowed,
+“gz” suffix. May also be used to verify that a file is not compressed where
+it does not apply. That is where <em>allowed</em> comes in. If “gz” is not allowed,
terminates the script on gzip files.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – String to put in front of the failure-message where gzip
-files are not allowed.</li>
-<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code on gzip files to be avoided, ends up in
-<code class="docutils literal"><span class="pre">$?</span></code> in the shell. <code class="docutils literal"><span class="pre">0</span></code> is traditionally reserved to
-successful commands.</li>
-<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
-<li><strong>allowed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Set to <code class="docutils literal"><span class="pre">False</span></code> if gzipped files are not allowed. Then the
-script will terminate if a gzip file is found.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message where gzip
+files are not allowed.</p></li>
+<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on gzip files to be avoided, ends up in
+<code class="docutils literal notranslate"><span class="pre">$?</span></code> in the shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to
+successful commands.</p></li>
+<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</p></li>
+<li><p><strong>allowed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Set to <code class="docutils literal notranslate"><span class="pre">False</span></code> if gzipped files are not allowed. Then the
+script will terminate if a gzip file is found.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Flag to indicate if file is gzipped (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Flag to indicate if file is gzipped (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>).</p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -209,45 +179,70 @@ script will terminate if a gzip file is found.</li>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a><ul>
-<li><a class="reference internal" href="#introduction">Introduction</a></li>
-<li><a class="reference internal" href="#messages">Messages</a></li>
-<li><a class="reference internal" href="#file-tests">File Tests</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
- <li>Previous: <a href="pm3argparse.html" title="previous chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="pm3argparse.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
<li>Next: <a href="geometry.html" title="next chapter">Geometry functions</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/core/helper.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -256,11 +251,11 @@ script will terminate if a gzip file is found.</li>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/core/helper.txt"
+ <a href="../_sources/core/helper.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 403c6aa8b1ff10c82c736caf8f8e2aa34e3c025f..520f3e50899fb5789c102e38d200a71059d422ae 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>core - ProMod3 Core Functionality — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>core - ProMod3 Core Functionality — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
<link rel="prev" title="Loading Precomputed Objects" href="../loop/load_loop_objects.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,18 +34,18 @@
<div class="body" role="main">
<div class="section" id="module-promod3.core">
-<span id="core-project-core-functionality"></span><h1><a class="reference internal" href="#module-promod3.core" title="promod3.core: Basic functionality, supporting standard tasks in your code."><code class="xref py py-mod docutils literal"><span class="pre">core</span></code></a> - ProMod3 Core Functionality<a class="headerlink" href="#module-promod3.core" title="Permalink to this headline">¶</a></h1>
+<span id="core-project-core-functionality"></span><h1><a class="reference internal" href="#module-promod3.core" title="promod3.core: Basic functionality, supporting standard tasks in your code."><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code></a> - ProMod3 Core Functionality<a class="headerlink" href="#module-promod3.core" title="Permalink to this headline">¶</a></h1>
<p>This module gathers functions and classes which are not devoted to homology
modeling per se but cover standard programming issues.</p>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
-<li class="toctree-l1"><a class="reference internal" href="pm3argparse.html"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="pm3argparse.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pm3argparse.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="pm3argparse.html#argument-parser">Argument Parser</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="helper.html"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="helper.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a><ul>
<li class="toctree-l2"><a class="reference internal" href="helper.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="helper.html#messages">Messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="helper.html#file-tests">File Tests</a></li>
@@ -78,34 +64,69 @@ modeling per se but cover standard programming issues.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li>Previous: <a href="../loop/load_loop_objects.html" title="previous chapter">Loading Precomputed Objects</a></li>
- <li>Next: <a href="pm3argparse.html" title="next chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+ <li>Next: <a href="pm3argparse.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/core/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -114,11 +135,11 @@ modeling per se but cover standard programming issues.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/core/index.txt"
+ <a href="../_sources/core/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 39e539ec170626f66df1c04d369a67d2ec5124ef..dbdf78f2bf0769f1ce5bc7c2821e065c7dfe975b 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>pm3argparse - Parsing Command Lines — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>pm3argparse - Parsing Command Lines — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
<link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,7 +34,7 @@
<div class="body" role="main">
<div class="section" id="module-promod3.core.pm3argparse">
-<span id="pm3argparse-parsing-command-lines"></span><h1><a class="reference internal" href="#module-promod3.core.pm3argparse" title="promod3.core.pm3argparse: Argument Parsing"><code class="xref py py-mod docutils literal"><span class="pre">pm3argparse</span></code></a> - Parsing Command Lines<a class="headerlink" href="#module-promod3.core.pm3argparse" title="Permalink to this headline">¶</a></h1>
+<span id="pm3argparse-parsing-command-lines"></span><h1><a class="reference internal" href="#module-promod3.core.pm3argparse" title="promod3.core.pm3argparse: Argument Parsing"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code></a> - Parsing Command Lines<a class="headerlink" href="#module-promod3.core.pm3argparse" title="Permalink to this headline">¶</a></h1>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
<p>A lot of the actions in ProMod3 have a bunch of command line parameters/
@@ -56,16 +42,16 @@ arguments in common. For example we need an input alignment quite often and
usually for an alignment we need information on what is the target sequence,
what identifies a template sequence and eventually a hint on the format. That
means we need the same functionality on the command line in several actions.
-There <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal"><span class="pre">PM3ArgumentParser</span></code></a> serves as a
+There <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal notranslate"><span class="pre">PM3ArgumentParser</span></code></a> serves as a
simplification. It provides a set of standard arguments you just need to
activate for your action plus it comes with some verification functionality for
input.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="sd">"""</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="sd">"""</span>
<span class="sd">Place the description of your script right in the file and import</span>
<span class="sd">it via '__doc__' as description to the parser ('-h', '--help').</span>
<span class="sd">"""</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">pm3argparse</span>
<span class="c1"># make sure we see output when passing '-h'</span>
<span class="kn">import</span> <span class="nn">ost</span>
@@ -77,302 +63,287 @@ input.</p>
<span class="n">opts</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">Parse</span><span class="p">()</span>
</pre></div>
</div>
-<p>When the example above is run with <code class="docutils literal"><span class="pre">pm</span></code> and no additional arguments, the
-script exits with a code 2. If it is run with an additional argument <code class="docutils literal"><span class="pre">-h</span></code> or
-<code class="docutils literal"><span class="pre">--help</span></code>, it exits with a code 0 and displays the help message given as a
+<p>When the example above is run with <code class="docutils literal notranslate"><span class="pre">pm</span></code> and no additional arguments, the
+script exits with a code 2. If it is run with an additional argument <code class="docutils literal notranslate"><span class="pre">-h</span></code> or
+<code class="docutils literal notranslate"><span class="pre">--help</span></code>, it exits with a code 0 and displays the help message given as a
docstring in your script.</p>
</div>
<div class="section" id="argument-parser">
<h2>Argument Parser<a class="headerlink" href="#argument-parser" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser">
-<em class="property">class </em><code class="descclassname">promod3.core.pm3argparse.</code><code class="descname">PM3ArgumentParser</code><span class="sig-paren">(</span><em>description</em>, <em>action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class is a child of <a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">argparse.ArgumentParser</span></code></a>. It provides a set
-of standard arguments which can be activated with <code class="xref py py-meth docutils literal"><span class="pre">Add*()</span></code> methods and
-then assembled with <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a>. This helps keeping up a common
+<em class="property">class </em><code class="sig-prename descclassname">promod3.core.pm3argparse.</code><code class="sig-name descname">PM3ArgumentParser</code><span class="sig-paren">(</span><em class="sig-param">description</em>, <em class="sig-param">action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="Permalink to this definition">¶</a></dt>
+<dd><p>This class is a child of <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a>. It provides a set
+of standard arguments which can be activated with <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods and
+then assembled with <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a>. This helps keeping up a common
naming scheme throughout all ProMod3 actions. As a real extension, this
-subclass provides checking of input parameters on <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>. Besides
-this, everything you can do with a ‘real’ <a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">ArgumentParser</span></code></a>
+subclass provides checking of input parameters on <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>. Besides
+this, everything you can do with a ‘real’ <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArgumentParser</span></code></a>
instance is possible here.</p>
-<p>Attributes beyond <a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">argparse.ArgumentParser</span></code></a>:</p>
+<p>Attributes beyond <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a>:</p>
<dl class="attribute">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.action">
-<code class="descname">action</code><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.action" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">action</code><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.action" title="Permalink to this definition">¶</a></dt>
<dd><p>Indicates if the calling script is a ProMod3 action.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.__init__">
-<code class="descname">__init__</code><span class="sig-paren">(</span><em>description</em>, <em>action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.__init__" title="Permalink to this definition">¶</a></dt>
-<dd><p>Create a new instance of <code class="xref py py-class docutils literal"><span class="pre">PM3ArgumentParser</span></code>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>description</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Help text for this script, handed down to
-<a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#description"><code class="xref py py-attr docutils literal"><span class="pre">description</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#argparse.ArgumentParser"><code class="xref py py-meth docutils literal"><span class="pre">argparse.ArgumentParser.__init__()</span></code></a>.</li>
-<li><strong>action</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Indicates if the calling script is a ProMod3 action.
-This influences <a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#prog"><code class="xref py py-attr docutils literal"><span class="pre">prog</span></code></a> of
-<a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">ArgumentParser</span></code></a> by clipping of the
+<code class="sig-name descname">__init__</code><span class="sig-paren">(</span><em class="sig-param">description</em>, <em class="sig-param">action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.__init__" title="Permalink to this definition">¶</a></dt>
+<dd><p>Create a new instance of <code class="xref py py-class docutils literal notranslate"><span class="pre">PM3ArgumentParser</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>description</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Help text for this script, handed down to
+<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#description"><code class="xref py py-attr docutils literal notranslate"><span class="pre">description</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">argparse.ArgumentParser.__init__()</span></code></a>.</p></li>
+<li><p><strong>action</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Indicates if the calling script is a ProMod3 action.
+This influences <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#prog"><code class="xref py py-attr docutils literal notranslate"><span class="pre">prog</span></code></a> of
+<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArgumentParser</span></code></a> by clipping of the
first 3 characters of the file name of the script. If
-<code class="docutils literal"><span class="pre">False</span></code>, default behaviour of
-<a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">ArgumentParser</span></code></a> kicks in.</li>
+<code class="docutils literal notranslate"><span class="pre">False</span></code>, default behaviour of
+<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArgumentParser</span></code></a> kicks in.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">argparse.ArgumentParser</span></code></a>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">
-<code class="descname">AddAlignment</code><span class="sig-paren">(</span><em>allow_multitemplate=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddAlignment</code><span class="sig-paren">(</span><em class="sig-param">allow_multitemplate=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline options for alignments.</p>
<p>Activate everything needed to load alignments to the argument parser.
-Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
-input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>allow_multitemplate</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – enable support for multitemplate alignments</td>
-</tr>
-</tbody>
-</table>
+Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> and the
+input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>allow_multitemplate</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – enable support for multitemplate alignments</p>
+</dd>
+</dl>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">-f/--fasta</span> <span class="pre"><FILE></span></code> - Target-template alignment in FASTA format.
-Target sequence is either named “trg” or “target” or the first
-sequence is used. File can be plain or gzipped.</li>
-<li><code class="docutils literal"><span class="pre">-c/--clustal</span> <span class="pre"><FILE></span></code> - Target-template alignment in CLUSTAL format.
-Target sequence is either named “trg” or “target” or the first
-sequence is used. File can be plain or gzipped.</li>
-<li><code class="docutils literal"><span class="pre">-j/--json</span> <span class="pre"><OBJECT>|<FILE></span></code> - Alignments provided as JSON
-file/object. File can be plain or gzipped.</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">-f/--fasta</span> <span class="pre"><FILE></span></code> - Target-template alignment in FASTA format.
+Target sequence is either named “trg” or “target” or the first
+sequence is used. File can be plain or gzipped.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">-c/--clustal</span> <span class="pre"><FILE></span></code> - Target-template alignment in CLUSTAL format.
+Target sequence is either named “trg” or “target” or the first
+sequence is used. File can be plain or gzipped.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">-j/--json</span> <span class="pre"><OBJECT>|<FILE></span></code> - Alignments provided as JSON
+file/object. File can be plain or gzipped.</p></li>
</ul>
<p>See <a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details on the file formats.</p>
-<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
+<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><code class="xref py py-attr docutils literal"><span class="pre">fasta</span></code> - filled with the input of the <code class="docutils literal"><span class="pre">--fasta</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> (filenames).</li>
-<li><code class="xref py py-attr docutils literal"><span class="pre">clustal</span></code> - filled with the input of the <code class="docutils literal"><span class="pre">--clustal</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> (filenames).</li>
-<li><code class="xref py py-attr docutils literal"><span class="pre">json</span></code> - filled with the input of the <code class="docutils literal"><span class="pre">--json</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>, where each string may be a filename
-or a JSON object string.</li>
-<li><code class="xref py py-attr docutils literal"><span class="pre">alignments</span></code> - <code class="xref py py-class docutils literal"><span class="pre">ost.AlignmentList</span></code>, same order as given.
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">fasta</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--fasta</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">clustal</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--clustal</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">json</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--json</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, where each string may be a filename
+or a JSON object string.</p></li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">alignments</span></code> - <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.AlignmentList</span></code>, same order as given.
First sequence of the alignment is the target sequence, if in doubt,
-check for sequence roles <code class="docutils literal"><span class="pre">TARGET</span></code> or <code class="docutils literal"><span class="pre">TEMPLATE</span></code></li>
-<li><code class="xref py py-attr docutils literal"><span class="pre">aln_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> with the original
-source(s) of the alignment: may be filename(s) or JSON strings.</li>
+check for sequence roles <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> or <code class="docutils literal notranslate"><span class="pre">TEMPLATE</span></code></p></li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">aln_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> with the original
+source(s) of the alignment: may be filename(s) or JSON strings.</p></li>
</ul>
<p>Exit codes related to alignment input:</p>
<ul class="simple">
-<li>12 - a given alignment file does not exist</li>
-<li>13 - never raised (parameter for checking gzip files)</li>
-<li>14 - gzip file cannot be opened</li>
-<li>15 - found an empty alignment file</li>
-<li>16 - unsupported number of sequences in alignment: only 1 sequence or
-(unless <em>allow_multitemplate</em> = True) more than 2 sequences</li>
-<li>17 - mutliple target sequences found in alignment</li>
-<li>18 - error when reading fasta/clustal file</li>
-<li>19 - problem with a JSON formatted file handed over to <code class="docutils literal"><span class="pre">--json</span></code></li>
-<li>20 - JSON file could not be decoded into a JSON object</li>
-<li>21 - JSON object has no ‘alignmentlist’ key</li>
-<li>22 - JSON object has no ‘target’/’template’ in the ‘alignmentlist’</li>
-<li>23 - JSON string could not be decoded</li>
-<li>24 - JSON object ‘alignmentlist’ does not point to a list</li>
-<li>25 - JSON object ‘alignmentlist’ member is not a dictionary</li>
-<li>26 - JSON object ‘alignmentlist’ ‘target’/’template’ does not point
-to a dictionary</li>
-<li>27 - JSON object ‘alignmentlist’ ‘target’/’template’ does not have
-a needed key</li>
-<li>28 - JSON object ‘alignmentlist’ ‘target’/’template’ has a value of
-wrong type</li>
+<li><p>12 - a given alignment file does not exist</p></li>
+<li><p>13 - never raised (parameter for checking gzip files)</p></li>
+<li><p>14 - gzip file cannot be opened</p></li>
+<li><p>15 - found an empty alignment file</p></li>
+<li><p>16 - unsupported number of sequences in alignment: only 1 sequence or
+(unless <em>allow_multitemplate</em> = True) more than 2 sequences</p></li>
+<li><p>17 - mutliple target sequences found in alignment</p></li>
+<li><p>18 - error when reading fasta/clustal file</p></li>
+<li><p>19 - problem with a JSON formatted file handed over to <code class="docutils literal notranslate"><span class="pre">--json</span></code></p></li>
+<li><p>20 - JSON file could not be decoded into a JSON object</p></li>
+<li><p>21 - JSON object has no ‘alignmentlist’ key</p></li>
+<li><p>22 - JSON object has no ‘target’/’template’ in the ‘alignmentlist’</p></li>
+<li><p>23 - JSON string could not be decoded</p></li>
+<li><p>24 - JSON object ‘alignmentlist’ does not point to a list</p></li>
+<li><p>25 - JSON object ‘alignmentlist’ member is not a dictionary</p></li>
+<li><p>26 - JSON object ‘alignmentlist’ ‘target’/’template’ does not point
+to a dictionary</p></li>
+<li><p>27 - JSON object ‘alignmentlist’ ‘target’/’template’ does not have
+a needed key</p></li>
+<li><p>28 - JSON object ‘alignmentlist’ ‘target’/’template’ has a value of
+wrong type</p></li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddFragments">
-<code class="descname">AddFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline option for usage of Fragments</p>
<p>Activate everything needed to setup
-<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.FraggerHandle</span></code></a> objects in the argument parser.
-Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
-input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
+<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a> objects in the argument parser.
+Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> and the
+input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">-r/--use-fragments</span></code> - Boolean flag whether to setup fragger handles.</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">-r/--use-fragments</span></code> - Boolean flag whether to setup fragger handles.</p></li>
</ul>
<p>Notes:</p>
<ul class="simple">
-<li>Fragger handles are setup to identify fragments in a
-<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.StructureDB</span></code></a>.</li>
-<li>If no profiles are provided as additional argument
-(<code class="docutils literal"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code>), fragments are identified based on BLOSUM62
-sequence similarity.</li>
-<li>If you provide profiles that are not in hhm format, fragments are
+<li><p>Fragger handles are setup to identify fragments in a
+<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.StructureDB</span></code></a>.</p></li>
+<li><p>If no profiles are provided as additional argument
+(<code class="docutils literal notranslate"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code>), fragments are identified based on BLOSUM62
+sequence similarity.</p></li>
+<li><p>If you provide profiles that are not in hhm format, fragments are
identified based on BLOSUM62 sequence similarity, sequence profile
-scoring and structural profile scoring.</li>
-<li>If you provide profiles in hhm format (optimal case), psipred
+scoring and structural profile scoring.</p></li>
+<li><p>If you provide profiles in hhm format (optimal case), psipred
predictions are fetched from there and fragments are identified based
on secondary structure agreement, secondary structure dependent
torsion probabilities, sequence profile scoring and structure
-profile scoring.</li>
+profile scoring.</p></li>
</ul>
-<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
+<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><code class="xref py py-attr docutils literal"><span class="pre">fragger_handles</span></code> - <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
-<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>, ordered to match the target
-sequences.</li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">fragger_handles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>, ordered to match the target
+sequences.</p></li>
</ul>
<p>Exit codes related to fragments input:</p>
<ul class="simple">
-<li>56 - cannot read psipred prediction from hhm file</li>
+<li><p>56 - cannot read psipred prediction from hhm file</p></li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">
-<code class="descname">AddProfile</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddProfile</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline options for profiles</p>
<p>Activate everything needed to load profiles to the argument parser.
-Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
-input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
+Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> and the
+input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code> - Sequence profile in any format readable
-by the <code class="xref py py-meth docutils literal"><span class="pre">ost.io.LoadSequenceProfile()</span></code> method. Format is chosen by
+<li><p><code class="docutils literal notranslate"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code> - Sequence profile in any format readable
+by the <code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.io.LoadSequenceProfile()</span></code> method. Format is chosen by
file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
.pssm.gz. Consider to use
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
-in a3m format at hand.</li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
+in a3m format at hand.</p></li>
</ul>
<p>Notes:</p>
<ul class="simple">
-<li>the profiles are mapped based on exact matches towards the gapless
+<li><p>the profiles are mapped based on exact matches towards the gapless
target sequences, i.e. one profile is mapped to several chains in
-case of homo-oligomers</li>
-<li>every profile must have a unique sequence to avoid ambiguities</li>
-<li>all or nothing - you cannot provide profiles for only a subset of
-target sequences</li>
+case of homo-oligomers</p></li>
+<li><p>every profile must have a unique sequence to avoid ambiguities</p></li>
+<li><p>all or nothing - you cannot provide profiles for only a subset of
+target sequences</p></li>
</ul>
-<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
+<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
-ordered to match the target sequences.</li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
+ordered to match the target sequences.</p></li>
</ul>
<p>Exit codes related to profile input:</p>
<ul class="simple">
-<li>51 - a given profile file does not exist</li>
-<li>52 - failure to read a given profile file</li>
-<li>53 - a profile cannot be mapped to any target sequence</li>
-<li>54 - profile sequences are not unique</li>
-<li>55 - only subset of target sequences is covered by profile</li>
+<li><p>51 - a given profile file does not exist</p></li>
+<li><p>52 - failure to read a given profile file</p></li>
+<li><p>53 - a profile cannot be mapped to any target sequence</p></li>
+<li><p>54 - profile sequences are not unique</p></li>
+<li><p>55 - only subset of target sequences is covered by profile</p></li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">
-<code class="descname">AddStructure</code><span class="sig-paren">(</span><em>attach_views=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddStructure</code><span class="sig-paren">(</span><em class="sig-param">attach_views=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline options for structures.</p>
<p>Activate everything needed to load structures to the argument parser.
-Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
-input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>attach_views</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True: attach views to alignments. Requires call
-to <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment"><code class="xref py py-meth docutils literal"><span class="pre">AddAlignment()</span></code></a>. Chains for each sequence
+Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> and the
+input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>attach_views</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True: attach views to alignments. Requires call
+to <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddAlignment()</span></code></a>. Chains for each sequence
are identified based on the sequence name of the
templates in the alignments (see
-<a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">-p/--pdb</span> <span class="pre"><FILE></span></code> - Structure in PDB format. File can be plain or
-gzipped.</li>
-<li><code class="docutils literal"><span class="pre">-e/--entity</span> <span class="pre"><FILE></span></code> - Structure in any format readable by the
-<code class="xref py py-meth docutils literal"><span class="pre">ost.io.LoadEntity()</span></code> method. Format is chosen by file ending.
-Recognized File Extensions: .ent, .pdb, .ent.gz, .pdb.gz, .cif, .cif.gz.</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">-p/--pdb</span> <span class="pre"><FILE></span></code> - Structure in PDB format. File can be plain or
+gzipped.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">-e/--entity</span> <span class="pre"><FILE></span></code> - Structure in any format readable by the
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code> method. Format is chosen by file ending.
+Recognized File Extensions: .ent, .pdb, .ent.gz, .pdb.gz, .cif, .cif.gz.</p></li>
</ul>
<p>Notes:</p>
<ul class="simple">
-<li>one of the inputs must be given and only one type of input acceptable</li>
-<li>callable multiple times (structures appended in given order)</li>
+<li><p>one of the inputs must be given and only one type of input acceptable</p></li>
+<li><p>callable multiple times (structures appended in given order)</p></li>
</ul>
-<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
+<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><code class="xref py py-attr docutils literal"><span class="pre">pdb</span></code> - filled with the input of the <code class="docutils literal"><span class="pre">--pdb</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> (filenames).</li>
-<li><code class="xref py py-attr docutils literal"><span class="pre">entity</span></code> - filled with the input of the <code class="docutils literal"><span class="pre">--entity</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> (filenames).</li>
-<li><code class="xref py py-attr docutils literal"><span class="pre">structures</span></code> - <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal"><span class="pre">ost.EntityHandle</span></code>, same
-order as given.</li>
-<li><code class="xref py py-attr docutils literal"><span class="pre">structure_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> with the
-original filenames of the structures.</li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">pdb</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--pdb</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">entity</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--entity</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">structures</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.EntityHandle</span></code>, same
+order as given.</p></li>
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">structure_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> with the
+original filenames of the structures.</p></li>
</ul>
<p>Exit codes related to alignment input:</p>
<ul class="simple">
-<li>32 - a given structure file does not exist</li>
-<li>33 - failure to read a given structure file</li>
-<li>34 - file ending is not a supported format</li>
+<li><p>32 - a given structure file does not exist</p></li>
+<li><p>33 - failure to read a given structure file</p></li>
+<li><p>34 - file ending is not a supported format</p></li>
</ul>
<p>Exit codes if <em>attach_views</em> = True:</p>
<ul class="simple">
-<li>41 - attach_views used without adding alignments</li>
-<li>42 - inconsistent offsets between seq. name and seq. in alignment</li>
-<li>43 - non-integer offset defined in seq. name</li>
-<li>44 - too many “|” in seq. name</li>
-<li>45 - chain to attach to sequence could not be identified</li>
+<li><p>41 - attach_views used without adding alignments</p></li>
+<li><p>42 - inconsistent offsets between seq. name and seq. in alignment</p></li>
+<li><p>43 - non-integer offset defined in seq. name</p></li>
+<li><p>44 - too many “|” in seq. name</p></li>
+<li><p>45 - chain to attach to sequence could not be identified</p></li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">
-<code class="descname">AssembleParser</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="Permalink to this definition">¶</a></dt>
-<dd><p>When adding options via the <code class="xref py py-meth docutils literal"><span class="pre">Add*()</span></code> methods, call this after you
+<code class="sig-name descname">AssembleParser</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="Permalink to this definition">¶</a></dt>
+<dd><p>When adding options via the <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods, call this after you
are done. Everything before just tells the parser that it should
contain those option sets but does not actually add anything.
-<a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> will put everything in place, in the right order
+<a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> will put everything in place, in the right order
and with the right constraints.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.Parse">
-<code class="descname">Parse</code><span class="sig-paren">(</span><em>args=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="Permalink to this definition">¶</a></dt>
-<dd><p>Parse an argument string. See <code class="xref py py-meth docutils literal"><span class="pre">Add*()</span></code> methods.</p>
-<p>Options/arguments added by default: <code class="docutils literal"><span class="pre">-h/--help</span></code> shows usage.</p>
+<code class="sig-name descname">Parse</code><span class="sig-paren">(</span><em class="sig-param">args=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="Permalink to this definition">¶</a></dt>
+<dd><p>Parse an argument string. See <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods.</p>
+<p>Options/arguments added by default: <code class="docutils literal notranslate"><span class="pre">-h/--help</span></code> shows usage.</p>
<p>General exit codes:</p>
<ul class="simple">
-<li>1 - an unhandled exception was raised</li>
-<li>2 - arguments cannot be parsed or required arguments are missing</li>
+<li><p>1 - an unhandled exception was raised</p></li>
+<li><p>2 - arguments cannot be parsed or required arguments are missing</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – The argument string. As default <a class="reference external" href="https://docs.python.org/3.6/library/sys.html#sys.argv"><code class="xref py py-attr docutils literal"><span class="pre">sys.argv</span></code></a> is used.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Namespace filled with attributes (see <code class="xref py py-meth docutils literal"><span class="pre">Add*()</span></code> methods).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>args</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – The argument string. As default <a class="reference external" href="https://docs.python.org/3.7/library/sys.html#sys.argv"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sys.argv</span></code></a> is used.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Namespace filled with attributes (see <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods).</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -387,44 +358,70 @@ and with the right constraints.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a><ul>
-<li><a class="reference internal" href="#introduction">Introduction</a></li>
-<li><a class="reference internal" href="#argument-parser">Argument Parser</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
- <li>Next: <a href="helper.html" title="next chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+ <li>Next: <a href="helper.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/core/pm3argparse.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -433,11 +430,11 @@ and with the right constraints.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/core/pm3argparse.txt"
+ <a href="../_sources/core/pm3argparse.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index d296ef538a708eb7b6b0c81cfd4bc0d8bb15c8cd..582468d7f5dc3c6264b06baf0f3e75ffa7d8c18d 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Runtime profiling — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Runtime profiling — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
<link rel="prev" title="Geometry functions" href="geometry.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -51,11 +37,11 @@
<h1>Runtime profiling<a class="headerlink" href="#runtime-profiling" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="promod3.core.StaticRuntimeProfiler">
-<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StaticRuntimeProfiler</code><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StaticRuntimeProfiler</code><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler" title="Permalink to this definition">¶</a></dt>
<dd><p>Defines functionality for runtime profiling.</p>
<p>All profiling is completely turned off by default and must be activated at
-compile-time by adding <code class="docutils literal"><span class="pre">-DPM3_RUNTIME_PROFILING_LEVEL=N</span></code> to your CMake
-call, where <code class="docutils literal"><span class="pre">N</span></code> must be larger than 0. If turned off, all these functions
+compile-time by adding <code class="docutils literal notranslate"><span class="pre">-DPM3_RUNTIME_PROFILING_LEVEL=N</span></code> to your CMake
+call, where <code class="docutils literal notranslate"><span class="pre">N</span></code> must be larger than 0. If turned off, all these functions
will still exist and work but will not do anything. Functionality in the C++
code is usually profiled at level 2, while Python functionality is profiled
at level 1. The default profiling only covers the steps of the modelling
@@ -65,99 +51,83 @@ generated considering the number of timings and the total runtime for that
timer. If a timer within another timed entity, the outer timer is paused,
while the inner one is running. Hence, the sum of all timers will be the
total time spent in any timer (nothing is counted twice!).</p>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.core.StaticRuntimeProfiler.Start">
-<em class="property">static </em><code class="descname">Start</code><span class="sig-paren">(</span><em>id</em>, <em>level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Start" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Start</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Start" title="Permalink to this definition">¶</a></dt>
<dd><p>Start a timer for the given <cite>id</cite>. This pauses any other currently running
timer.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Identifier for this timer.</li>
-<li><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Identifier for this timer.</p></li>
+<li><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.core.StaticRuntimeProfiler.StartScoped">
-<em class="property">static </em><code class="descname">StartScoped</code><span class="sig-paren">(</span><em>id</em>, <em>level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.StartScoped" title="Permalink to this definition">¶</a></dt>
-<dd><p>Start a timer for the given <cite>id</cite> as in <a class="reference internal" href="#promod3.core.StaticRuntimeProfiler.Start" title="promod3.core.StaticRuntimeProfiler.Start"><code class="xref py py-meth docutils literal"><span class="pre">Start()</span></code></a>, but this will stop it
+<em class="property">static </em><code class="sig-name descname">StartScoped</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.StartScoped" title="Permalink to this definition">¶</a></dt>
+<dd><p>Start a timer for the given <cite>id</cite> as in <a class="reference internal" href="#promod3.core.StaticRuntimeProfiler.Start" title="promod3.core.StaticRuntimeProfiler.Start"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Start()</span></code></a>, but this will stop it
automatically when the returned variable goes out of scope.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Identifier for this timer.</li>
-<li><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Identifier for this timer.</p></li>
+<li><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Object that will call <a class="reference internal" href="#promod3.core.StaticRuntimeProfiler.Stop" title="promod3.core.StaticRuntimeProfiler.Stop"><code class="xref py py-meth docutils literal"><span class="pre">Stop()</span></code></a> when it goes out of scope</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Object that will call <a class="reference internal" href="#promod3.core.StaticRuntimeProfiler.Stop" title="promod3.core.StaticRuntimeProfiler.Stop"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Stop()</span></code></a> when it goes out of scope</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.core.StaticRuntimeProfiler.Stop">
-<em class="property">static </em><code class="descname">Stop</code><span class="sig-paren">(</span><em>id</em>, <em>level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Stop" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Stop</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Stop" title="Permalink to this definition">¶</a></dt>
<dd><p>Stop the currently running timer. If a timer was paused when starting this
timer, it will be resumed now. Note that there is no error checking here, so
this will fail miserably if no timer is currently running.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Timer only stopped if level <= <code class="docutils literal"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only stopped if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.core.StaticRuntimeProfiler.PrintSummary">
-<em class="property">static </em><code class="descname">PrintSummary</code><span class="sig-paren">(</span><em>max_to_show=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.PrintSummary" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">PrintSummary</code><span class="sig-paren">(</span><em class="sig-param">max_to_show=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.PrintSummary" title="Permalink to this definition">¶</a></dt>
<dd><p>Display a summary of all timed entities. The timers are collected by id and
-sorted by total runtime. If more than 10 entries are shown and the used id’s
-have the form “GROUP::NAME”, an additional summary is shown with the total
-times spent in each “GROUP”.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>max_to_show</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – if >= 0, show only top <cite>max_to_show</cite> entries.</td>
-</tr>
-</tbody>
-</table>
+sorted by total runtime. If more than 10 entries are shown and the used id’s
+have the form “GROUP::NAME”, an additional summary is shown with the total
+times spent in each “GROUP”.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>max_to_show</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – if >= 0, show only top <cite>max_to_show</cite> entries.</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.core.StaticRuntimeProfiler.IsEnabled">
-<em class="property">static </em><code class="descname">IsEnabled</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.IsEnabled" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if <code class="docutils literal"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code> > 0. Otherwise, profiling
-is completely turned off.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">IsEnabled</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.IsEnabled" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code> > 0. Otherwise, profiling
+is completely turned off.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.core.StaticRuntimeProfiler.Clear">
-<em class="property">static </em><code class="descname">Clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Clear" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Clear" title="Permalink to this definition">¶</a></dt>
<dd><p>Clears all timed entries. Note that there is no error checking here, so this
will fail miserably if timers are currently running.</p>
</dd></dl>
@@ -172,12 +142,46 @@ will fail miserably if timers are currently running.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
<li>Previous: <a href="geometry.html" title="previous chapter">Geometry functions</a></li>
<li>Next: <a href="graph_minimizer.html" title="next chapter">Graph Minimizer</a></li>
</ul></li>
@@ -185,23 +189,24 @@ will fail miserably if timers are currently running.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/core/runtime_profiling.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -210,11 +215,11 @@ will fail miserably if timers are currently running.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/core/runtime_profiling.txt"
+ <a href="../_sources/core/runtime_profiling.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 7e638ed7070920d70ffd609d27ed378ef541dbf7..1d70eb8ef4e399229e0f50fa86da6976d9f135e0 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>SetCompoundsChemlib() — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>SetCompoundsChemlib() — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Contributing" href="../user_contributions.html" />
<link rel="prev" title="Graph Minimizer" href="graph_minimizer.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,8 +34,8 @@
<div class="body" role="main">
<div class="section" id="setcompoundschemlib">
-<h1><a class="reference internal" href="#promod3.SetCompoundsChemlib" title="promod3.SetCompoundsChemlib"><code class="xref py py-func docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a><a class="headerlink" href="#setcompoundschemlib" title="Permalink to this headline">¶</a></h1>
-<p>This is the one function defined on the highest level of ProMod3‘s module
+<h1><a class="reference internal" href="#promod3.SetCompoundsChemlib" title="promod3.SetCompoundsChemlib"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a><a class="headerlink" href="#setcompoundschemlib" title="Permalink to this headline">¶</a></h1>
+<p>This is the one function defined on the highest level of ProMod3’s module
hierarchy. It is used to load an OST compound library to avoid running
Python code via the ancient OST wrapper. Applying this function at
top-level, we can set a decent default by CMake plus the library is
@@ -58,17 +44,14 @@ need to call this function, only if you want to load a different chemical
components dictionary.</p>
<dl class="function">
<dt id="promod3.SetCompoundsChemlib">
-<code class="descclassname">promod3.</code><code class="descname">SetCompoundsChemlib</code><span class="sig-paren">(</span><em>path_to_chemlib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.SetCompoundsChemlib" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.</code><code class="sig-name descname">SetCompoundsChemlib</code><span class="sig-paren">(</span><em class="sig-param">path_to_chemlib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.SetCompoundsChemlib" title="Permalink to this definition">¶</a></dt>
<dd><p>Load a compounds library. Does not return anything, the library is just
enabled globally.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>path_to_chemlib</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Points to the file to be loaded.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>path_to_chemlib</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Points to the file to be loaded.</p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -79,7 +62,41 @@ enabled globally.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
@@ -90,23 +107,24 @@ enabled globally.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/core/setcompoundschemlib.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -115,11 +133,11 @@ enabled globally.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/core/setcompoundschemlib.txt"
+ <a href="../_sources/core/setcompoundschemlib.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 2ce0d2e68bdda8b310541a5cf0183c5f619f173e..2fbffee7db4c76ed82c28399265785a34c4ca09e 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>ProMod3 Setup — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>ProMod3 Setup — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="Contributing" href="contributing.html" />
<link rel="prev" title="Documentation For Developers" href="developers.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -55,29 +41,29 @@ Git branches, the directory structure and tightly linked with this also
CMake.</p>
<div class="section" id="git-branches">
<span id="id1"></span><h2>Git Branches<a class="headerlink" href="#git-branches" title="Permalink to this headline">¶</a></h2>
-<p>Basically we have two, sometimes three major branches. <code class="docutils literal"><span class="pre">master</span></code>, <code class="docutils literal"><span class="pre">develop</span></code>
+<p>Basically we have two, sometimes three major branches. <code class="docutils literal notranslate"><span class="pre">master</span></code>, <code class="docutils literal notranslate"><span class="pre">develop</span></code>
and in front of a new release a dedicated release branch. For bugs, hotfix
branches of a rather short life are used.</p>
-<p><code class="docutils literal"><span class="pre">master</span></code> is the stable branch, corresponding to a released version. It is
+<p><code class="docutils literal notranslate"><span class="pre">master</span></code> is the stable branch, corresponding to a released version. It is
solely fed by a release or hotfix branch.</p>
-<p>Release branches, usually labelled <code class="docutils literal"><span class="pre">release-<VERSION></span></code>, are branched of
-<code class="docutils literal"><span class="pre">develop</span></code> to fix features and thoroughly test them before a new major
+<p>Release branches, usually labelled <code class="docutils literal notranslate"><span class="pre">release-<VERSION></span></code>, are branched of
+<code class="docutils literal notranslate"><span class="pre">develop</span></code> to fix features and thoroughly test them before a new major
release. Once everything looks trustworthy, such a branch is merged into
-<code class="docutils literal"><span class="pre">master</span></code> and since there should be a few bug fixes in, <code class="docutils literal"><span class="pre">master</span></code> is merged
-into <code class="docutils literal"><span class="pre">develop</span></code>. Bugs are fixed in dedicated hotfix branches, which should
+<code class="docutils literal notranslate"><span class="pre">master</span></code> and since there should be a few bug fixes in, <code class="docutils literal notranslate"><span class="pre">master</span></code> is merged
+into <code class="docutils literal notranslate"><span class="pre">develop</span></code>. Bugs are fixed in dedicated hotfix branches, which should
only exist for the fix and testing itself. Those are forged from release
-branches or <code class="docutils literal"><span class="pre">master</span></code>. If created for <code class="docutils literal"><span class="pre">master</span></code>, they are also merged back
-into <code class="docutils literal"><span class="pre">develop</span></code>.</p>
-<p>The <code class="docutils literal"><span class="pre">develop</span></code> branch exists to introduce new features up to the level of
+branches or <code class="docutils literal notranslate"><span class="pre">master</span></code>. If created for <code class="docutils literal notranslate"><span class="pre">master</span></code>, they are also merged back
+into <code class="docutils literal notranslate"><span class="pre">develop</span></code>.</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">develop</span></code> branch exists to introduce new features up to the level of
whole projects extending ProMod3 and see that they work seamlessly together
with the rest of the system. There do exist a couple of rather strict rules for
what goes into this branch:</p>
<ul class="simple">
-<li>Your code must have been (briefly) reviewed by others</li>
-<li>There have to be unit tests</li>
-<li>It needs to pass <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code> <strong>including</strong> <code class="docutils literal"><span class="pre">doctest</span></code> & <code class="docutils literal"><span class="pre">linkcheck</span></code></li>
-<li>Your project needs documentation</li>
-<li>It must not break the ability of out-of-source builds</li>
+<li><p>Your code must have been (briefly) reviewed by others</p></li>
+<li><p>There have to be unit tests</p></li>
+<li><p>It needs to pass <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> <strong>including</strong> <code class="docutils literal notranslate"><span class="pre">doctest</span></code> & <code class="docutils literal notranslate"><span class="pre">linkcheck</span></code></p></li>
+<li><p>Your project needs documentation</p></li>
+<li><p>It must not break the ability of out-of-source builds</p></li>
</ul>
<p>The reason to be a bit restrictive on branches which end up in actual releases,
should be mostly obvious: ProMod3 is used by productive services as a third
@@ -90,20 +76,20 @@ the end for you, fixing the problems.</p>
<p>The place where you may get messy is your own Git branch within the ProMod3
repository. This is basically where you should develop your project. Once you
created something that could go into a release, tidy things up according to the
-rules from above and merge it into <code class="docutils literal"><span class="pre">develop</span></code>. From there it will
+rules from above and merge it into <code class="docutils literal notranslate"><span class="pre">develop</span></code>. From there it will
automatically find its way into the next release.</p>
-<p>To set up your own branch, start from a current <code class="docutils literal"><span class="pre">develop</span></code> branch:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop <span class="c1"># switch to branch develop</span>
+<p>To set up your own branch, start from a current <code class="docutils literal notranslate"><span class="pre">develop</span></code> branch:</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop <span class="c1"># switch to branch develop</span>
<span class="gp">$</span> git pull --rebase <span class="c1"># update branch develop</span>
<span class="gp">$</span> git checkout -b <BRANCHNAME> <span class="c1"># create branch <BRANCHNAME> and switch to it</span>
</pre></div>
</div>
-<p>Over time, <code class="docutils literal"><span class="pre">develop</span></code> may recognise some changes, e.g. new features, which you
+<p>Over time, <code class="docutils literal notranslate"><span class="pre">develop</span></code> may recognise some changes, e.g. new features, which you
want to make use of in your project. Keeping your branch up to date is a three
step process. Git does not allow updates on top of changed code, so either
changes have to be committed, or if in the middle of implementing something,
stored away temporarily. Making commits is straight forward:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit -m <span class="s1">'<DESCRIPTION>'</span> <span class="c1"># commit changes including a comment</span>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit -m <span class="s1">'<DESCRIPTION>'</span> <span class="c1"># commit changes including a comment</span>
</pre></div>
</div>
<p>Hiding your changes away from Git just for updating files is a bit more
@@ -114,15 +100,15 @@ you have changed, too, and stashed away, this may end up in a non-resolvable
merge conflict and your changes are lost. Usually the log tells you, which
files were recently modified. Moving all current changes to the stack is
achieved by:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash save
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash save
</pre></div>
</div>
<p>To revive them, use:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash pop
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash pop
</pre></div>
</div>
-<p>After cleaning up your branch, switch to <code class="docutils literal"><span class="pre">develop</span></code>, update it and switch back:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
+<p>After cleaning up your branch, switch to <code class="docutils literal notranslate"><span class="pre">develop</span></code>, update it and switch back:</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
<span class="gp">$</span> git pull --rebase
<span class="gp">$</span> git checkout <BRANCHNAME>
</pre></div>
@@ -130,12 +116,12 @@ achieved by:</p>
<p>Now for actually updating your branch, there are two different ways: merging
and rebasing. A rebase may only be done, if you <strong>never</strong> pushed your branch to
the origin of the repository (otherwise you will mess up history, in the worst
-case <code class="docutils literal"><span class="pre">develop</span></code> may be unusable once you merge):</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git rebase develop
+case <code class="docutils literal notranslate"><span class="pre">develop</span></code> may be unusable once you merge):</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git rebase develop
</pre></div>
</div>
<p>For branches which are available to others, do a proper merge:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git merge develop
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git merge develop
</pre></div>
</div>
<p>This may require some manual conflict solving and will end up in a merge commit.</p>
@@ -144,17 +130,17 @@ case <code class="docutils literal"><span class="pre">develop</span></code> may
<h2>Git Hooks<a class="headerlink" href="#git-hooks" title="Permalink to this headline">¶</a></h2>
<p>Git hooks are scripts invoked by Git in connection to certain commands.
ProMod3 currently provides one for <strong class="command">commit</strong>. It is installed by</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
</pre></div>
</div>
<p>Its task is applying coding standards and doing a bunch of other checks on the
files involved in a commit. Everything around the script is hosted in
-<code class="file docutils literal"><span class="pre">extras/pre_commit/</span></code>. The checks can be manually executed with</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> python .git/hooks/pre-commit
+<code class="file docutils literal notranslate"><span class="pre">extras/pre_commit/</span></code>. The checks can be manually executed with</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> python .git/hooks/pre-commit
</pre></div>
</div>
<p>If you ever have to skip the hook,</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit --no-verify
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit --no-verify
</pre></div>
</div>
<p>does the trick. <strong>But</strong> checks are always run on the complete file containing
@@ -167,20 +153,20 @@ PEP 8 sounds overly restrictive but it may help with performance and
compatibility with Python 3. For ProMod3 it is also important that the code
looks similar throughout the various modules. So do not disable a check because
it just seems inconvenient or you do not understand why Pylint is croaking at
-what looks like ‘working’ code. But then there are also cases where Pylint is
+what looks like ‘working’ code. But then there are also cases where Pylint is
not smart enough to cope with valid PEP 8 code. For changes with valid cause,
the configuration flushed into Pylint may be found at
-<code class="file docutils literal"><span class="pre">extras/pre_commit/pm3_csc/filecheck/pylintrc</span></code> and
-<code class="file docutils literal"><span class="pre">extras/pre_commit/pm3_csc/filecheck/pylint-unittest-rc</span></code>. The latter one
+<code class="file docutils literal notranslate"><span class="pre">extras/pre_commit/pm3_csc/filecheck/pylintrc</span></code> and
+<code class="file docutils literal notranslate"><span class="pre">extras/pre_commit/pm3_csc/filecheck/pylint-unittest-rc</span></code>. The latter one
is invoked on unit test code, where we may go a little bit less restrictive.</p>
</div>
<div class="section" id="directory-structure">
<h2>Directory Structure<a class="headerlink" href="#directory-structure" title="Permalink to this headline">¶</a></h2>
-<p>The directory structure of the ProMod3 repository is supposed to ‘keep
-everything together that belongs together’. That is, code, documentation and
+<p>The directory structure of the ProMod3 repository is supposed to ‘keep
+everything together that belongs together’. That is, code, documentation and
extra data should be gathered on a per-module basis immediately in the
repository root. The directory structure of your module should look like this:</p>
-<div class="highlight-text"><div class="highlight"><pre><span></span>promod3.git/ Project folder
+<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>promod3.git/ Project folder
your_module/ Module directory
CMakeLists.txt CMake configuration
data/ Extra data (if needed)
@@ -211,22 +197,22 @@ repository root. The directory structure of your module should look like this:</
</div>
<p>Additionally to the module directories there are a few extra folders:</p>
<ul class="simple">
-<li><code class="file docutils literal"><span class="pre">actions</span></code>: Scripts callable as <code class="docutils literal"><span class="pre">pm</span> <span class="pre"><ACTION_NAME></span></code>.
-See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span class="std std-ref">here</span></a> for details.</li>
-<li><code class="file docutils literal"><span class="pre">cmake_support</span></code>: Helper functions for CMake.
-See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a> for details.</li>
-<li><code class="file docutils literal"><span class="pre">doc</span></code>: High-level documentation, test scripts (<code class="file docutils literal"><span class="pre">doc/tests</span></code>) and a
-copy of the generated html documentation (<code class="file docutils literal"><span class="pre">doc/html</span></code>). The latter must
-be kept up-to-date at least on the <code class="docutils literal"><span class="pre">master</span></code> branch.
-See <a class="reference internal" href="contributing.html#writing-documentation"><span class="std std-ref">here</span></a> for details.</li>
-<li><code class="file docutils literal"><span class="pre">extras</span></code>: Extra data and information that doesn’t fit anywhere
-else (e.g. Git hooks or scripts to recreate the binary files).</li>
-<li><code class="file docutils literal"><span class="pre">scripts</span></code>: Input for scripts that end up in <code class="file docutils literal"><span class="pre">stage/bin</span></code></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">actions</span></code>: Scripts callable as <code class="docutils literal notranslate"><span class="pre">pm</span> <span class="pre"><ACTION_NAME></span></code>.
+See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span class="std std-ref">here</span></a> for details.</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">cmake_support</span></code>: Helper functions for CMake.
+See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a> for details.</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">doc</span></code>: High-level documentation, test scripts (<code class="file docutils literal notranslate"><span class="pre">doc/tests</span></code>) and a
+copy of the generated html documentation (<code class="file docutils literal notranslate"><span class="pre">doc/html</span></code>). The latter must
+be kept up-to-date at least on the <code class="docutils literal notranslate"><span class="pre">master</span></code> branch.
+See <a class="reference internal" href="contributing.html#writing-documentation"><span class="std std-ref">here</span></a> for details.</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">extras</span></code>: Extra data and information that doesn’t fit anywhere
+else (e.g. Git hooks or scripts to recreate the binary files).</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">scripts</span></code>: Input for scripts that end up in <code class="file docutils literal notranslate"><span class="pre">stage/bin</span></code></p></li>
</ul>
</div>
<div class="section" id="cmake">
<h2>CMake<a class="headerlink" href="#cmake" title="Permalink to this headline">¶</a></h2>
-<p>The attentive reader may have noticed all the <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> files in
+<p>The attentive reader may have noticed all the <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code> files in
the directory structure. Those are needed to configure the build system, e.g.
tell it which files have to be considered packaging, compiling, etc.. Also
Python modules are declared there as well as which files belong to the
@@ -239,12 +225,12 @@ CMake documentation all by yourself and on your own responsibility. You have
been warned.</p>
</div>
<div class="section" id="the-stage-directory">
-<h2>The <code class="file docutils literal"><span class="pre">stage</span></code> Directory<a class="headerlink" href="#the-stage-directory" title="Permalink to this headline">¶</a></h2>
-<p>Once you hit <strong class="command">make</strong> in your build directory, a directory <code class="file docutils literal"><span class="pre">stage</span></code>
+<h2>The <code class="file docutils literal notranslate"><span class="pre">stage</span></code> Directory<a class="headerlink" href="#the-stage-directory" title="Permalink to this headline">¶</a></h2>
+<p>Once you hit <strong class="command">make</strong> in your build directory, a directory <code class="file docutils literal notranslate"><span class="pre">stage</span></code>
in this path will be populated. It just resembles a directory structure as of a
usual Unix file system filled with the build products of ProMod3. The
-<code class="file docutils literal"><span class="pre">stage</span></code> directory tree can already be utilised. You may import Python
-modules from there, use the binaries from <code class="file docutils literal"><span class="pre">stage/bin</span></code>, etc..</p>
+<code class="file docutils literal notranslate"><span class="pre">stage</span></code> directory tree can already be utilised. You may import Python
+modules from there, use the binaries from <code class="file docutils literal notranslate"><span class="pre">stage/bin</span></code>, etc..</p>
</div>
</div>
@@ -255,17 +241,26 @@ modules from there, use the binaries from <code class="file docutils literal"><s
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">ProMod3 Setup</a><ul>
-<li><a class="reference internal" href="#git-branches">Git Branches</a></li>
-<li><a class="reference internal" href="#git-hooks">Git Hooks</a></li>
-<li><a class="reference internal" href="#directory-structure">Directory Structure</a></li>
-<li><a class="reference internal" href="#cmake">CMake</a></li>
-<li><a class="reference internal" href="#the-stage-directory">The <code class="file docutils literal"><span class="pre">stage</span></code> Directory</a></li>
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
</ul>
-</li>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -277,23 +272,24 @@ modules from there, use the binaries from <code class="file docutils literal"><s
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/dev_setup.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -302,11 +298,11 @@ modules from there, use the binaries from <code class="file docutils literal"><s
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/dev_setup.txt"
+ <a href="_sources/dev_setup.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 0105fb59fa8f87c8f46088308f34097fb1fde1a2..ab1e42355b429ad3c73807a44dbeacabd2ab44f3 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -1,32 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Documentation For Developers — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Documentation For Developers — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
<link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
<link rel="prev" title="Contributing" href="user_contributions.html" />
@@ -35,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -59,7 +46,7 @@ new features.</p>
<li class="toctree-l2"><a class="reference internal" href="dev_setup.html#git-hooks">Git Hooks</a></li>
<li class="toctree-l2"><a class="reference internal" href="dev_setup.html#directory-structure">Directory Structure</a></li>
<li class="toctree-l2"><a class="reference internal" href="dev_setup.html#cmake">CMake</a></li>
-<li class="toctree-l2"><a class="reference internal" href="dev_setup.html#the-stage-directory">The <code class="file docutils literal"><span class="pre">stage</span></code> Directory</a></li>
+<li class="toctree-l2"><a class="reference internal" href="dev_setup.html#the-stage-directory">The <code class="file docutils literal notranslate"><span class="pre">stage</span></code> Directory</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a><ul>
@@ -73,12 +60,12 @@ new features.</p>
<li class="toctree-l2"><a class="reference internal" href="contributing.html#third-party-contributions-license-issues">Third Party Contributions (License Issues)</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="actions/index_dev.html"><code class="docutils literal"><span class="pre">test_actions</span></code> - Testing Actions</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="actions/index_dev.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="actions/index_dev.html#creating-an-action-unit-test-script">Creating an Action Unit Test Script</a></li>
<li class="toctree-l2"><a class="reference internal" href="actions/index_dev.html#unit-test-actions-api">Unit Test Actions API</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="cmake/index.html">ProMod3‘s Share Of CMake</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="cmake/index.html">ProMod3’s Share Of CMake</a><ul>
<li class="toctree-l2"><a class="reference internal" href="cmake/index.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="cmake/index.html#functions-for-module-action-maintenance">Functions For Module/ Action Maintenance</a></li>
</ul>
@@ -100,7 +87,28 @@ new features.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
+</ul>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
@@ -109,23 +117,24 @@ new features.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/developers.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -134,11 +143,11 @@ new features.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/developers.txt"
+ <a href="_sources/developers.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 017b3982636d84c192d45bbaabe7fce5b19acde7..1677805e2e2dbb9ebd1aff421fce54cf8e316f07 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -1,41 +1,28 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Index — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Index — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -76,3984 +63,2230 @@
</div>
<h2 id="Symbols">Symbols</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li>
-f, --energy_function
- </dt>
- <dd><dl>
-
- <dt><a href="actions/index.html#cmdoption-f">command line option</a>
- </dt>
-
- </dl></dd>
-
- <dt>
+ <ul>
+ <li><a href="actions/index.html#cmdoption-f">command line option</a>
+</li>
+ </ul></li>
+ <li>
-i, --backbone-independent
- </dt>
- <dd><dl>
-
- <dt><a href="actions/index.html#cmdoption-i">command line option</a>
- </dt>
-
- </dl></dd>
-
- <dt>
+ <ul>
+ <li><a href="actions/index.html#cmdoption-i">command line option</a>
+</li>
+ </ul></li>
+ <li>
-k, --keep-sidechains
- </dt>
- <dd><dl>
-
- <dt><a href="actions/index.html#cmdoption-k">command line option</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt>
+ <ul>
+ <li><a href="actions/index.html#cmdoption-k">command line option</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li>
-n, --no-disulfids
- </dt>
- <dd><dl>
-
- <dt><a href="actions/index.html#cmdoption-n">command line option</a>
- </dt>
-
- </dl></dd>
-
- <dt>
+ <ul>
+ <li><a href="actions/index.html#cmdoption-n">command line option</a>
+</li>
+ </ul></li>
+ <li>
-r, --rigid-rotamers
- </dt>
- <dd><dl>
-
- <dt><a href="actions/index.html#cmdoption-r">command line option</a>
- </dt>
-
- </dl></dd>
-
- <dt>
+ <ul>
+ <li><a href="actions/index.html#cmdoption-r">command line option</a>
+</li>
+ </ul></li>
+ <li>
-s, --no-subrotamer-optimization
- </dt>
- <dd><dl>
-
- <dt><a href="actions/index.html#cmdoption-s">command line option</a>
- </dt>
-
- </dl></dd>
- </dl></td>
+ <ul>
+ <li><a href="actions/index.html#cmdoption-s">command line option</a>
+</li>
+ </ul></li>
+ </ul></td>
</tr></table>
<h2 id="_">_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.__getitem__">__getitem__() (promod3.loop.Fragger method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap.__getitem__">(promod3.loop.FraggerMap method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.__getitem__">(promod3.scoring.AllAtomOverallScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.__getitem__">(promod3.scoring.BackboneOverallScorer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.__getitem__">(promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.__getitem__">(promod3.sidechain.FRMRotamerGroup method)</a>
- </dt>
-
-
- <dt><a href="sidechain/frame.html#promod3.sidechain.FrameResidue.__getitem__">(promod3.sidechain.FrameResidue method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.__getitem__">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.__getitem__">(promod3.sidechain.RRMRotamerGroup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.__init__">__init__() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.__len__">__len__() (promod3.loop.BackboneList method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.__len__">(promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.__len__">(promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.__len__">(promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.__len__">(promod3.sidechain.FRMRotamerGroup method)</a>
- </dt>
-
-
- <dt><a href="sidechain/frame.html#promod3.sidechain.FrameResidue.__len__">(promod3.sidechain.FrameResidue method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.__len__">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.__len__">(promod3.sidechain.RRMRotamerGroup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap.__setitem__">__setitem__() (promod3.loop.FraggerMap method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.__setitem__">(promod3.scoring.AllAtomOverallScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.__setitem__">(promod3.scoring.BackboneOverallScorer method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.__getitem__">__getitem__() (promod3.loop.Fragger method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap.__getitem__">(promod3.loop.FraggerMap method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.__getitem__">(promod3.scoring.AllAtomOverallScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.__getitem__">(promod3.scoring.BackboneOverallScorer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.__getitem__">(promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.__getitem__">(promod3.sidechain.FRMRotamerGroup method)</a>
+</li>
+ <li><a href="sidechain/frame.html#promod3.sidechain.FrameResidue.__getitem__">(promod3.sidechain.FrameResidue method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.__getitem__">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.__getitem__">(promod3.sidechain.RRMRotamerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.__init__">__init__() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.__len__">__len__() (promod3.loop.BackboneList method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.__len__">(promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.__len__">(promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.__len__">(promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.__len__">(promod3.sidechain.FRMRotamerGroup method)</a>
+</li>
+ <li><a href="sidechain/frame.html#promod3.sidechain.FrameResidue.__len__">(promod3.sidechain.FrameResidue method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.__len__">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.__len__">(promod3.sidechain.RRMRotamerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap.__setitem__">__setitem__() (promod3.loop.FraggerMap method)</a>
+
+ <ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.__setitem__">(promod3.scoring.AllAtomOverallScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.__setitem__">(promod3.scoring.BackboneOverallScorer method)</a>
+</li>
+ </ul></li>
+ </ul></td>
</tr></table>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.AAToRotID">AAToRotID() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.action">action (promod3.core.pm3argparse.PM3ArgumentParser attribute)</a>
- </dt>
-
-
- <dt><a href="actions/index_dev.html#test_actions.ActionTestCase">ActionTestCase (class in test_actions)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.Add">Add() (promod3.loop.PsipredPrediction method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.Add">(promod3.modelling.LoopCandidates method)</a>
- </dt>
-
- </dl></dd>
-
- <dt>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.AAToRotID">AAToRotID() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.action">action (promod3.core.pm3argparse.PM3ArgumentParser attribute)</a>
+</li>
+ <li><a href="actions/index_dev.html#test_actions.ActionTestCase">ActionTestCase (class in test_actions)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.Add">Add() (promod3.loop.PsipredPrediction method)</a>
+
+ <ul>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.Add">(promod3.modelling.LoopCandidates method)</a>
+</li>
+ </ul></li>
+ <li>
add_doc_dependency
- </dt>
- <dd><dl>
-
- <dt><a href="cmake/index.html#command:add_doc_dependency"><strong>command</strong></a>
- </dt>
-
- </dl></dd>
-
- <dt>
+ <ul>
+ <li><a href="cmake/index.html#command:add_doc_dependency"><strong>command</strong></a>
+</li>
+ </ul></li>
+ <li>
add_doc_source
- </dt>
-
- <dd><dl>
-
- <dt><a href="cmake/index.html#index-0-command:add_doc_source">command</a>, <a href="cmake/index.html#index-1-command:add_doc_source">[1]</a>, <a href="cmake/index.html#command:add_doc_source"><strong>[2]</strong></a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">AddAlignment() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddCARestraint">AddCARestraint() (promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddCBRestraint">AddCBRestraint() (promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.AddCoordinates">AddCoordinates() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddCRestraint">AddCRestraint() (promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AddEdge">AddEdge() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.AddFragmentInfo">AddFragmentInfo() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments">AddFragments() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.AddFragments">(promod3.loop.FragDB method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.AddFrameEnergy">AddFrameEnergy() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.AddFrameEnergy">[1]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.AddFrameEnergy">(promod3.sidechain.FRMRotamerGroup method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.AddFrameEnergy">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.AddFrameEnergy">(promod3.sidechain.RRMRotamerGroup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.AddModellingIssue">AddModellingIssue() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AddNode">AddNode() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddNRestraint">AddNRestraint() (promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddORestraint">AddORestraint() (promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction">AddPairwiseFunction() (promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">AddProfile() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.AddRotamer">AddRotamer() (promod3.sidechain.BBDepRotamerLib method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.AddRotamer">(promod3.sidechain.RotamerLib method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSeqIDParameters">AddSeqIDParameters() (promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSeqSimParameters">AddSeqSimParameters() (promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSequenceProfileParameters">AddSequenceProfileParameters() (promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSSAgreeParameters">AddSSAgreeParameters() (promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">AddStructure() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddStructureProfileParameters">AddStructureProfileParameters() (promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.AddSubrotamerDefinition">AddSubrotamerDefinition() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddTorsionProbabilityParameters">AddTorsionProbabilityParameters() (promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.after">after (promod3.modelling.StructuralGap attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.alignment">alignment (promod3.modelling.MotifMatch attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer">all_atom_scorer (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer_env">all_atom_scorer_env (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_sidechain_env">all_atom_sidechain_env (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.all_pos">all_pos (promod3.loop.AllAtomEnvPositions attribute)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer">AllAtomClashScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnv">AllAtomEnv (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions">AllAtomEnvPositions (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer">AllAtomInteractionScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer">AllAtomOverallScorer (class in promod3.scoring)</a>
- </dt>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer">AllAtomPackingScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions">AllAtomPositions (class in promod3.loop)</a>
- </dt>
+ <ul>
+ <li><a href="cmake/index.html#index-0-command:add_doc_source">command</a>, <a href="cmake/index.html#index-1-command:add_doc_source">[1]</a>, <a href="cmake/index.html#command:add_doc_source"><strong>[2]</strong></a>
+</li>
+ </ul></li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">AddAlignment() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddCARestraint">AddCARestraint() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddCBRestraint">AddCBRestraint() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.AddCoordinates">AddCoordinates() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddCRestraint">AddCRestraint() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AddEdge">AddEdge() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.AddFragmentInfo">AddFragmentInfo() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments">AddFragments() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.AddFragments">(promod3.loop.FragDB method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.AddFrameEnergy">AddFrameEnergy() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.AddFrameEnergy">[1]</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.AddFrameEnergy">(promod3.sidechain.FRMRotamerGroup method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.AddFrameEnergy">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.AddFrameEnergy">(promod3.sidechain.RRMRotamerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.AddModellingIssue">AddModellingIssue() (in module promod3.modelling)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AddNode">AddNode() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddNRestraint">AddNRestraint() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddORestraint">AddORestraint() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction">AddPairwiseFunction() (promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">AddProfile() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.AddRotamer">AddRotamer() (promod3.sidechain.BBDepRotamerLib method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.AddRotamer">(promod3.sidechain.RotamerLib method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.AddSeqIDParameters">AddSeqIDParameters() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.AddSeqSimParameters">AddSeqSimParameters() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.AddSequenceProfileParameters">AddSequenceProfileParameters() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.AddSSAgreeParameters">AddSSAgreeParameters() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">AddStructure() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.AddStructureProfileParameters">AddStructureProfileParameters() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.AddSubrotamerDefinition">AddSubrotamerDefinition() (promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.AddTorsionProbabilityParameters">AddTorsionProbabilityParameters() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.after">after (promod3.modelling.StructuralGap attribute)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.alignment">alignment (promod3.modelling.MotifMatch attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer">all_atom_scorer (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer_env">all_atom_scorer_env (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_sidechain_env">all_atom_sidechain_env (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.all_pos">all_pos (promod3.loop.AllAtomEnvPositions attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer">AllAtomClashScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv">AllAtomEnv (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions">AllAtomEnvPositions (class in promod3.loop)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer">AllAtomInteractionScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer">AllAtomOverallScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer">AllAtomPackingScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions">AllAtomPositions (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">AllAtomPositions() (promod3.loop.AllAtomPositions method)</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">[1]</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">[2]</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">[3]</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer">AllAtomRelaxer (class in promod3.modelling)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer">AllAtomScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidAtom">AminoAcidAtom (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidHydrogen">AminoAcidHydrogen (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup">AminoAcidLookup (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.angle">angle (promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.angle">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant">angle_force_constant (promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_four">angle_four (promod3.core.StemPairOrientation attribute)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_one">angle_one (promod3.core.StemPairOrientation attribute)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_three">angle_three (promod3.core.StemPairOrientation attribute)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_two">angle_two (promod3.core.StemPairOrientation attribute)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.append">append() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.ApplyCCD">ApplyCCD() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.ApplyDEE">ApplyDEE() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.ApplyEdgeDecomposition">ApplyEdgeDecomposition() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.ApplyKIC">ApplyKIC() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ApplyOnResidue">ApplyOnResidue() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ApplyOnResidue">[1]</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.ApplyOnResidue">(promod3.sidechain.FRMRotamerGroup method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.ApplyOnResidue">(promod3.sidechain.RRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.ApplyOnResidue">[1]</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.ApplyOnResidue">(promod3.sidechain.RRMRotamerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction">ApplyPairwiseFunction() (promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh">ApplySelfEnergyThresh() (promod3.sidechain.FRMRotamerGroup method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh">(promod3.sidechain.RRMRotamerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.ApplyTransform">ApplyTransform() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.ApplyTransform">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.ApplyTransform">[2]</a>
+</li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">AssembleParser() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.AssignInternalEnergies">AssignInternalEnergies() (promod3.sidechain.RotamerConstructor method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL3RotamerConstructor method)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL4RotamerConstructor method)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies">(promod3.sidechain.VINARotamerConstructor method)</a>
+</li>
+ </ul></li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AStarSolve">AStarSolve() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor.AttachEnvironment">AttachEnvironment() (promod3.modelling.SidechainReconstructor method)</a>
+
+ <ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.AttachEnvironment">(promod3.scoring.AllAtomOverallScorer method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer.AttachEnvironment">(promod3.scoring.AllAtomScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.AttachEnvironment">(promod3.scoring.BackboneOverallScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer.AttachEnvironment">(promod3.scoring.BackboneScorer method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">AllAtomPositions() (promod3.loop.AllAtomPositions method)</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">[1]</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">[2]</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.AllAtomPositions">[3]</a>
- </dt>
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.backbone_scorer">backbone_scorer (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.backbone_scorer_env">backbone_scorer_env (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList">BackboneList (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">BackboneList() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[2]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[3]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[4]</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer">BackboneOverallScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer">BackboneRelaxer (class in promod3.modelling)</a>, <a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer">[1]</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv">BackboneScoreEnv (class in promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer">BackboneScorer (class in promod3.scoring)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib">BBDepRotamerLib (class in promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.before">before (promod3.modelling.StructuralGap attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant">bond_force_constant (promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.bond_length">bond_length (promod3.loop.ForcefieldBondInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.BuildFromRawModel">BuildFromRawModel() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.BuildRawModel">BuildRawModel() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.BuildSidechains">BuildSidechains() (in module promod3.modelling)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer">AllAtomRelaxer (class in promod3.modelling)</a>
- </dt>
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="core/geometry.html#promod3.core.StemCoords.c_coord">c_coord (promod3.core.StemCoords attribute)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemCoords.ca_coord">ca_coord (promod3.core.StemCoords attribute)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.Calculate">Calculate() (promod3.scoring.BackboneOverallScorer method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateAllAtomScores">CalculateAllAtomScores() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateBackboneScores">CalculateBackboneScores() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination">CalculateLinearCombination() (promod3.scoring.AllAtomOverallScorer method)</a>
+
+ <ul>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination">(promod3.scoring.BackboneOverallScorer method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer.CalculateScore">CalculateScore() (promod3.scoring.AllAtomScorer method)</a>
+
+ <ul>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer.CalculateScore">(promod3.scoring.BackboneScorer method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer.CalculateScoreProfile">CalculateScoreProfile() (promod3.scoring.AllAtomScorer method)</a>
+
+ <ul>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer.CalculateScoreProfile">(promod3.scoring.BackboneScorer method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores">CalculateSequenceProfileScores() (promod3.modelling.LoopCandidates method)</a>, <a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores">[1]</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStemRMSDs">CalculateStemRMSDs() (promod3.modelling.LoopCandidates method)</a>, <a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStemRMSDs">[1]</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStructureProfileScores">CalculateStructureProfileScores() (promod3.modelling.LoopCandidates method)</a>, <a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStructureProfileScores">[1]</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.CARMSD">CARMSD() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer">CBetaScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer">CBPackingScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.CCD">CCD (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.CCD.CCD">CCD() (promod3.modelling.CCD method)</a>, <a href="modelling/loop_closing.html#promod3.modelling.CCD.CCD">[1]</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CCDCloser">CCDCloser (class in promod3.modelling)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragmentInfo.chain_index">chain_index (promod3.loop.FragmentInfo attribute)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.CoordInfo.chain_name">chain_name (promod3.loop.CoordInfo attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.CheckFinalModel">CheckFinalModel() (in module promod3.modelling)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi1">chi1 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi2">chi2 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi3">chi3 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi4">chi4 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer">ClashScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.Clear">Clear() (promod3.core.StaticRuntimeProfiler static method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.clear">clear() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.ClearEnvironment">ClearEnvironment() (promod3.loop.AllAtomEnv method)</a>
+
+ <ul>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ClearEnvironment">(promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.ClearGaps">ClearGaps() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearPos">ClearPos() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearResidue">ClearResidue() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.CCD.Close">Close() (promod3.modelling.CCD method)</a>
+
+ <ul>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CCDCloser.Close">(promod3.modelling.CCDCloser method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser.Close">(promod3.modelling.CTerminalCloser method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase.Close">(promod3.modelling.CloserBase method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser.Close">(promod3.modelling.DeNovoCloser method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser.Close">(promod3.modelling.DirtyCCDCloser method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.KIC.Close">(promod3.modelling.KIC method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.KICCloser.Close">(promod3.modelling.KICCloser method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.NTerminalCloser.Close">(promod3.modelling.NTerminalCloser method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.CloseGaps">CloseGaps() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.CloseLargeDeletions">CloseLargeDeletions() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase">CloserBase (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.CloseSmallDeletions">CloseSmallDeletions() (in module promod3.modelling)</a>
+</li>
+ <li>
+ command
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer">AllAtomScorer (class in promod3.scoring)</a>
- </dt>
+ <ul>
+ <li><a href="cmake/index.html#command:add_doc_dependency"><strong>add_doc_dependency</strong></a>
+</li>
+ <li><a href="cmake/index.html#index-0-command:add_doc_source">add_doc_source</a>, <a href="cmake/index.html#index-1-command:add_doc_source">[1]</a>, <a href="cmake/index.html#command:add_doc_source"><strong>[2]</strong></a>
+</li>
+ <li><a href="cmake/index.html#command:convert_module_data"><strong>convert_module_data</strong></a>
+</li>
+ <li><a href="cmake/index.html#command:module"><strong>module</strong></a>
+</li>
+ <li><a href="contributing.html#index-0-command:pm_action">pm_action</a>, <a href="cmake/index.html#command:pm_action"><strong>[1]</strong></a>
+</li>
+ <li><a href="cmake/index.html#index-0-command:promod3_unittest">promod3_unittest</a>, <a href="cmake/index.html#index-1-command:promod3_unittest">[1]</a>, <a href="cmake/index.html#command:promod3_unittest"><strong>[2]</strong></a>
+</li>
+ <li><a href="cmake/index.html#command:pymod"><strong>pymod</strong></a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li>
+ command line option
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidAtom">AminoAcidAtom (class in promod3.loop)</a>
- </dt>
+ <ul>
+ <li><a href="actions/index.html#cmdoption-f">-f, --energy_function</a>
+</li>
+ <li><a href="actions/index.html#cmdoption-i">-i, --backbone-independent</a>
+</li>
+ <li><a href="actions/index.html#cmdoption-k">-k, --keep-sidechains</a>
+</li>
+ <li><a href="actions/index.html#cmdoption-n">-n, --no-disulfids</a>
+</li>
+ <li><a href="actions/index.html#cmdoption-r">-r, --rigid-rotamers</a>
+</li>
+ <li><a href="actions/index.html#cmdoption-s">-s, --no-subrotamer-optimization</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.ConstraintFunction">ConstraintFunction (class in promod3.scoring)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.ConstructAtomPos">ConstructAtomPos() (in module promod3.core)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue">ConstructBackboneFrameResidue() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue">[1]</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.ConstructCBetaPos">ConstructCBetaPos() (in module promod3.core)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.ConstructCTerminalOxygens">ConstructCTerminalOxygens() (in module promod3.core)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">ConstructFrameResidue() (promod3.sidechain.SCWRL4RotamerConstructor method)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">ConstructFrameResidueHeuristic() (promod3.sidechain.SCWRL4RotamerConstructor method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">(promod3.sidechain.VINARotamerConstructor method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">ConstructFRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[3]</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">ConstructRRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">ConstructSidechainFrameResidue() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">[1]</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.ContactFunction">ContactFunction (class in promod3.scoring)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap.Contains">Contains() (promod3.loop.FraggerMap method)</a>
+
+ <ul>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Contains">(promod3.modelling.ScoreContainer method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.Contains">(promod3.scoring.AllAtomOverallScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.Contains">(promod3.scoring.BackboneOverallScorer method)</a>
+</li>
+ </ul></li>
+ <li>
+ convert_module_data
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidHydrogen">AminoAcidHydrogen (class in promod3.loop)</a>
- </dt>
+ <ul>
+ <li><a href="cmake/index.html#command:convert_module_data"><strong>command</strong></a>
+</li>
+ </ul></li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase">CoolerBase (class in promod3.modelling)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.CoordInfo">CoordInfo (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.Copy">Copy() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.Copy">(promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.Copy">(promod3.modelling.ModellingHandle method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Copy">(promod3.modelling.ScoreContainer method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.Copy">(promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Copy">(promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.CountEnclosedGaps">CountEnclosedGaps() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.CountEnclosedInsertions">CountEnclosedInsertions() (in module promod3.modelling)</a>
+</li>
+ <li><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.CreateFromFRMList">CreateFromFRMList() (promod3.sidechain.RotamerGraph static method)</a>
+</li>
+ <li><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.CreateFromRRMList">CreateFromRRMList() (promod3.sidechain.RotamerGraph static method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL3Particle">CreateSCWRL3Particle() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL4Particle">CreateSCWRL4Particle() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.CreateVINAParticle">CreateVINAParticle() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser">CTerminalCloser (class in promod3.modelling)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup">AminoAcidLookup (class in promod3.loop)</a>
- </dt>
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/pipeline.html#promod3.modelling.DeleteGapCols">DeleteGapCols() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser">DeNovoCloser (class in promod3.modelling)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.DihedralConfiguration">DihedralConfiguration (class in promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser">DirtyCCDCloser (class in promod3.modelling)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.DiscoContainer">DiscoContainer (class in promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.DiscoContainer.AddStructuralInfo">DiscoContainer.AddStructuralInfo() (in module promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.DiscoContainer.AttachConstraints">DiscoContainer.AttachConstraints() (in module promod3.scoring)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemPairOrientation.distance">distance (promod3.core.StemPairOrientation attribute)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.disulfid_bridges">disulfid_bridges (promod3.modelling.SidechainReconstructionData attribute)</a>
+</li>
+ <li><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoExternalScores">DoExternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
+
+ <ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoExternalScores">(promod3.scoring.AllAtomInteractionScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoExternalScores">(promod3.scoring.CBetaScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoExternalScores">(promod3.scoring.ClashScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoExternalScores">(promod3.scoring.HBondScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoExternalScores">(promod3.scoring.PairwiseScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoExternalScores">(promod3.scoring.ReducedScorer method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoInternalScores">DoInternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
+
+ <ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoInternalScores">(promod3.scoring.AllAtomInteractionScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoInternalScores">(promod3.scoring.CBetaScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoInternalScores">(promod3.scoring.ClashScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoInternalScores">(promod3.scoring.HBondScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoInternalScores">(promod3.scoring.PairwiseScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoInternalScores">(promod3.scoring.ReducedScorer method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoNormalize">DoNormalize() (promod3.scoring.AllAtomClashScorer method)</a>
+
+ <ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoNormalize">(promod3.scoring.AllAtomInteractionScorer method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.DoNormalize">(promod3.scoring.AllAtomPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.DoNormalize">(promod3.scoring.CBPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoNormalize">(promod3.scoring.CBetaScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoNormalize">(promod3.scoring.ClashScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoNormalize">(promod3.scoring.HBondScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoNormalize">(promod3.scoring.PairwiseScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoNormalize">(promod3.scoring.ReducedScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.DoNormalize">(promod3.scoring.SSAgreementScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.DoNormalize">(promod3.scoring.TorsionScorer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">Draw() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">[1]</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPhiGivenPsi">DrawPhiGivenPsi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPhiGivenPsi">[1]</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPsiGivenPhi">DrawPsiGivenPhi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPsiGivenPhi">[1]</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.angle">angle (promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
- </dt>
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.empty">empty() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.env_pos">env_pos (promod3.modelling.SidechainReconstructionData attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.epsilon">epsilon (promod3.loop.ForcefieldLJPairInfo attribute)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.EvaluateGromacsPosRule">EvaluateGromacsPosRule() (in module promod3.core)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler">ExponentialCooler (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.FullGapExtender.Extend">Extend() (promod3.modelling.FullGapExtender method)</a>
+
+ <ul>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.GapExtender.Extend">(promod3.modelling.GapExtender method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Extend">(promod3.modelling.ScoreContainer method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.ScoringGapExtender.Extend">(promod3.modelling.ScoringGapExtender method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.ShiftExtension.Extend">(promod3.modelling.ShiftExtension method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.ExtendAtCTerm">ExtendAtCTerm() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.ExtendAtNTerm">ExtendAtNTerm() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.Extract">Extract() (promod3.loop.AllAtomPositions method)</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.Extract">[1]</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.Extract">(promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.Extract">(promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.Extract">(promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Extract">(promod3.modelling.ScoreContainer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ExtractBackbone">ExtractBackbone() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.ExtractLoopPositions">ExtractLoopPositions() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.ExtractStatistics">ExtractStatistics() (promod3.loop.TorsionSampler method)</a>
+</li>
+ </ul></td>
+</tr></table>
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.angle">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
- </dt>
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="core/helper.html#promod3.core.helper.FileExists">FileExists() (in module promod3.core.helper)</a>
+</li>
+ <li><a href="core/helper.html#promod3.core.helper.FileExtension">FileExtension() (in module promod3.core.helper)</a>
+</li>
+ <li><a href="core/helper.html#promod3.core.helper.FileGzip">FileGzip() (in module promod3.core.helper)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.Fill">Fill() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.FillFromDatabase">FillFromDatabase() (promod3.modelling.LoopCandidates static method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler">FillFromMonteCarloSampler() (promod3.modelling.LoopCandidates static method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.FillLoopsByDatabase">FillLoopsByDatabase() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.FillLoopsByMonteCarlo">FillLoopsByMonteCarlo() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.FilterCandidates">FilterCandidates() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.FilterCandidatesWithSC">FilterCandidatesWithSC() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FindMotifs">FindMotifs() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.force_constant">force_constant (promod3.loop.ForcefieldBondInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.force_constant">(promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.force_constant">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldAminoAcid">ForcefieldAminoAcid (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo">ForcefieldBondInfo (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity">ForcefieldConnectivity (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo">ForcefieldHarmonicAngleInfo (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo">ForcefieldHarmonicImproperInfo (class in promod3.loop)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo">ForcefieldLJPairInfo (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup">ForcefieldLookup (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo">ForcefieldPeriodicDihedralInfo (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo">ForcefieldUreyBradleyAngleInfo (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB">FragDB (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger">Fragger (class in promod3.loop)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.fragger_handles">fragger_handles (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle">FraggerHandle (class in promod3.modelling)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap">FraggerMap (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragmentInfo">FragmentInfo (class in promod3.loop)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.FragmentSampler">FragmentSampler (class in promod3.modelling)</a>
+</li>
+ <li><a href="sidechain/frame.html#promod3.sidechain.Frame">Frame (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/frame.html#promod3.sidechain.FrameResidue">FrameResidue (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer">FRMRotamer (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup">FRMRotamerGroup (class in promod3.sidechain)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.FromHHM">FromHHM() (promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.FromHoriz">FromHoriz() (promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.FromResidue">FromResidue() (promod3.sidechain.RotamerLibEntry static method)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.FromResidue">[1]</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.full_seq">full_seq (promod3.modelling.StructuralGap attribute)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.FullGapExtender">FullGapExtender (class in promod3.modelling)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
- </dt>
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.GapExtender">GapExtender (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.gaps">gaps (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.GenerateDeNovoTrajectories">GenerateDeNovoTrajectories() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GenerateStructureProfile">GenerateStructureProfile() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.Get">Get() (promod3.modelling.FraggerHandle method)</a>
+
+ <ul>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Get">(promod3.modelling.ScoreContainer method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.Get">(promod3.scoring.AllAtomOverallScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.Get">(promod3.scoring.BackboneOverallScorer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetAA">GetAA() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAA">(promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetAA">(promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetAA">(promod3.loop.ForcefieldLookup method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAAA">GetAAA() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAAH">GetAAH() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetActiveSubrotamer">GetActiveSubrotamer() (promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.GetAllAtomPositions">GetAllAtomPositions() (promod3.loop.AllAtomEnv method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys">GetAllAtomScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetAllAtomWeights">GetAllAtomWeights() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAnchorAtomIndex">GetAnchorAtomIndex() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.GetAngularBinSize">GetAngularBinSize() (promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAtomName">GetAtomName() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAtomNameAmber">GetAtomNameAmber() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAtomNameCharmm">GetAtomNameCharmm() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetBackboneList">GetBackboneList() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetBackboneScoringKeys">GetBackboneScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetBackboneWeights">GetBackboneWeights() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetBinSize">GetBinSize() (promod3.loop.TorsionSampler method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetBinsPerDimension">GetBinsPerDimension() (promod3.loop.TorsionSampler method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetBounds">GetBounds() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetC">GetC() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetCA">GetCA() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetCB">GetCB() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetChain">GetChain() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetChainIndex">GetChainIndex() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetChainName">GetChainName() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetCharges">GetCharges() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetClusteredCandidates">GetClusteredCandidates() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetClusters">GetClusters() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetCollisionDistance">GetCollisionDistance() (promod3.sidechain.Particle method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetConfidence">GetConfidence() (promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetConfidences">GetConfidences() (promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetCoordIdx">GetCoordIdx() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetCoordInfo">GetCoordInfo() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetCpuPlatformSupport">GetCpuPlatformSupport() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetDefault">GetDefault() (promod3.loop.ForcefieldLookup static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetDihedralAngles">GetDihedralAngles() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetDihedralConfiguration">GetDihedralConfiguration() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.GetDistBinSize">GetDistBinSize() (promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetDisulfidBridges">GetDisulfidBridges() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity">GetDisulfidConnectivity() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetDSSPStates">GetDSSPStates() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetElement">GetElement() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.GetEnvironment">GetEnvironment() (promod3.loop.AllAtomEnv method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetEpsilons">GetEpsilons() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetFirstIndex">GetFirstIndex() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetForcefieldAminoAcids">GetForcefieldAminoAcids() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.GetFragmentInfo">GetFragmentInfo() (promod3.loop.Fragger method)</a>
+
+ <ul>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetFragmentInfo">(promod3.modelling.LoopCandidates method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetFrameEnergy">GetFrameEnergy() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetFrameEnergy">[1]</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetFrameEnergy">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetFudgeLJ">GetFudgeLJ() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetFudgeQQ">GetFudgeQQ() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetH1Index">GetH1Index() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetH2Index">GetH2Index() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetH3Index">GetH3Index() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetHeavyIndex">GetHeavyIndex() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetHistogramIndex">GetHistogramIndex() (promod3.loop.TorsionSampler method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetHistogramIndices">GetHistogramIndices() (promod3.loop.TorsionSampler method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetHNIndex">GetHNIndex() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetHydrogenIndex">GetHydrogenIndex() (promod3.loop.AminoAcidLookup static method)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetHydrogenIndex">(promod3.loop.ForcefieldLookup method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetIdentifiers">GetIdentifiers() (promod3.modelling.MotifQuery method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetIndex">GetIndex() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetIndex">(promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetIndexing">GetIndexing() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetInternalConnectivity">GetInternalConnectivity() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetInternalEnergy">GetInternalEnergy() (promod3.sidechain.FRMRotamer method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetInternalEnergy">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor">GetInternalEnergyPrefactor() (promod3.sidechain.FRMRotamer method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetLargestCluster">GetLargestCluster() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetLastIndex">GetLastIndex() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetLength">GetLength() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.GetList">GetList() (promod3.modelling.FraggerHandle method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetLoopLengths">GetLoopLengths() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetLoopStartIndices">GetLoopStartIndices() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetMasses">GetMasses() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetMaxNumAtoms">GetMaxNumAtoms() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetMaxNumHydrogens">GetMaxNumHydrogens() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetN">GetN() (promod3.loop.BackboneList method)</a>
+
+ <ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetN">(promod3.modelling.MotifQuery method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetName">GetName() (promod3.sidechain.Particle method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.GetNonBondedCutoff">GetNonBondedCutoff() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetNumAtoms">GetNumAtoms() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetNumAtoms">(promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetNumAtoms">(promod3.loop.ForcefieldLookup method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.GetNumCandidates">GetNumCandidates() (promod3.modelling.ScoreContainer method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetNumCoords">GetNumCoords() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.GetNumFragments">GetNumFragments() (promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetNumHydrogens">GetNumHydrogens() (promod3.loop.AminoAcidLookup static method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetNumLoopResidues">GetNumLoopResidues() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetNumResidues">GetNumResidues() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetNumResidues">(promod3.loop.MmSystemCreator method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.GetNumStemPairs">GetNumStemPairs() (promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetNumSubrotamers">GetNumSubrotamers() (promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetO">GetO() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetOLC">GetOLC() (promod3.loop.AminoAcidLookup static method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetOLC">(promod3.loop.BackboneList method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetOmegaTorsion">GetOmegaTorsion() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetOmegaTorsion">(promod3.loop.BackboneList method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetOXTIndex">GetOXTIndex() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity">GetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">GetPhiProbabilityGivenPsi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">[1]</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetPhiTorsion">GetPhiTorsion() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetPhiTorsion">(promod3.loop.BackboneList method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetPos">GetPos() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetPos">(promod3.sidechain.Particle method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetPositions">GetPositions() (promod3.modelling.MotifQuery method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetPrediction">GetPrediction() (promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetPredictions">GetPredictions() (promod3.loop.PsipredPrediction method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetProbability">GetProbability() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetProbability">[1]</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetProbability">(promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetProbability">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">GetPsiProbabilityGivenPhi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">[1]</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetPsiTorsion">GetPsiTorsion() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetPsiTorsion">(promod3.loop.BackboneList method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetResidueDepths">GetResidueDepths() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.GetRingPunches">GetRingPunches() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.GetRings">GetRings() (in module promod3.modelling)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetRotamericConfiguration">GetRotamericConfiguration() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">GetScore() (promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
+
+ <ul>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer.GetScore">(promod3.modelling.LinearScorer method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase.GetScore">(promod3.modelling.ScorerBase method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetScoringFunction">GetScoringFunction() (promod3.sidechain.Particle method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetSelfEnergy">GetSelfEnergy() (promod3.sidechain.FRMRotamer method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetSelfEnergy">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.GetSeqres">GetSeqres() (promod3.loop.AllAtomEnv method)</a>
+
+ <ul>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.GetSeqres">(promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetSequence">GetSequence() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetSequence">(promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSequence">(promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetSequence">(promod3.modelling.LoopCandidates method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSequenceProfile">GetSequenceProfile() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey">GetSequenceProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetSigmas">GetSigmas() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetSimulation">GetSimulation() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSolventAccessibilitites">GetSolventAccessibilitites() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetStemRMSDsKey">GetStemRMSDsKey() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetStructureProfile">GetStructureProfile() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetStructureProfileScoresKey">GetStructureProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSubDB">GetSubDB() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetSubrotamerDefinition">GetSubrotamerDefinition() (promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer.GetSystemCreator">GetSystemCreator() (promod3.modelling.AllAtomRelaxer method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.GetTemperature">GetTemperature() (promod3.modelling.CoolerBase method)</a>
+
+ <ul>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.GetTemperature">(promod3.modelling.ExponentialCooler method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetTemperature">(promod3.sidechain.FRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.GetTransform">GetTransform() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.GetTransform">[1]</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetWeights">GetWeights() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer">GraphMinimizer (class in promod3.core)</a>
+</li>
+ </ul></td>
+</tr></table>
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant">angle_force_constant (promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
- </dt>
+<h2 id="H">H</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.harmonic_angles">harmonic_angles (promod3.loop.ForcefieldConnectivity attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.harmonic_bonds">harmonic_bonds (promod3.loop.ForcefieldConnectivity attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.harmonic_impropers">harmonic_impropers (promod3.loop.ForcefieldConnectivity attribute)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.HasData">HasData() (promod3.loop.StructureDB method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.HasFragLength">HasFragLength() (promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.HasFragmentInfos">HasFragmentInfos() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.HasRingPunches">HasRingPunches() (in module promod3.modelling)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer">HBondScorer (class in promod3.scoring)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_four">angle_four (promod3.core.StemPairOrientation attribute)</a>
- </dt>
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/structure_db.html#promod3.loop.CoordInfo.id">id (promod3.loop.CoordInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_four">index_four (promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_four">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.index_one">index_one (promod3.loop.ForcefieldBondInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.index_one">(promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_one">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.index_one">(promod3.loop.ForcefieldLJPairInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.index_three">index_three (promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_three">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_three">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.index_two">index_two (promod3.loop.ForcefieldBondInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.index_two">(promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_two">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.index_two">(promod3.loop.ForcefieldLJPairInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_two">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.FragmentSampler.Initialize">Initialize() (promod3.modelling.FragmentSampler method)</a>
+
+ <ul>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.PhiPsiSampler.Initialize">(promod3.modelling.PhiPsiSampler method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.Initialize">(promod3.modelling.SamplerBase method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.Initialize">(promod3.modelling.SoftSampler method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.InsertInto">InsertInto() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.InsertInto">(promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.InsertInto">[1]</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.InsertLoop">InsertLoop() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.InsertLoopClearGaps">InsertLoopClearGaps() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.is_c_ter">is_c_ter (promod3.modelling.SidechainReconstructionData attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.is_major">is_major() (promod3.modelling.ModellingIssue method)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.is_n_ter">is_n_ter (promod3.modelling.SidechainReconstructionData attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.IsAllAtomScoringSetUp">IsAllAtomScoringSetUp() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsAllSet">IsAllSet() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsAnySet">IsAnySet() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.IsBackboneScoringSetUp">IsBackboneScoringSetUp() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.IsCTerminal">IsCTerminal() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.IsEmpty">IsEmpty() (promod3.modelling.ScoreContainer method)</a>
+</li>
+ <li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.IsEnabled">IsEnabled() (promod3.core.StaticRuntimeProfiler static method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.IsNTerminal">IsNTerminal() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsSet">IsSet() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.IsSimilar">IsSimilar() (promod3.sidechain.RotamerLibEntry method)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.IsSimilar">[1]</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.IsTerminal">IsTerminal() (promod3.modelling.StructuralGap method)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_one">angle_one (promod3.core.StemPairOrientation attribute)</a>
- </dt>
+<h2 id="K">K</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.KIC">KIC (class in promod3.modelling)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.KIC.KIC">KIC() (promod3.modelling.KIC method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.KICCloser">KICCloser (class in promod3.modelling)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_three">angle_three (promod3.core.StemPairOrientation attribute)</a>
- </dt>
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragmentInfo.length">length (promod3.loop.FragmentInfo attribute)</a>
+
+ <ul>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.length">(promod3.modelling.StructuralGap attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.LinearCombine">LinearCombine() (promod3.modelling.ScoreContainer method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer">LinearScorer (class in promod3.modelling)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.lj_pairs">lj_pairs (promod3.loop.ForcefieldConnectivity attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.Load">Load() (promod3.loop.ForcefieldLookup static method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.Load">(promod3.loop.FragDB static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap.Load">(promod3.loop.FraggerMap method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.Load">(promod3.loop.StructureDB static method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Load">(promod3.loop.TorsionSampler static method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Load">(promod3.modelling.MotifQuery static method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Load">(promod3.scoring.AllAtomInteractionScorer static method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.Load">(promod3.scoring.AllAtomPackingScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.Load">(promod3.scoring.CBPackingScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.Load">(promod3.scoring.CBetaScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.Load">(promod3.scoring.HBondScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.Load">(promod3.scoring.ReducedScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.Load">(promod3.scoring.SSAgreementScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.Load">(promod3.scoring.TorsionScorer static method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.Load">(promod3.sidechain.BBDepRotamerLib static method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.Load">(promod3.sidechain.RotamerLib static method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.LoadAllAtomInteractionScorer">LoadAllAtomInteractionScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.LoadAllAtomPackingScorer">LoadAllAtomPackingScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap.LoadBB">LoadBB() (promod3.loop.FraggerMap method)</a>
+</li>
+ <li><a href="sidechain/loading.html#promod3.sidechain.LoadBBDepLib">LoadBBDepLib() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.LoadCached">LoadCached() (promod3.modelling.FraggerHandle method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadCBetaScorer">LoadCBetaScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadCBPackingScorer">LoadCBPackingScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.LoadCHARMM">LoadCHARMM() (promod3.loop.ForcefieldLookup static method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.LoadDefaultAllAtomOverallScorer">LoadDefaultAllAtomOverallScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadDefaultBackboneOverallScorer">LoadDefaultBackboneOverallScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="loop/load_loop_objects.html#promod3.loop.LoadFragDB">LoadFragDB() (in module promod3.loop)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadHBondScorer">LoadHBondScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="sidechain/loading.html#promod3.sidechain.LoadLib">LoadLib() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.LoadPortable">LoadPortable() (promod3.loop.ForcefieldLookup static method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.LoadPortable">(promod3.loop.FragDB static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.LoadPortable">(promod3.loop.StructureDB static method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.LoadPortable">(promod3.loop.TorsionSampler static method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.LoadPortable">(promod3.scoring.AllAtomInteractionScorer static method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.LoadPortable">(promod3.scoring.AllAtomPackingScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.LoadPortable">(promod3.scoring.CBPackingScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.LoadPortable">(promod3.scoring.CBetaScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.LoadPortable">(promod3.scoring.HBondScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.LoadPortable">(promod3.scoring.ReducedScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.LoadPortable">(promod3.scoring.SSAgreementScorer static method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.LoadPortable">(promod3.scoring.TorsionScorer static method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.LoadPortable">(promod3.sidechain.BBDepRotamerLib static method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.LoadPortable">(promod3.sidechain.RotamerLib static method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadReducedScorer">LoadReducedScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadSSAgreementScorer">LoadSSAgreementScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="loop/load_loop_objects.html#promod3.loop.LoadStructureDB">LoadStructureDB() (in module promod3.loop)</a>
+</li>
+ <li><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSampler">LoadTorsionSampler() (in module promod3.loop)</a>
+</li>
+ <li><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSamplerCoil">LoadTorsionSamplerCoil() (in module promod3.loop)</a>
+</li>
+ <li><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSamplerExtended">LoadTorsionSamplerExtended() (in module promod3.loop)</a>
+</li>
+ <li><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSamplerHelical">LoadTorsionSamplerHelical() (in module promod3.loop)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadTorsionScorer">LoadTorsionScorer() (in module promod3.scoring)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.loop_lengths">loop_lengths (promod3.modelling.SidechainReconstructionData attribute)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.loop_start_indices">loop_start_indices (promod3.modelling.SidechainReconstructionData attribute)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates">LoopCandidates (class in promod3.modelling)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="core/geometry.html#promod3.core.StemPairOrientation.angle_two">angle_two (promod3.core.StemPairOrientation attribute)</a>
- </dt>
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.Severity.MAJOR">MAJOR (promod3.modelling.ModellingIssue.Severity attribute)</a>
+</li>
+ <li><a href="buildsystem.html#index-1">make check</a>
+</li>
+ <li><a href="buildsystem.html#index-4">make doc</a>
+</li>
+ <li><a href="buildsystem.html#index-5">make help</a>
+</li>
+ <li><a href="buildsystem.html#index-2">make html</a>
+</li>
+ <li><a href="buildsystem.html#index-3">make man</a>
+</li>
+ <li><a href="buildsystem.html#index-0">Make targets</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.MakeStatic">MakeStatic() (promod3.sidechain.BBDepRotamerLib method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.MakeStatic">(promod3.sidechain.RotamerLib method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.mat">mat (promod3.modelling.MotifMatch attribute)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.MaxFragLength">MaxFragLength() (promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.MCSolve">MCSolve() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.Merge">Merge() (promod3.sidechain.FRMRotamerGroup method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.Merge">(promod3.sidechain.RRMRotamerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.MergeGaps">MergeGaps() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.MergeGapsByDistance">MergeGapsByDistance() (in module promod3.modelling)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/pipeline.html#promod3.modelling.MergeMHandle">MergeMHandle() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.MinCADistance">MinCADistance() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.MinimizeModelEnergy">MinimizeModelEnergy() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.Severity.MINOR">MINOR (promod3.modelling.ModellingIssue.Severity attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator">MmSystemCreator (class in promod3.loop)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.model">model (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.modelling_issues">modelling_issues (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle">ModellingHandle (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue">ModellingIssue (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.Severity">ModellingIssue.Severity (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModelTermini">ModelTermini() (in module promod3.modelling)</a>
+</li>
+ <li>
+ module
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.append">append() (promod3.loop.BackboneList method)</a>
- </dt>
+ <ul>
+ <li><a href="cmake/index.html#command:module"><strong>command</strong></a>
+</li>
+ </ul></li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifMatch">MotifMatch (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifQuery">MotifQuery (class in promod3.modelling)</a>
+</li>
+ <li><a href="core/helper.html#promod3.core.helper.MsgErrorAndExit">MsgErrorAndExit() (in module promod3.core.helper)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity">multiplicity (promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.ApplyCCD">ApplyCCD() (promod3.modelling.LoopCandidates method)</a>
- </dt>
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="core/geometry.html#promod3.core.StemCoords.n_coord">n_coord (promod3.core.StemCoords attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.NaiveSolve">NaiveSolve() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.NTerminalCloser">NTerminalCloser (class in promod3.modelling)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.ApplyDEE">ApplyDEE() (promod3.core.GraphMinimizer method)</a>
- </dt>
+<h2 id="O">O</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/structure_db.html#promod3.loop.CoordInfo.offset">offset (promod3.loop.CoordInfo attribute)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragmentInfo.offset">(promod3.loop.FragmentInfo attribute)</a>
+</li>
+ </ul></li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.ApplyEdgeDecomposition">ApplyEdgeDecomposition() (promod3.core.GraphMinimizer method)</a>
- </dt>
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.PairwiseFunction">PairwiseFunction (class in promod3.scoring)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.PairwiseFunctionType">PairwiseFunctionType (class in promod3.scoring)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.Particle.PairwiseScore">PairwiseScore() (promod3.sidechain.Particle method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer">PairwiseScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.Parse">Parse() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.Particle">Particle (class in promod3.sidechain)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.periodic_dihedrals">periodic_dihedrals (promod3.loop.ForcefieldConnectivity attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.periodic_impropers">periodic_impropers (promod3.loop.ForcefieldConnectivity attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.phase">phase (promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.PhiPsiSampler">PhiPsiSampler (class in promod3.modelling)</a>
+</li>
+ <li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser">PM3ArgumentParser (class in promod3.core.pm3argparse)</a>
+</li>
+ <li>
+ pm_action
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.ApplyKIC">ApplyKIC() (promod3.modelling.LoopCandidates method)</a>
- </dt>
+ <ul>
+ <li><a href="contributing.html#index-0-command:pm_action">command</a>, <a href="cmake/index.html#command:pm_action"><strong>[1]</strong></a>
+</li>
+ </ul></li>
+ <li><a href="actions/index_dev.html#test_actions.ActionTestCase.pm_action">pm_action (test_actions.ActionTestCase attribute)</a>
+</li>
+ <li><a href="actions/index_dev.html#test_actions.ActionTestCase.pm_bin">pm_bin (test_actions.ActionTestCase attribute)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Pop">Pop() (promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.PrintStatistics">PrintStatistics() (promod3.loop.FragDB method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.PrintStatistics">(promod3.loop.StructureDB method)</a>
+</li>
+ </ul></li>
+ <li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.PrintSummary">PrintSummary() (promod3.core.StaticRuntimeProfiler static method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.probability">probability (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.profiles">profiles (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="core/index.html#module-promod3.core">promod3.core (module)</a>
+</li>
+ <li><a href="core/helper.html#module-promod3.core.helper">promod3.core.helper (module)</a>
+</li>
+ <li><a href="core/pm3argparse.html#module-promod3.core.pm3argparse">promod3.core.pm3argparse (module)</a>
+</li>
+ <li><a href="loop/index.html#module-promod3.loop">promod3.loop (module)</a>
+</li>
+ <li><a href="modelling/index.html#module-promod3.modelling">promod3.modelling (module)</a>
+</li>
+ <li><a href="scoring/index.html#module-promod3.scoring">promod3.scoring (module)</a>
+</li>
+ <li><a href="sidechain/index.html#module-promod3.sidechain">promod3.sidechain (module)</a>
+</li>
+ <li>
+ promod3_unittest
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ApplyOnResidue">ApplyOnResidue() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ApplyOnResidue">[1]</a>
- </dt>
+ <ul>
+ <li><a href="cmake/index.html#index-0-command:promod3_unittest">command</a>, <a href="cmake/index.html#index-1-command:promod3_unittest">[1]</a>, <a href="cmake/index.html#command:promod3_unittest"><strong>[2]</strong></a>
+</li>
+ </ul></li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.FragmentSampler.ProposeStep">ProposeStep() (promod3.modelling.FragmentSampler method)</a>
+
+ <ul>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.PhiPsiSampler.ProposeStep">(promod3.modelling.PhiPsiSampler method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.ProposeStep">(promod3.modelling.SamplerBase method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.ProposeStep">(promod3.modelling.SoftSampler method)</a>
+</li>
+ </ul></li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.Prune">Prune() (promod3.core.GraphMinimizer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.PScoringFunction">PScoringFunction (class in promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.psipred_predictions">psipred_predictions (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction">PsipredPrediction (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.PsipredPrediction">PsipredPrediction() (promod3.loop.PsipredPrediction method)</a>, <a href="loop/structure_db.html#promod3.loop.PsipredPrediction.PsipredPrediction">[1]</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.PullTerminalDeletions">PullTerminalDeletions() (in module promod3.modelling)</a>
+</li>
+ <li>
+ pymod
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.ApplyOnResidue">(promod3.sidechain.FRMRotamerGroup method)</a>
- </dt>
+ <ul>
+ <li><a href="cmake/index.html#command:pymod"><strong>command</strong></a>
+</li>
+ </ul></li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.ApplyOnResidue">(promod3.sidechain.RRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.ApplyOnResidue">[1]</a>
- </dt>
+<h2 id="Q">Q</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.query_idx">query_idx (promod3.modelling.MotifMatch attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.QueryLib">QueryLib() (promod3.sidechain.BBDepRotamerLib method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.QueryLib">(promod3.sidechain.RotamerLib method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.ApplyOnResidue">(promod3.sidechain.RRMRotamerGroup method)</a>
- </dt>
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="sidechain/loading.html#promod3.sidechain.ReadDunbrackFile">ReadDunbrackFile() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor.Reconstruct">Reconstruct() (promod3.modelling.SidechainReconstructor method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructCBetaPositions">ReconstructCBetaPositions() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructCStemOxygen">ReconstructCStemOxygen() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructOxygenPositions">ReconstructOxygenPositions() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains">ReconstructSidechains() (in module promod3.modelling)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer">ReducedScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.Remove">Remove() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.RemoveCoordinates">RemoveCoordinates() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.RemoveTerminalGaps">RemoveTerminalGaps() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ReorderGaps">ReorderGaps() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.ReplaceFragment">ReplaceFragment() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.ReportMolProbityScores">ReportMolProbityScores() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.res_indices">res_indices (promod3.loop.AllAtomEnvPositions attribute)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.Reset">Reset() (promod3.core.GraphMinimizer method)</a>
+
+ <ul>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.Reset">(promod3.modelling.CoolerBase method)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.Reset">(promod3.modelling.ExponentialCooler method)</a>
+</li>
+ </ul></li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.residue_list">residue_list (promod3.modelling.ModellingIssue attribute)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.resize">resize() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="sidechain/disulfid.html#promod3.sidechain.ResolveCysteins">ResolveCysteins() (in module promod3.sidechain)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">RigidBlocks() (in module promod3.modelling)</a>, <a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">[1]</a>, <a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">[2]</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.RMSD">RMSD() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.rotamer_res_indices">rotamer_res_indices (promod3.modelling.SidechainReconstructionData attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor">RotamerConstructor (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph">RotamerGraph (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RotamerID">RotamerID (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib">RotamerLib (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">RotamerLibEntry (class in promod3.sidechain)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">[1]</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundOmegaTorsion">RotateAroundOmegaTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion">RotateAroundPhiPsiTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPhiTorsion">RotateAroundPhiTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPsiTorsion">RotateAroundPsiTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.RotationAroundLine">RotationAroundLine() (in module promod3.core)</a>, <a href="core/geometry.html#promod3.core.RotationAroundLine">[1]</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer">RRMRotamer (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup">RRMRotamerGroup (class in promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer.Run">Run() (promod3.modelling.AllAtomRelaxer method)</a>
+
+ <ul>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.Run">(promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ </ul></li>
+ <li><a href="actions/index_dev.html#test_actions.ActionTestCase.RunAction">RunAction() (test_actions.ActionTestCase method)</a>
+</li>
+ <li><a href="actions/index_dev.html#test_actions.ActionTestCase.RunExitStatusTest">RunExitStatusTest() (test_actions.ActionTestCase method)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.RunMolProbity">RunMolProbity() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.RunMolProbityEntity">RunMolProbityEntity() (in module promod3.modelling)</a>
+</li>
+ </ul></td>
+</tr></table>
- </dl></dd>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction">ApplyPairwiseFunction() (promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.SampleMonteCarlo">SampleMonteCarlo() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase">SamplerBase (class in promod3.modelling)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.Save">Save() (promod3.loop.ForcefieldLookup method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.Save">(promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap.Save">(promod3.loop.FraggerMap method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.Save">(promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Save">(promod3.loop.TorsionSampler method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Save">(promod3.modelling.MotifQuery method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Save">(promod3.scoring.AllAtomInteractionScorer method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.Save">(promod3.scoring.AllAtomPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.Save">(promod3.scoring.CBPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.Save">(promod3.scoring.CBetaScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.Save">(promod3.scoring.HBondScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.Save">(promod3.scoring.ReducedScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.Save">(promod3.scoring.SSAgreementScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.Save">(promod3.scoring.TorsionScorer method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.Save">(promod3.sidechain.BBDepRotamerLib method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.Save">(promod3.sidechain.RotamerLib method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/structure_db.html#promod3.loop.FraggerMap.SaveBB">SaveBB() (promod3.loop.FraggerMap method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.SaveCached">SaveCached() (promod3.modelling.FraggerHandle method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SavePortable">SavePortable() (promod3.loop.ForcefieldLookup method)</a>
+
+ <ul>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.SavePortable">(promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.SavePortable">(promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.SavePortable">(promod3.loop.TorsionSampler method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.SavePortable">(promod3.scoring.AllAtomInteractionScorer method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.SavePortable">(promod3.scoring.AllAtomPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.SavePortable">(promod3.scoring.CBPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.SavePortable">(promod3.scoring.CBetaScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.SavePortable">(promod3.scoring.HBondScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.SavePortable">(promod3.scoring.ReducedScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.SavePortable">(promod3.scoring.SSAgreementScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.SavePortable">(promod3.scoring.TorsionScorer method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.SavePortable">(promod3.sidechain.BBDepRotamerLib method)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.SavePortable">(promod3.sidechain.RotamerLib method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.PairwiseFunction.Score">Score() (promod3.scoring.PairwiseFunction method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer">ScoreContainer (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase">ScorerBase (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.ScoringGapExtender">ScoringGapExtender (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights">ScoringWeights (class in promod3.modelling)</a>
+</li>
+ <li><a href="scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore">SCWRL3DisulfidScore() (in module promod3.scoring)</a>
+</li>
+ <li><a href="scoring/other_scoring_functions.html#promod3.scoring.SCWRL3PairwiseScore">SCWRL3PairwiseScore() (in module promod3.scoring)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor">SCWRL3RotamerConstructor (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.SCWRL4ParticleType">SCWRL4ParticleType (class in promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor">SCWRL4RotamerConstructor (class in promod3.sidechain)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.FragDB.SearchDB">SearchDB() (promod3.loop.FragDB method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.seq">seq (promod3.modelling.StructuralGap attribute)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.seqres">seqres (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.Set">Set() (promod3.loop.BackboneList method)</a>
+
+ <ul>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Set">(promod3.modelling.ScoreContainer method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetAA">SetAA() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetActiveSubrotamer">SetActiveSubrotamer() (promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetAllAtomScoringKeys">SetAllAtomScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundOmegaTorsion">SetAroundOmegaTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundPhiPsiTorsion">SetAroundPhiPsiTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundPhiTorsion">SetAroundPhiTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundPsiTorsion">SetAroundPsiTorsion() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetBackboneScoringKeys">SetBackboneScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetBackrub">SetBackrub() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.SetBackrub">[1]</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetC">SetC() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetCA">SetCA() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetCB">SetCB() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetCharges">SetCharges() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">SetCompoundsChemlib() (in module promod3)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.SetCpuPlatformSupport">SetCpuPlatformSupport() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetDefault">SetDefault() (promod3.loop.ForcefieldLookup static method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetDisulfidConnectivity">SetDisulfidConnectivity() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.SetEnergy">SetEnergy() (promod3.scoring.AllAtomInteractionScorer method)</a>
+
+ <ul>
+ <li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.SetEnergy">(promod3.scoring.AllAtomPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.SetEnergy">(promod3.scoring.CBPackingScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.SetEnergy">(promod3.scoring.CBetaScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.SetEnergy">(promod3.scoring.HBondScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.SetEnergy">(promod3.scoring.ReducedScorer method)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.SetEnergy">(promod3.scoring.TorsionScorer method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.SetEnvironment">SetEnvironment() (promod3.loop.AllAtomEnv method)</a>
+
+ <ul>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetEnvironment">(promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetEpsilons">SetEpsilons() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.SetFraggerHandles">SetFraggerHandles() (in module promod3.modelling)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetFrameEnergy">SetFrameEnergy() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetFrameEnergy">[1]</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.SetFrameEnergy">(promod3.sidechain.FRMRotamerGroup method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetFrameEnergy">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.SetFrameEnergy">(promod3.sidechain.RRMRotamerGroup method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetFudgeLJ">SetFudgeLJ() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetFudgeQQ">SetFudgeQQ() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.SetInitialEnvironment">SetInitialEnvironment() (promod3.loop.AllAtomEnv method)</a>
+
+ <ul>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetInitialEnvironment">(promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ </ul></li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetInternalConnectivity">SetInternalConnectivity() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetInternalEnergy">SetInternalEnergy() (promod3.sidechain.FRMRotamer method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetInternalEnergy">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor">SetInternalEnergyPrefactor() (promod3.sidechain.FRMRotamer method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.SetInterpolate">SetInterpolate() (promod3.sidechain.BBDepRotamerLib method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetMasses">SetMasses() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetN">SetN() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.SetNonBondedCutoff">SetNonBondedCutoff() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetO">SetO() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetOLC">SetOLC() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity">SetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.SetPos">SetPos() (promod3.loop.AllAtomPositions method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetProbability">SetProbability() (promod3.sidechain.FRMRotamer method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetProbability">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction">SetPsipredPrediction() (promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.SetPsipredPredictions">SetPsipredPredictions() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.SetResidue">SetResidue() (promod3.loop.AllAtomPositions method)</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.SetResidue">[1]</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.SetScore">SetScore() (promod3.scoring.SSAgreementScorer method)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SetSequence">SetSequence() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.SetSequenceProfiles">SetSequenceProfiles() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey">SetSequenceProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetSigmas">SetSigmas() (promod3.loop.ForcefieldLookup method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetStemRMSDsKey">SetStemRMSDsKey() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB.SetStructureProfile">SetStructureProfile() (promod3.loop.StructureDB method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetStructureProfileScoresKey">SetStructureProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetTemperature">SetTemperature() (promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring">SetupDefaultAllAtomScoring() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.SetupDefaultBackboneScoring">SetupDefaultBackboneScoring() (in module promod3.modelling)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.SetupSystem">SetupSystem() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetWeights">SetWeights() (promod3.modelling.ScoringWeights static method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.severity">severity (promod3.modelling.ModellingIssue attribute)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.CoordInfo.shift">shift (promod3.loop.CoordInfo attribute)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.ShiftCTerminal">ShiftCTerminal() (promod3.modelling.StructuralGap method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.ShiftExtension">ShiftExtension (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.sidechain_reconstructor">sidechain_reconstructor (promod3.modelling.ModellingHandle attribute)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData">SidechainReconstructionData (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor">SidechainReconstructor (class in promod3.modelling)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig1">sig1 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig2">sig2 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig3">sig3 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig4">sig4 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.sigma">sigma (promod3.loop.ForcefieldLJPairInfo attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.SimilarDihedral">SimilarDihedral() (promod3.sidechain.RotamerLibEntry method)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.SimilarDihedral">[1]</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.CoordInfo.size">size (promod3.loop.CoordInfo attribute)</a>
+</li>
+ <li><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler">SoftSampler (class in promod3.modelling)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer">SSAgreementScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.Start">Start() (promod3.core.StaticRuntimeProfiler static method)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.CoordInfo.start_resnum">start_resnum (promod3.loop.CoordInfo attribute)</a>
+</li>
+ <li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.StartScoped">StartScoped() (promod3.core.StaticRuntimeProfiler static method)</a>
+</li>
+ <li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Stash">Stash() (promod3.scoring.BackboneScoreEnv method)</a>
+</li>
+ <li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler">StaticRuntimeProfiler (class in promod3.core)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemCoords">StemCoords (class in promod3.core)</a>
+</li>
+ <li><a href="core/geometry.html#promod3.core.StemPairOrientation">StemPairOrientation (class in promod3.core)</a>
+</li>
+ <li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.Stop">Stop() (promod3.core.StaticRuntimeProfiler static method)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap">StructuralGap (class in promod3.modelling)</a>
+</li>
+ <li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGapList">StructuralGapList (class in promod3.modelling)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDB">StructureDB (class in promod3.loop)</a>
+</li>
+ <li><a href="loop/structure_db.html#promod3.loop.StructureDBDataType">StructureDBDataType (class in promod3.loop)</a>
+</li>
+ <li><a href="sidechain/subrotamer_optimizer.html#promod3.sidechain.SubrotamerOptimizer">SubrotamerOptimizer() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.SuperposeOnto">SuperposeOnto() (promod3.loop.BackboneList method)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh">ApplySelfEnergyThresh() (promod3.sidechain.FRMRotamerGroup method)</a>
- </dt>
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="actions/index_dev.html#module-test_actions">test_actions (module)</a>
+</li>
+ <li><a href="actions/index_dev.html#test_actions.ActionTestCase.testPMExists">testPMExists() (test_actions.ActionTestCase method)</a>
+</li>
+ <li><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.text">text (promod3.modelling.ModellingIssue attribute)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.TLCToRotID">TLCToRotID() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.ToDensity">ToDensity() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ToEntity">ToEntity() (promod3.loop.AllAtomPositions method)</a>
+
+ <ul>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.ToEntity">(promod3.loop.BackboneList method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ToFrameResidue">ToFrameResidue() (promod3.sidechain.FRMRotamer method)</a>
+
+ <ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.ToFrameResidue">(promod3.sidechain.RRMRotamer method)</a>
+</li>
+ </ul></li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ToRRMRotamer">ToRRMRotamer() (promod3.sidechain.FRMRotamer method)</a>
+</li>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler">TorsionSampler (class in promod3.loop)</a>
+</li>
+ <li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer">TorsionScorer (class in promod3.scoring)</a>
+</li>
+ <li><a href="loop/backbone.html#promod3.loop.BackboneList.TransOmegaTorsions">TransOmegaTorsions() (promod3.loop.BackboneList method)</a>
+</li>
+ <li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.TreeSolve">TreeSolve() (promod3.core.GraphMinimizer method)</a>
+</li>
+ </ul></td>
+</tr></table>
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh">(promod3.sidechain.RRMRotamerGroup method)</a>
- </dt>
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.UpdateDistributions">UpdateDistributions() (promod3.loop.TorsionSampler method)</a>
+</li>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.UpdatePositions">UpdatePositions() (promod3.loop.MmSystemCreator method)</a>
+
+ <ul>
+ <li><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer.UpdatePositions">(promod3.modelling.AllAtomRelaxer method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.urey_bradley_angles">urey_bradley_angles (promod3.loop.ForcefieldConnectivity attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
- </dl></dd>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ApplyTransform">ApplyTransform() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.ApplyTransform">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.ApplyTransform">[2]</a>
- </dt>
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.VINAParticleType">VINAParticleType (class in promod3.sidechain)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor">VINARotamerConstructor (class in promod3.sidechain)</a>
+</li>
+ </ul></td>
+</tr></table>
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">AssembleParser() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
- </dt>
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.AssignInternalEnergies">AssignInternalEnergies() (promod3.sidechain.RotamerConstructor method)</a>
- </dt>
- <dd><dl>
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL3RotamerConstructor method)</a>
- </dt>
+ </div>
+
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL4RotamerConstructor method)</a>
- </dt>
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies">(promod3.sidechain.VINARotamerConstructor method)</a>
- </dt>
- </dl></dd>
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AStarSolve">AStarSolve() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor.AttachEnvironment">AttachEnvironment() (promod3.modelling.SidechainReconstructor method)</a>
- </dt>
- <dd><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.AttachEnvironment">(promod3.scoring.AllAtomOverallScorer method)</a>
- </dt>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer.AttachEnvironment">(promod3.scoring.AllAtomScorer method)</a>
- </dt>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.AttachEnvironment">(promod3.scoring.BackboneOverallScorer method)</a>
- </dt>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer.AttachEnvironment">(promod3.scoring.BackboneScorer method)</a>
- </dt>
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
- </dl></dd>
- </dl></td>
-</tr></table>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
+ <form class="search" action="search.html" method="get">
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
+ </form>
+ </div>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
-<h2 id="B">B</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.backbone_scorer">backbone_scorer (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.backbone_scorer_env">backbone_scorer_env (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList">BackboneList (class in promod3.loop)</a>
- </dt>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">BackboneList() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[2]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[3]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[4]</a>
- </dt>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer">BackboneOverallScorer (class in promod3.scoring)</a>
- </dt>
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer">BackboneRelaxer (class in promod3.modelling)</a>, <a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer">[1]</a>
- </dt>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv">BackboneScoreEnv (class in promod3.scoring)</a>
- </dt>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer">BackboneScorer (class in promod3.scoring)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib">BBDepRotamerLib (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.before">before (promod3.modelling.StructuralGap attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant">bond_force_constant (promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.bond_length">bond_length (promod3.loop.ForcefieldBondInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.BuildFromRawModel">BuildFromRawModel() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.BuildRawModel">BuildRawModel() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.BuildSidechains">BuildSidechains() (in module promod3.modelling)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="C">C</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="core/geometry.html#promod3.core.StemCoords.c_coord">c_coord (promod3.core.StemCoords attribute)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.StemCoords.ca_coord">ca_coord (promod3.core.StemCoords attribute)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.Calculate">Calculate() (promod3.scoring.BackboneOverallScorer method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateAllAtomScores">CalculateAllAtomScores() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateBackboneScores">CalculateBackboneScores() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination">CalculateLinearCombination() (promod3.scoring.AllAtomOverallScorer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination">(promod3.scoring.BackboneOverallScorer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer.CalculateScore">CalculateScore() (promod3.scoring.AllAtomScorer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer.CalculateScore">(promod3.scoring.BackboneScorer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomScorer.CalculateScoreProfile">CalculateScoreProfile() (promod3.scoring.AllAtomScorer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer.CalculateScoreProfile">(promod3.scoring.BackboneScorer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores">CalculateSequenceProfileScores() (promod3.modelling.LoopCandidates method)</a>, <a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores">[1]</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStemRMSDs">CalculateStemRMSDs() (promod3.modelling.LoopCandidates method)</a>, <a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStemRMSDs">[1]</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStructureProfileScores">CalculateStructureProfileScores() (promod3.modelling.LoopCandidates method)</a>, <a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.CalculateStructureProfileScores">[1]</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.CARMSD">CARMSD() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer">CBetaScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer">CBPackingScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.CCD">CCD (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.CCD.CCD">CCD() (promod3.modelling.CCD method)</a>, <a href="modelling/loop_closing.html#promod3.modelling.CCD.CCD">[1]</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CCDCloser">CCDCloser (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo.chain_index">chain_index (promod3.loop.FragmentInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.chain_name">chain_name (promod3.loop.CoordInfo attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.CheckFinalModel">CheckFinalModel() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi1">chi1 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi2">chi2 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi3">chi3 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi4">chi4 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer">ClashScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.Clear">Clear() (promod3.core.StaticRuntimeProfiler static method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.clear">clear() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.ClearEnvironment">ClearEnvironment() (promod3.loop.AllAtomEnv method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ClearEnvironment">(promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.ClearGaps">ClearGaps() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearPos">ClearPos() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearResidue">ClearResidue() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.CCD.Close">Close() (promod3.modelling.CCD method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CCDCloser.Close">(promod3.modelling.CCDCloser method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser.Close">(promod3.modelling.CTerminalCloser method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase.Close">(promod3.modelling.CloserBase method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser.Close">(promod3.modelling.DeNovoCloser method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser.Close">(promod3.modelling.DirtyCCDCloser method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.KIC.Close">(promod3.modelling.KIC method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.KICCloser.Close">(promod3.modelling.KICCloser method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.NTerminalCloser.Close">(promod3.modelling.NTerminalCloser method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.CloseGaps">CloseGaps() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.CloseLargeDeletions">CloseLargeDeletions() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase">CloserBase (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.CloseSmallDeletions">CloseSmallDeletions() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt>
- command
- </dt>
-
- <dd><dl>
-
- <dt><a href="cmake/index.html#command:add_doc_dependency"><strong>add_doc_dependency</strong></a>
- </dt>
-
-
- <dt><a href="cmake/index.html#index-0-command:add_doc_source">add_doc_source</a>, <a href="cmake/index.html#index-1-command:add_doc_source">[1]</a>, <a href="cmake/index.html#command:add_doc_source"><strong>[2]</strong></a>
- </dt>
-
-
- <dt><a href="cmake/index.html#command:convert_module_data"><strong>convert_module_data</strong></a>
- </dt>
-
-
- <dt><a href="cmake/index.html#command:module"><strong>module</strong></a>
- </dt>
-
-
- <dt><a href="contributing.html#index-0-command:pm_action">pm_action</a>, <a href="cmake/index.html#command:pm_action"><strong>[1]</strong></a>
- </dt>
-
-
- <dt><a href="cmake/index.html#index-0-command:promod3_unittest">promod3_unittest</a>, <a href="cmake/index.html#index-1-command:promod3_unittest">[1]</a>, <a href="cmake/index.html#command:promod3_unittest"><strong>[2]</strong></a>
- </dt>
-
-
- <dt><a href="cmake/index.html#command:pymod"><strong>pymod</strong></a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt>
- command line option
- </dt>
-
- <dd><dl>
-
- <dt><a href="actions/index.html#cmdoption-f">-f, --energy_function</a>
- </dt>
-
-
- <dt><a href="actions/index.html#cmdoption-i">-i, --backbone-independent</a>
- </dt>
-
-
- <dt><a href="actions/index.html#cmdoption-k">-k, --keep-sidechains</a>
- </dt>
-
-
- <dt><a href="actions/index.html#cmdoption-n">-n, --no-disulfids</a>
- </dt>
-
-
- <dt><a href="actions/index.html#cmdoption-r">-r, --rigid-rotamers</a>
- </dt>
-
-
- <dt><a href="actions/index.html#cmdoption-s">-s, --no-subrotamer-optimization</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.ConstraintFunction">ConstraintFunction (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.ConstructAtomPos">ConstructAtomPos() (in module promod3.core)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue">ConstructBackboneFrameResidue() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue">[1]</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.ConstructCBetaPos">ConstructCBetaPos() (in module promod3.core)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.ConstructCTerminalOxygens">ConstructCTerminalOxygens() (in module promod3.core)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">ConstructFrameResidue() (promod3.sidechain.SCWRL4RotamerConstructor method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">ConstructFrameResidueHeuristic() (promod3.sidechain.SCWRL4RotamerConstructor method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">(promod3.sidechain.VINARotamerConstructor method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">ConstructFRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[3]</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">ConstructRRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">ConstructSidechainFrameResidue() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">[1]</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.ContactFunction">ContactFunction (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap.Contains">Contains() (promod3.loop.FraggerMap method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Contains">(promod3.modelling.ScoreContainer method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.Contains">(promod3.scoring.AllAtomOverallScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.Contains">(promod3.scoring.BackboneOverallScorer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt>
- convert_module_data
- </dt>
-
- <dd><dl>
-
- <dt><a href="cmake/index.html#command:convert_module_data"><strong>command</strong></a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase">CoolerBase (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo">CoordInfo (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.Copy">Copy() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.Copy">(promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.Copy">(promod3.modelling.ModellingHandle method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Copy">(promod3.modelling.ScoreContainer method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.Copy">(promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Copy">(promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.CountEnclosedGaps">CountEnclosedGaps() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.CountEnclosedInsertions">CountEnclosedInsertions() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.CreateFromFRMList">CreateFromFRMList() (promod3.sidechain.RotamerGraph static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.CreateFromRRMList">CreateFromRRMList() (promod3.sidechain.RotamerGraph static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL3Particle">CreateSCWRL3Particle() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL4Particle">CreateSCWRL4Particle() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateVINAParticle">CreateVINAParticle() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser">CTerminalCloser (class in promod3.modelling)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="D">D</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser">DeNovoCloser (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.DihedralConfiguration">DihedralConfiguration (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser">DirtyCCDCloser (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.DiscoContainer">DiscoContainer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.DiscoContainer.AddStructuralInfo">DiscoContainer.AddStructuralInfo() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.DiscoContainer.AttachConstraints">DiscoContainer.AttachConstraints() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.StemPairOrientation.distance">distance (promod3.core.StemPairOrientation attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.disulfid_bridges">disulfid_bridges (promod3.modelling.SidechainReconstructionData attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoExternalScores">DoExternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoExternalScores">(promod3.scoring.AllAtomInteractionScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoExternalScores">(promod3.scoring.CBetaScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoExternalScores">(promod3.scoring.ClashScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoExternalScores">(promod3.scoring.HBondScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoExternalScores">(promod3.scoring.PairwiseScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoExternalScores">(promod3.scoring.ReducedScorer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoInternalScores">DoInternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoInternalScores">(promod3.scoring.AllAtomInteractionScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoInternalScores">(promod3.scoring.CBetaScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoInternalScores">(promod3.scoring.ClashScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoInternalScores">(promod3.scoring.HBondScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoInternalScores">(promod3.scoring.PairwiseScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoInternalScores">(promod3.scoring.ReducedScorer method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoNormalize">DoNormalize() (promod3.scoring.AllAtomClashScorer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoNormalize">(promod3.scoring.AllAtomInteractionScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.DoNormalize">(promod3.scoring.AllAtomPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.DoNormalize">(promod3.scoring.CBPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoNormalize">(promod3.scoring.CBetaScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoNormalize">(promod3.scoring.ClashScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoNormalize">(promod3.scoring.HBondScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoNormalize">(promod3.scoring.PairwiseScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoNormalize">(promod3.scoring.ReducedScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.DoNormalize">(promod3.scoring.SSAgreementScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.DoNormalize">(promod3.scoring.TorsionScorer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">Draw() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">[1]</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPhiGivenPsi">DrawPhiGivenPsi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPhiGivenPsi">[1]</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPsiGivenPhi">DrawPsiGivenPhi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPsiGivenPhi">[1]</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="E">E</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.empty">empty() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.env_pos">env_pos (promod3.modelling.SidechainReconstructionData attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.epsilon">epsilon (promod3.loop.ForcefieldLJPairInfo attribute)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.EvaluateGromacsPosRule">EvaluateGromacsPosRule() (in module promod3.core)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler">ExponentialCooler (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.FullGapExtender.Extend">Extend() (promod3.modelling.FullGapExtender method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.GapExtender.Extend">(promod3.modelling.GapExtender method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Extend">(promod3.modelling.ScoreContainer method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.ScoringGapExtender.Extend">(promod3.modelling.ScoringGapExtender method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.ShiftExtension.Extend">(promod3.modelling.ShiftExtension method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.ExtendAtCTerm">ExtendAtCTerm() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.ExtendAtNTerm">ExtendAtNTerm() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.Extract">Extract() (promod3.loop.AllAtomPositions method)</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.Extract">[1]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.Extract">(promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.Extract">(promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.Extract">(promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Extract">(promod3.modelling.ScoreContainer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ExtractBackbone">ExtractBackbone() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.ExtractLoopPositions">ExtractLoopPositions() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.ExtractStatistics">ExtractStatistics() (promod3.loop.TorsionSampler method)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="F">F</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="core/helper.html#promod3.core.helper.FileExists">FileExists() (in module promod3.core.helper)</a>
- </dt>
-
-
- <dt><a href="core/helper.html#promod3.core.helper.FileExtension">FileExtension() (in module promod3.core.helper)</a>
- </dt>
-
-
- <dt><a href="core/helper.html#promod3.core.helper.FileGzip">FileGzip() (in module promod3.core.helper)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.Fill">Fill() (promod3.loop.Fragger method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.FillFromDatabase">FillFromDatabase() (promod3.modelling.LoopCandidates static method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler">FillFromMonteCarloSampler() (promod3.modelling.LoopCandidates static method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.FillLoopsByDatabase">FillLoopsByDatabase() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.FillLoopsByMonteCarlo">FillLoopsByMonteCarlo() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.FilterCandidates">FilterCandidates() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.FilterCandidatesWithSC">FilterCandidatesWithSC() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.FindMotifs">FindMotifs() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.force_constant">force_constant (promod3.loop.ForcefieldBondInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.force_constant">(promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.force_constant">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldAminoAcid">ForcefieldAminoAcid (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo">ForcefieldBondInfo (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity">ForcefieldConnectivity (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo">ForcefieldHarmonicAngleInfo (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo">ForcefieldHarmonicImproperInfo (class in promod3.loop)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo">ForcefieldLJPairInfo (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup">ForcefieldLookup (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo">ForcefieldPeriodicDihedralInfo (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo">ForcefieldUreyBradleyAngleInfo (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB">FragDB (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger">Fragger (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.fragger_handles">fragger_handles (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle">FraggerHandle (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap">FraggerMap (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo">FragmentInfo (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.FragmentSampler">FragmentSampler (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="sidechain/frame.html#promod3.sidechain.Frame">Frame (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/frame.html#promod3.sidechain.FrameResidue">FrameResidue (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer">FRMRotamer (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup">FRMRotamerGroup (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.FromHHM">FromHHM() (promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.FromHoriz">FromHoriz() (promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.FromResidue">FromResidue() (promod3.sidechain.RotamerLibEntry static method)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.FromResidue">[1]</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.full_seq">full_seq (promod3.modelling.StructuralGap attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.FullGapExtender">FullGapExtender (class in promod3.modelling)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="G">G</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.GapExtender">GapExtender (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.gaps">gaps (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.GenerateDeNovoTrajectories">GenerateDeNovoTrajectories() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GenerateStructureProfile">GenerateStructureProfile() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.Get">Get() (promod3.modelling.FraggerHandle method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Get">(promod3.modelling.ScoreContainer method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer.Get">(promod3.scoring.AllAtomOverallScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.Get">(promod3.scoring.BackboneOverallScorer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetAA">GetAA() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAA">(promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetAA">(promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetAA">(promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAAA">GetAAA() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAAH">GetAAH() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetActiveSubrotamer">GetActiveSubrotamer() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.GetAllAtomPositions">GetAllAtomPositions() (promod3.loop.AllAtomEnv method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys">GetAllAtomScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetAllAtomWeights">GetAllAtomWeights() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAnchorAtomIndex">GetAnchorAtomIndex() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetAngularBinSize">GetAngularBinSize() (promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAtomName">GetAtomName() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAtomNameAmber">GetAtomNameAmber() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetAtomNameCharmm">GetAtomNameCharmm() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetBackboneList">GetBackboneList() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetBackboneScoringKeys">GetBackboneScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetBackboneWeights">GetBackboneWeights() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetBinSize">GetBinSize() (promod3.loop.TorsionSampler method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetBinsPerDimension">GetBinsPerDimension() (promod3.loop.TorsionSampler method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetBounds">GetBounds() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetC">GetC() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetCA">GetCA() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetCB">GetCB() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetChain">GetChain() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetChainIndex">GetChainIndex() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetChainName">GetChainName() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetCharges">GetCharges() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetClusteredCandidates">GetClusteredCandidates() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetClusters">GetClusters() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetCollisionDistance">GetCollisionDistance() (promod3.sidechain.Particle method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetConfidence">GetConfidence() (promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetConfidences">GetConfidences() (promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetCoordIdx">GetCoordIdx() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetCoordInfo">GetCoordInfo() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetCpuPlatformSupport">GetCpuPlatformSupport() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetDefault">GetDefault() (promod3.loop.ForcefieldLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetDihedralAngles">GetDihedralAngles() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetDihedralConfiguration">GetDihedralConfiguration() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetDistBinSize">GetDistBinSize() (promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetDisulfidBridges">GetDisulfidBridges() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity">GetDisulfidConnectivity() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetDSSPStates">GetDSSPStates() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetElement">GetElement() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.GetEnvironment">GetEnvironment() (promod3.loop.AllAtomEnv method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetEpsilons">GetEpsilons() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetFirstIndex">GetFirstIndex() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetForcefieldAminoAcids">GetForcefieldAminoAcids() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetFragmentInfo">GetFragmentInfo() (promod3.loop.Fragger method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetFragmentInfo">(promod3.modelling.LoopCandidates method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetFrameEnergy">GetFrameEnergy() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetFrameEnergy">[1]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetFrameEnergy">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetFudgeLJ">GetFudgeLJ() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetFudgeQQ">GetFudgeQQ() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetH1Index">GetH1Index() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetH2Index">GetH2Index() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetH3Index">GetH3Index() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetHeavyIndex">GetHeavyIndex() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetHistogramIndex">GetHistogramIndex() (promod3.loop.TorsionSampler method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetHistogramIndices">GetHistogramIndices() (promod3.loop.TorsionSampler method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetHNIndex">GetHNIndex() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetHydrogenIndex">GetHydrogenIndex() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetHydrogenIndex">(promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetIdentifiers">GetIdentifiers() (promod3.modelling.MotifQuery method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetIndex">GetIndex() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetIndex">(promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetIndexing">GetIndexing() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetInternalConnectivity">GetInternalConnectivity() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetInternalEnergy">GetInternalEnergy() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetInternalEnergy">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor">GetInternalEnergyPrefactor() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetLargestCluster">GetLargestCluster() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetLastIndex">GetLastIndex() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetLength">GetLength() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.GetList">GetList() (promod3.modelling.FraggerHandle method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetLoopLengths">GetLoopLengths() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetLoopStartIndices">GetLoopStartIndices() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetMasses">GetMasses() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetMaxNumAtoms">GetMaxNumAtoms() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetMaxNumHydrogens">GetMaxNumHydrogens() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetN">GetN() (promod3.loop.BackboneList method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetN">(promod3.modelling.MotifQuery method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetName">GetName() (promod3.sidechain.Particle method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.GetNonBondedCutoff">GetNonBondedCutoff() (promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetNumAtoms">GetNumAtoms() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetNumAtoms">(promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetNumAtoms">(promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.GetNumCandidates">GetNumCandidates() (promod3.modelling.ScoreContainer method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetNumCoords">GetNumCoords() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetNumFragments">GetNumFragments() (promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetNumHydrogens">GetNumHydrogens() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetNumLoopResidues">GetNumLoopResidues() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetNumResidues">GetNumResidues() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetNumResidues">(promod3.loop.MmSystemCreator method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetNumStemPairs">GetNumStemPairs() (promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetNumSubrotamers">GetNumSubrotamers() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetO">GetO() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetOLC">GetOLC() (promod3.loop.AminoAcidLookup static method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetOLC">(promod3.loop.BackboneList method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetOmegaTorsion">GetOmegaTorsion() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetOmegaTorsion">(promod3.loop.BackboneList method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetOXTIndex">GetOXTIndex() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity">GetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">GetPhiProbabilityGivenPsi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">[1]</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetPhiTorsion">GetPhiTorsion() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetPhiTorsion">(promod3.loop.BackboneList method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetPos">GetPos() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetPos">(promod3.sidechain.Particle method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetPositions">GetPositions() (promod3.modelling.MotifQuery method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetPrediction">GetPrediction() (promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetPredictions">GetPredictions() (promod3.loop.PsipredPrediction method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetProbability">GetProbability() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetProbability">[1]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetProbability">(promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetProbability">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">GetPsiProbabilityGivenPhi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">[1]</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetPsiTorsion">GetPsiTorsion() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetPsiTorsion">(promod3.loop.BackboneList method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetResidueDepths">GetResidueDepths() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.GetRingPunches">GetRingPunches() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.GetRings">GetRings() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetRotamericConfiguration">GetRotamericConfiguration() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">GetScore() (promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer.GetScore">(promod3.modelling.LinearScorer method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase.GetScore">(promod3.modelling.ScorerBase method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetScoringFunction">GetScoringFunction() (promod3.sidechain.Particle method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetSelfEnergy">GetSelfEnergy() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetSelfEnergy">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.GetSeqres">GetSeqres() (promod3.loop.AllAtomEnv method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.GetSeqres">(promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetSequence">GetSequence() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetSequence">(promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSequence">(promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetSequence">(promod3.modelling.LoopCandidates method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSequenceProfile">GetSequenceProfile() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey">GetSequenceProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetSigmas">GetSigmas() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetSimulation">GetSimulation() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSolventAccessibilitites">GetSolventAccessibilitites() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetStemRMSDsKey">GetStemRMSDsKey() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetStructureProfile">GetStructureProfile() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetStructureProfileScoresKey">GetStructureProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSubDB">GetSubDB() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetSubrotamerDefinition">GetSubrotamerDefinition() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer.GetSystemCreator">GetSystemCreator() (promod3.modelling.AllAtomRelaxer method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.GetTemperature">GetTemperature() (promod3.modelling.CoolerBase method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.GetTemperature">(promod3.modelling.ExponentialCooler method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetTemperature">(promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetTransform">GetTransform() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.GetTransform">[1]</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetWeights">GetWeights() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer">GraphMinimizer (class in promod3.core)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="H">H</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.harmonic_angles">harmonic_angles (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.harmonic_bonds">harmonic_bonds (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.harmonic_impropers">harmonic_impropers (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.HasData">HasData() (promod3.loop.StructureDB method)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.HasFragLength">HasFragLength() (promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.HasFragmentInfos">HasFragmentInfos() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.HasRingPunches">HasRingPunches() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer">HBondScorer (class in promod3.scoring)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="I">I</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.id">id (promod3.loop.CoordInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_four">index_four (promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_four">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.index_one">index_one (promod3.loop.ForcefieldBondInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.index_one">(promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_one">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.index_one">(promod3.loop.ForcefieldLJPairInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.index_three">index_three (promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_three">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_three">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.index_two">index_two (promod3.loop.ForcefieldBondInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicAngleInfo.index_two">(promod3.loop.ForcefieldHarmonicAngleInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_two">(promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.index_two">(promod3.loop.ForcefieldLJPairInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.index_two">(promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.FragmentSampler.Initialize">Initialize() (promod3.modelling.FragmentSampler method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.PhiPsiSampler.Initialize">(promod3.modelling.PhiPsiSampler method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.Initialize">(promod3.modelling.SamplerBase method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.Initialize">(promod3.modelling.SoftSampler method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.InsertInto">InsertInto() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.InsertInto">(promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.InsertInto">[1]</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.InsertLoop">InsertLoop() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.InsertLoopClearGaps">InsertLoopClearGaps() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.is_c_ter">is_c_ter (promod3.modelling.SidechainReconstructionData attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.is_major">is_major() (promod3.modelling.ModellingIssue method)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.is_n_ter">is_n_ter (promod3.modelling.SidechainReconstructionData attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.IsAllAtomScoringSetUp">IsAllAtomScoringSetUp() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsAllSet">IsAllSet() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsAnySet">IsAnySet() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.IsBackboneScoringSetUp">IsBackboneScoringSetUp() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.IsCTerminal">IsCTerminal() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.IsEmpty">IsEmpty() (promod3.modelling.ScoreContainer method)</a>
- </dt>
-
-
- <dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.IsEnabled">IsEnabled() (promod3.core.StaticRuntimeProfiler static method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.IsNTerminal">IsNTerminal() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsSet">IsSet() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.IsSimilar">IsSimilar() (promod3.sidechain.RotamerLibEntry method)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.IsSimilar">[1]</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.IsTerminal">IsTerminal() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="K">K</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.KIC">KIC (class in promod3.modelling)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.KIC.KIC">KIC() (promod3.modelling.KIC method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.KICCloser">KICCloser (class in promod3.modelling)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="L">L</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo.length">length (promod3.loop.FragmentInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.length">(promod3.modelling.StructuralGap attribute)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.LinearCombine">LinearCombine() (promod3.modelling.ScoreContainer method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer">LinearScorer (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.lj_pairs">lj_pairs (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.Load">Load() (promod3.loop.ForcefieldLookup static method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.Load">(promod3.loop.FragDB static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap.Load">(promod3.loop.FraggerMap method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.Load">(promod3.loop.StructureDB static method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Load">(promod3.loop.TorsionSampler static method)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Load">(promod3.modelling.MotifQuery static method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Load">(promod3.scoring.AllAtomInteractionScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.Load">(promod3.scoring.AllAtomPackingScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.Load">(promod3.scoring.CBPackingScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.Load">(promod3.scoring.CBetaScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.Load">(promod3.scoring.HBondScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.Load">(promod3.scoring.ReducedScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.Load">(promod3.scoring.SSAgreementScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.Load">(promod3.scoring.TorsionScorer static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.Load">(promod3.sidechain.BBDepRotamerLib static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.Load">(promod3.sidechain.RotamerLib static method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.LoadAllAtomInteractionScorer">LoadAllAtomInteractionScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.LoadAllAtomPackingScorer">LoadAllAtomPackingScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap.LoadBB">LoadBB() (promod3.loop.FraggerMap method)</a>
- </dt>
-
-
- <dt><a href="sidechain/loading.html#promod3.sidechain.LoadBBDepLib">LoadBBDepLib() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.LoadCached">LoadCached() (promod3.modelling.FraggerHandle method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadCBetaScorer">LoadCBetaScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadCBPackingScorer">LoadCBPackingScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.LoadCHARMM">LoadCHARMM() (promod3.loop.ForcefieldLookup static method)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.LoadDefaultAllAtomOverallScorer">LoadDefaultAllAtomOverallScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadDefaultBackboneOverallScorer">LoadDefaultBackboneOverallScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/load_loop_objects.html#promod3.loop.LoadFragDB">LoadFragDB() (in module promod3.loop)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadHBondScorer">LoadHBondScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="sidechain/loading.html#promod3.sidechain.LoadLib">LoadLib() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.LoadPortable">LoadPortable() (promod3.loop.ForcefieldLookup static method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.LoadPortable">(promod3.loop.FragDB static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.LoadPortable">(promod3.loop.StructureDB static method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.LoadPortable">(promod3.loop.TorsionSampler static method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.LoadPortable">(promod3.scoring.AllAtomInteractionScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.LoadPortable">(promod3.scoring.AllAtomPackingScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.LoadPortable">(promod3.scoring.CBPackingScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.LoadPortable">(promod3.scoring.CBetaScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.LoadPortable">(promod3.scoring.HBondScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.LoadPortable">(promod3.scoring.ReducedScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.LoadPortable">(promod3.scoring.SSAgreementScorer static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.LoadPortable">(promod3.scoring.TorsionScorer static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.LoadPortable">(promod3.sidechain.BBDepRotamerLib static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.LoadPortable">(promod3.sidechain.RotamerLib static method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadReducedScorer">LoadReducedScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadSSAgreementScorer">LoadSSAgreementScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/load_loop_objects.html#promod3.loop.LoadStructureDB">LoadStructureDB() (in module promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSampler">LoadTorsionSampler() (in module promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSamplerCoil">LoadTorsionSamplerCoil() (in module promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSamplerExtended">LoadTorsionSamplerExtended() (in module promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/load_loop_objects.html#promod3.loop.LoadTorsionSamplerHelical">LoadTorsionSamplerHelical() (in module promod3.loop)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadTorsionScorer">LoadTorsionScorer() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.loop_lengths">loop_lengths (promod3.modelling.SidechainReconstructionData attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.loop_start_indices">loop_start_indices (promod3.modelling.SidechainReconstructionData attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates">LoopCandidates (class in promod3.modelling)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="M">M</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.Severity.MAJOR">MAJOR (promod3.modelling.ModellingIssue.Severity attribute)</a>
- </dt>
-
-
- <dt><a href="buildsystem.html#index-1">make check</a>
- </dt>
-
-
- <dt><a href="buildsystem.html#index-4">make doc</a>
- </dt>
-
-
- <dt><a href="buildsystem.html#index-5">make help</a>
- </dt>
-
-
- <dt><a href="buildsystem.html#index-2">make html</a>
- </dt>
-
-
- <dt><a href="buildsystem.html#index-3">make man</a>
- </dt>
-
-
- <dt><a href="buildsystem.html#index-0">Make targets</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.MakeStatic">MakeStatic() (promod3.sidechain.BBDepRotamerLib method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.MakeStatic">(promod3.sidechain.RotamerLib method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.mat">mat (promod3.modelling.MotifMatch attribute)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.MaxFragLength">MaxFragLength() (promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.MCSolve">MCSolve() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.Merge">Merge() (promod3.sidechain.FRMRotamerGroup method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.Merge">(promod3.sidechain.RRMRotamerGroup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.MergeGaps">MergeGaps() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.MergeGapsByDistance">MergeGapsByDistance() (in module promod3.modelling)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.MergeMHandle">MergeMHandle() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.MinCADistance">MinCADistance() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.MinimizeModelEnergy">MinimizeModelEnergy() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.Severity.MINOR">MINOR (promod3.modelling.ModellingIssue.Severity attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator">MmSystemCreator (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.model">model (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.modelling_issues">modelling_issues (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle">ModellingHandle (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue">ModellingIssue (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.Severity">ModellingIssue.Severity (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModelTermini">ModelTermini() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt>
- module
- </dt>
-
- <dd><dl>
-
- <dt><a href="cmake/index.html#command:module"><strong>command</strong></a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch">MotifMatch (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery">MotifQuery (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="core/helper.html#promod3.core.helper.MsgErrorAndExit">MsgErrorAndExit() (in module promod3.core.helper)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity">multiplicity (promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="N">N</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="core/geometry.html#promod3.core.StemCoords.n_coord">n_coord (promod3.core.StemCoords attribute)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.NaiveSolve">NaiveSolve() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.NTerminalCloser">NTerminalCloser (class in promod3.modelling)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="O">O</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.offset">offset (promod3.loop.CoordInfo attribute)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo.offset">(promod3.loop.FragmentInfo attribute)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
-</tr></table>
-
-<h2 id="P">P</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.PairwiseFunction">PairwiseFunction (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.PairwiseFunctionType">PairwiseFunctionType (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.PairwiseScore">PairwiseScore() (promod3.sidechain.Particle method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer">PairwiseScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.Parse">Parse() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle">Particle (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.periodic_dihedrals">periodic_dihedrals (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.periodic_impropers">periodic_impropers (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo.phase">phase (promod3.loop.ForcefieldPeriodicDihedralInfo attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.PhiPsiSampler">PhiPsiSampler (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser">PM3ArgumentParser (class in promod3.core.pm3argparse)</a>
- </dt>
-
-
- <dt>
- pm_action
- </dt>
-
- <dd><dl>
-
- <dt><a href="contributing.html#index-0-command:pm_action">command</a>, <a href="cmake/index.html#command:pm_action"><strong>[1]</strong></a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="actions/index_dev.html#test_actions.ActionTestCase.pm_action">pm_action (test_actions.ActionTestCase attribute)</a>
- </dt>
-
-
- <dt><a href="actions/index_dev.html#test_actions.ActionTestCase.pm_bin">pm_bin (test_actions.ActionTestCase attribute)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Pop">Pop() (promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.PrintStatistics">PrintStatistics() (promod3.loop.FragDB method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.PrintStatistics">(promod3.loop.StructureDB method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.PrintSummary">PrintSummary() (promod3.core.StaticRuntimeProfiler static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.probability">probability (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.profiles">profiles (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="core/index.html#module-promod3.core">promod3.core (module)</a>
- </dt>
-
-
- <dt><a href="core/helper.html#module-promod3.core.helper">promod3.core.helper (module)</a>
- </dt>
-
-
- <dt><a href="core/pm3argparse.html#module-promod3.core.pm3argparse">promod3.core.pm3argparse (module)</a>
- </dt>
-
-
- <dt><a href="loop/index.html#module-promod3.loop">promod3.loop (module)</a>
- </dt>
-
-
- <dt><a href="modelling/index.html#module-promod3.modelling">promod3.modelling (module)</a>
- </dt>
-
-
- <dt><a href="scoring/index.html#module-promod3.scoring">promod3.scoring (module)</a>
- </dt>
-
-
- <dt><a href="sidechain/index.html#module-promod3.sidechain">promod3.sidechain (module)</a>
- </dt>
-
-
- <dt>
- promod3_unittest
- </dt>
-
- <dd><dl>
-
- <dt><a href="cmake/index.html#index-0-command:promod3_unittest">command</a>, <a href="cmake/index.html#index-1-command:promod3_unittest">[1]</a>, <a href="cmake/index.html#command:promod3_unittest"><strong>[2]</strong></a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.FragmentSampler.ProposeStep">ProposeStep() (promod3.modelling.FragmentSampler method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.PhiPsiSampler.ProposeStep">(promod3.modelling.PhiPsiSampler method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.ProposeStep">(promod3.modelling.SamplerBase method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.ProposeStep">(promod3.modelling.SoftSampler method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.Prune">Prune() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.PScoringFunction">PScoringFunction (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.psipred_predictions">psipred_predictions (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction">PsipredPrediction (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.PsipredPrediction">PsipredPrediction() (promod3.loop.PsipredPrediction method)</a>, <a href="loop/structure_db.html#promod3.loop.PsipredPrediction.PsipredPrediction">[1]</a>
- </dt>
-
-
- <dt>
- pymod
- </dt>
-
- <dd><dl>
-
- <dt><a href="cmake/index.html#command:pymod"><strong>command</strong></a>
- </dt>
-
- </dl></dd>
- </dl></td>
-</tr></table>
-
-<h2 id="Q">Q</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.query_idx">query_idx (promod3.modelling.MotifMatch attribute)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.QueryLib">QueryLib() (promod3.sidechain.BBDepRotamerLib method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.QueryLib">(promod3.sidechain.RotamerLib method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
-</tr></table>
-
-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="sidechain/loading.html#promod3.sidechain.ReadDunbrackFile">ReadDunbrackFile() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor.Reconstruct">Reconstruct() (promod3.modelling.SidechainReconstructor method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructCBetaPositions">ReconstructCBetaPositions() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructCStemOxygen">ReconstructCStemOxygen() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructOxygenPositions">ReconstructOxygenPositions() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains">ReconstructSidechains() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer">ReducedScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.Remove">Remove() (promod3.modelling.LoopCandidates method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.RemoveCoordinates">RemoveCoordinates() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.RemoveTerminalGaps">RemoveTerminalGaps() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ReorderGaps">ReorderGaps() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ReplaceFragment">ReplaceFragment() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.ReportMolProbityScores">ReportMolProbityScores() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.res_indices">res_indices (promod3.loop.AllAtomEnvPositions attribute)</a>
- </dt>
-
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.Reset">Reset() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.Reset">(promod3.modelling.CoolerBase method)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.Reset">(promod3.modelling.ExponentialCooler method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.residue_list">residue_list (promod3.modelling.ModellingIssue attribute)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.resize">resize() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="sidechain/disulfid.html#promod3.sidechain.ResolveCysteins">ResolveCysteins() (in module promod3.sidechain)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">RigidBlocks() (in module promod3.modelling)</a>, <a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">[1]</a>, <a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">[2]</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.RMSD">RMSD() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.rotamer_res_indices">rotamer_res_indices (promod3.modelling.SidechainReconstructionData attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor">RotamerConstructor (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph">RotamerGraph (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RotamerID">RotamerID (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib">RotamerLib (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">RotamerLibEntry (class in promod3.sidechain)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">[1]</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundOmegaTorsion">RotateAroundOmegaTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion">RotateAroundPhiPsiTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPhiTorsion">RotateAroundPhiTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPsiTorsion">RotateAroundPsiTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.RotationAroundLine">RotationAroundLine() (in module promod3.core)</a>, <a href="core/geometry.html#promod3.core.RotationAroundLine">[1]</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer">RRMRotamer (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup">RRMRotamerGroup (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer.Run">Run() (promod3.modelling.AllAtomRelaxer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.Run">(promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="actions/index_dev.html#test_actions.ActionTestCase.RunAction">RunAction() (test_actions.ActionTestCase method)</a>
- </dt>
-
-
- <dt><a href="actions/index_dev.html#test_actions.ActionTestCase.RunExitStatusTest">RunExitStatusTest() (test_actions.ActionTestCase method)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.RunMolProbity">RunMolProbity() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/model_checking.html#promod3.modelling.RunMolProbityEntity">RunMolProbityEntity() (in module promod3.modelling)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.SampleMonteCarlo">SampleMonteCarlo() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase">SamplerBase (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.Save">Save() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.Save">(promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap.Save">(promod3.loop.FraggerMap method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.Save">(promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Save">(promod3.loop.TorsionSampler method)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Save">(promod3.modelling.MotifQuery method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Save">(promod3.scoring.AllAtomInteractionScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.Save">(promod3.scoring.AllAtomPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.Save">(promod3.scoring.CBPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.Save">(promod3.scoring.CBetaScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.Save">(promod3.scoring.HBondScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.Save">(promod3.scoring.ReducedScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.Save">(promod3.scoring.SSAgreementScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.Save">(promod3.scoring.TorsionScorer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.Save">(promod3.sidechain.BBDepRotamerLib method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.Save">(promod3.sidechain.RotamerLib method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerMap.SaveBB">SaveBB() (promod3.loop.FraggerMap method)</a>
- </dt>
-
-
- <dt><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.SaveCached">SaveCached() (promod3.modelling.FraggerHandle method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SavePortable">SavePortable() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.SavePortable">(promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.SavePortable">(promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.SavePortable">(promod3.loop.TorsionSampler method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.SavePortable">(promod3.scoring.AllAtomInteractionScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.SavePortable">(promod3.scoring.AllAtomPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.SavePortable">(promod3.scoring.CBPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.SavePortable">(promod3.scoring.CBetaScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.SavePortable">(promod3.scoring.HBondScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.SavePortable">(promod3.scoring.ReducedScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.SavePortable">(promod3.scoring.SSAgreementScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.SavePortable">(promod3.scoring.TorsionScorer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.SavePortable">(promod3.sidechain.BBDepRotamerLib method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.SavePortable">(promod3.sidechain.RotamerLib method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.PairwiseFunction.Score">Score() (promod3.scoring.PairwiseFunction method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer">ScoreContainer (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase">ScorerBase (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.ScoringGapExtender">ScoringGapExtender (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights">ScoringWeights (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore">SCWRL3DisulfidScore() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="scoring/other_scoring_functions.html#promod3.scoring.SCWRL3PairwiseScore">SCWRL3PairwiseScore() (in module promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor">SCWRL3RotamerConstructor (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.SCWRL4ParticleType">SCWRL4ParticleType (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor">SCWRL4RotamerConstructor (class in promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.SearchDB">SearchDB() (promod3.loop.FragDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.seq">seq (promod3.modelling.StructuralGap attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.seqres">seqres (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.Set">Set() (promod3.loop.BackboneList method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoreContainer.Set">(promod3.modelling.ScoreContainer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetAA">SetAA() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetActiveSubrotamer">SetActiveSubrotamer() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetAllAtomScoringKeys">SetAllAtomScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundOmegaTorsion">SetAroundOmegaTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundPhiPsiTorsion">SetAroundPhiPsiTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundPhiTorsion">SetAroundPhiTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetAroundPsiTorsion">SetAroundPsiTorsion() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetBackboneScoringKeys">SetBackboneScoringKeys() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetBackrub">SetBackrub() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.SetBackrub">[1]</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetC">SetC() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetCA">SetCA() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetCB">SetCB() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetCharges">SetCharges() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">SetCompoundsChemlib() (in module promod3)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.SetCpuPlatformSupport">SetCpuPlatformSupport() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetDefault">SetDefault() (promod3.loop.ForcefieldLookup static method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetDisulfidConnectivity">SetDisulfidConnectivity() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.SetEnergy">SetEnergy() (promod3.scoring.AllAtomInteractionScorer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.SetEnergy">(promod3.scoring.AllAtomPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.SetEnergy">(promod3.scoring.CBPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.SetEnergy">(promod3.scoring.CBetaScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.SetEnergy">(promod3.scoring.HBondScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.SetEnergy">(promod3.scoring.ReducedScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.SetEnergy">(promod3.scoring.TorsionScorer method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.SetEnvironment">SetEnvironment() (promod3.loop.AllAtomEnv method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetEnvironment">(promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetEpsilons">SetEpsilons() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.SetFraggerHandles">SetFraggerHandles() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetFrameEnergy">SetFrameEnergy() (promod3.sidechain.FRMRotamer method)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetFrameEnergy">[1]</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.SetFrameEnergy">(promod3.sidechain.FRMRotamerGroup method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetFrameEnergy">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.SetFrameEnergy">(promod3.sidechain.RRMRotamerGroup method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetFudgeLJ">SetFudgeLJ() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetFudgeQQ">SetFudgeQQ() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.SetInitialEnvironment">SetInitialEnvironment() (promod3.loop.AllAtomEnv method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetInitialEnvironment">(promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetInternalConnectivity">SetInternalConnectivity() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetInternalEnergy">SetInternalEnergy() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetInternalEnergy">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor">SetInternalEnergyPrefactor() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.SetInterpolate">SetInterpolate() (promod3.sidechain.BBDepRotamerLib method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetMasses">SetMasses() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetN">SetN() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.SetNonBondedCutoff">SetNonBondedCutoff() (promod3.modelling.BackboneRelaxer method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetO">SetO() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetOLC">SetOLC() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity">SetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.SetPos">SetPos() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetProbability">SetProbability() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.SetProbability">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction">SetPsipredPrediction() (promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.SetPsipredPredictions">SetPsipredPredictions() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.SetResidue">SetResidue() (promod3.loop.AllAtomPositions method)</a>, <a href="loop/all_atom.html#promod3.loop.AllAtomPositions.SetResidue">[1]</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.SetScore">SetScore() (promod3.scoring.SSAgreementScorer method)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetSequence">SetSequence() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.SetSequenceProfiles">SetSequenceProfiles() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey">SetSequenceProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetSigmas">SetSigmas() (promod3.loop.ForcefieldLookup method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetStemRMSDsKey">SetStemRMSDsKey() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.SetStructureProfile">SetStructureProfile() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetStructureProfileScoresKey">SetStructureProfileScoresKey() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetTemperature">SetTemperature() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring">SetupDefaultAllAtomScoring() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.SetupDefaultBackboneScoring">SetupDefaultBackboneScoring() (in module promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.SetupSystem">SetupSystem() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
-
- <dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetWeights">SetWeights() (promod3.modelling.ScoringWeights static method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.severity">severity (promod3.modelling.ModellingIssue attribute)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.shift">shift (promod3.loop.CoordInfo attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.ShiftCTerminal">ShiftCTerminal() (promod3.modelling.StructuralGap method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.ShiftExtension">ShiftExtension (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.sidechain_reconstructor">sidechain_reconstructor (promod3.modelling.ModellingHandle attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData">SidechainReconstructionData (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor">SidechainReconstructor (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig1">sig1 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig2">sig2 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig3">sig3 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig4">sig4 (promod3.sidechain.RotamerLibEntry attribute)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo.sigma">sigma (promod3.loop.ForcefieldLJPairInfo attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.SimilarDihedral">SimilarDihedral() (promod3.sidechain.RotamerLibEntry method)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.SimilarDihedral">[1]</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.size">size (promod3.loop.CoordInfo attribute)</a>
- </dt>
-
-
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler">SoftSampler (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer">SSAgreementScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.Start">Start() (promod3.core.StaticRuntimeProfiler static method)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.start_resnum">start_resnum (promod3.loop.CoordInfo attribute)</a>
- </dt>
-
-
- <dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.StartScoped">StartScoped() (promod3.core.StaticRuntimeProfiler static method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Stash">Stash() (promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
-
- <dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler">StaticRuntimeProfiler (class in promod3.core)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.StemCoords">StemCoords (class in promod3.core)</a>
- </dt>
-
-
- <dt><a href="core/geometry.html#promod3.core.StemPairOrientation">StemPairOrientation (class in promod3.core)</a>
- </dt>
-
-
- <dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.Stop">Stop() (promod3.core.StaticRuntimeProfiler static method)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap">StructuralGap (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGapList">StructuralGapList (class in promod3.modelling)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB">StructureDB (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDBDataType">StructureDBDataType (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="sidechain/subrotamer_optimizer.html#promod3.sidechain.SubrotamerOptimizer">SubrotamerOptimizer() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SuperposeOnto">SuperposeOnto() (promod3.loop.BackboneList method)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="T">T</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="actions/index_dev.html#module-test_actions">test_actions (module)</a>
- </dt>
-
-
- <dt><a href="actions/index_dev.html#test_actions.ActionTestCase.testPMExists">testPMExists() (test_actions.ActionTestCase method)</a>
- </dt>
-
-
- <dt><a href="modelling/pipeline.html#promod3.modelling.ModellingIssue.text">text (promod3.modelling.ModellingIssue attribute)</a>
- </dt>
-
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.TLCToRotID">TLCToRotID() (in module promod3.sidechain)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ToDensity">ToDensity() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ToEntity">ToEntity() (promod3.loop.AllAtomPositions method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ToEntity">(promod3.loop.BackboneList method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ToFrameResidue">ToFrameResidue() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.ToFrameResidue">(promod3.sidechain.RRMRotamer method)</a>
- </dt>
-
- </dl></dd>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ToRRMRotamer">ToRRMRotamer() (promod3.sidechain.FRMRotamer method)</a>
- </dt>
-
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler">TorsionSampler (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer">TorsionScorer (class in promod3.scoring)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.TransOmegaTorsions">TransOmegaTorsions() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
- <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.TreeSolve">TreeSolve() (promod3.core.GraphMinimizer method)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="U">U</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.UpdateDistributions">UpdateDistributions() (promod3.loop.TorsionSampler method)</a>
- </dt>
-
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.UpdatePositions">UpdatePositions() (promod3.loop.MmSystemCreator method)</a>
- </dt>
-
- <dd><dl>
-
- <dt><a href="modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer.UpdatePositions">(promod3.modelling.AllAtomRelaxer method)</a>
- </dt>
-
- </dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.urey_bradley_angles">urey_bradley_angles (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-<h2 id="V">V</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.VINAParticleType">VINAParticleType (class in promod3.sidechain)</a>
- </dt>
-
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor">VINARotamerConstructor (class in promod3.sidechain)</a>
- </dt>
-
- </dl></td>
-</tr></table>
-
-
-
- </div>
-
- </div>
- </div>
- <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
-
- <div class="relations">
-<h3>Related Topics</h3>
-<ul>
- <li><a href="index.html">Documentation overview</a><ul>
- </ul></li>
-</ul>
-</div>
-
-<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
- <form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
- </form>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
@@ -4062,7 +2295,7 @@
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
</div>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 040ad96124524394294b078c836828783f13f37c..8fba122262a8eed50b127feb14beb80ea9a93a39 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Getting Started — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Getting Started — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="ProMod3 Actions" href="actions/index.html" />
<link rel="prev" title="Documentation For Users" href="users.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -51,34 +37,30 @@
<h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
<div class="section" id="get-and-run-project">
<h2>Get and Run ProMod3<a class="headerlink" href="#get-and-run-project" title="Permalink to this headline">¶</a></h2>
-<p>First steps to get ProMod3 up and running:</p>
+<p>Either utilize <a class="reference internal" href="container/index.html#container"><span class="std std-ref">containers</span></a> or start from source code:</p>
<ol class="arabic">
-<li><p class="first">Fetch the source code from <a class="reference external" href="https://git.scicore.unibas.ch/schwede/ProMod3.git">https://git.scicore.unibas.ch/schwede/ProMod3.git</a>.
+<li><p>Fetch the source code from <a class="reference external" href="https://git.scicore.unibas.ch/schwede/ProMod3.git">https://git.scicore.unibas.ch/schwede/ProMod3.git</a>.
Or directly pull it with git:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git clone https://git.scicore.unibas.ch/schwede/ProMod3.git <DIR>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git clone https://git.scicore.unibas.ch/schwede/ProMod3.git <DIR>
</pre></div>
</div>
</li>
-<li><p class="first">Obtain all dependencies and compile ProMod3 with <code class="docutils literal"><span class="pre">cmake</span></code> and <code class="docutils literal"><span class="pre">make</span></code>
-(see <a class="reference internal" href="buildsystem.html#building-promod"><span class="std std-ref">here</span></a>).</p>
-</li>
-<li><p class="first">Ensure that you have a <code class="docutils literal"><span class="pre">stage/bin</span></code> folder which includes a <code class="docutils literal"><span class="pre">pm</span></code> executable.
-For convenience, add the folder to your <code class="docutils literal"><span class="pre">PATH</span></code> env. variable.</p>
-</li>
-<li><p class="first">You can now execute ProMod3 by running the following in your terminal:</p>
-</li>
+<li><p>Obtain all dependencies and compile ProMod3 with <code class="docutils literal notranslate"><span class="pre">cmake</span></code> and <code class="docutils literal notranslate"><span class="pre">make</span></code>
+(see <a class="reference internal" href="buildsystem.html#building-promod"><span class="std std-ref">here</span></a>).</p></li>
+<li><p>Ensure that you have a <code class="docutils literal notranslate"><span class="pre">stage/bin</span></code> folder which includes a <code class="docutils literal notranslate"><span class="pre">pm</span></code> executable.
+For convenience, add the folder to your <code class="docutils literal notranslate"><span class="pre">PATH</span></code> env. variable.</p></li>
+<li><p>You can now execute ProMod3 by running the following in your terminal:</p></li>
</ol>
<blockquote>
-<div><div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm <COMMAND>
+<div><div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pm <COMMAND>
</pre></div>
</div>
-<p>Here <code class="docutils literal"><span class="pre"><COMMAND></span></code> can be:</p>
+<p>Here <code class="docutils literal notranslate"><span class="pre"><COMMAND></span></code> can be:</p>
<ul>
-<li><p class="first">a predefined “action” (see <a class="reference internal" href="actions/index.html#promod-actions"><span class="std std-ref">here</span></a>)</p>
-</li>
-<li><p class="first">the path to a python script, such as the following example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<li><p>a predefined “action” (see <a class="reference internal" href="actions/index.html#promod-actions"><span class="std std-ref">here</span></a>)</p></li>
+<li><p>the path to a python script, such as the following example:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
<span class="c1"># generate backbone with dihedrals of a helix and store it</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="s2">"HELLYEAH"</span>
@@ -86,8 +68,8 @@ For convenience, add the folder to your <code class="docutils literal"><span cla
<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"test.pdb"</span><span class="p">)</span>
</pre></div>
</div>
-<p>The execution of this script should generate a <code class="docutils literal"><span class="pre">test.pdb</span></code> file, which you
-can visualize with any pdb reader (e.g. <code class="docutils literal"><span class="pre">dng</span></code> from OST).</p>
+<p>The execution of this script should generate a <code class="docutils literal notranslate"><span class="pre">test.pdb</span></code> file, which you
+can visualize with any pdb reader (e.g. <code class="docutils literal notranslate"><span class="pre">dng</span></code> from OST).</p>
</li>
</ul>
</div></blockquote>
@@ -98,19 +80,19 @@ can visualize with any pdb reader (e.g. <code class="docutils literal"><span cla
Commonly, your input is a template structure and an alignment of the template to
the desired target sequence. The modelling steps then are:</p>
<ul class="simple">
-<li>Build a raw model from a template by copying the part of the template which
-is conserved</li>
-<li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> module)</li>
-<li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> module)</li>
-<li>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+<li><p>Build a raw model from a template by copying the part of the template which
+is conserved</p></li>
+<li><p>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> module)</p></li>
+<li><p>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> module)</p></li>
+<li><p>Minimize energy of final model using molecular mechanics
+(using <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</p></li>
</ul>
<p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
-try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
+try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
included and working on any hardware supported by OpenMM). If the platform is
-not available, we use the slower “Reference” platform. For the “CPU” platform,
+not available, we use the slower “Reference” platform. For the “CPU” platform,
multiple CPU threads can be used by setting the env. variable
-<code class="docutils literal"><span class="pre">PM3_OPENMM_CPU_THREADS</span></code> to the number of desired threads. If the variable is
+<code class="docutils literal notranslate"><span class="pre">PM3_OPENMM_CPU_THREADS</span></code> to the number of desired threads. If the variable is
not set, 1 thread will be used by default.</p>
</div>
</div>
@@ -122,14 +104,39 @@ not set, 1 thread will be used by default.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Getting Started</a><ul>
-<li><a class="reference internal" href="#get-and-run-project">Get and Run ProMod3</a></li>
-<li><a class="reference internal" href="#modelling-pipeline">Modelling pipeline</a></li>
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="users.html">Users</a><ul class="current">
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -141,23 +148,24 @@ not set, 1 thread will be used by default.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/gettingstarted.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -166,11 +174,11 @@ not set, 1 thread will be used by default.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/gettingstarted.txt"
+ <a href="_sources/gettingstarted.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/index.html b/doc/html/index.html
index 52816f747ceea71e4a33ae55f42b5ab7bb71c0ee..90ecac33833d41e08f0775ae0397144035079adb 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -1,32 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>ProMod3 — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>ProMod3 — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="#" />
<link rel="next" title="Documentation For Users" href="users.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -34,8 +22,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -47,7 +34,7 @@
<div class="section" id="promod3">
<h1>ProMod3<a class="headerlink" href="#promod3" title="Permalink to this headline">¶</a></h1>
-<p>ProMod3 is a modelling engine based on the <a class="reference external" href="https://openstructure.org">OpenStructure</a> <a class="reference internal" href="references.html#biasini2013" id="id1">[biasini2013]</a>
+<p>ProMod3 is a modelling engine based on the <a class="reference external" href="https://openstructure.org">OpenStructure</a> <a class="reference internal" href="references.html#biasini2013" id="id1"><span>[biasini2013]</span></a>
computational structural biology framework that can perform all steps required
to generate a protein model by homology. Its modular design aims at
implementing flexible modelling pipelines and fast prototyping of novel
@@ -63,12 +50,12 @@ algorithms.</p>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -91,13 +78,26 @@ algorithms.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="#">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">ProMod3</a></li>
-<li><a class="reference internal" href="#documentation">Documentation</a><ul>
+<h1 class="logo"><a href="#">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
</ul>
-</li>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
@@ -106,23 +106,24 @@ algorithms.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -131,11 +132,11 @@ algorithms.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/index.txt"
+ <a href="_sources/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/license.html b/doc/html/license.html
index 04058dbcd20c214e5d0fc8ed7c6253aa21ac0014..5631dc84db1225f2ebba1fe37ad759121728e5fe 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -1,32 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>License — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>License — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
<link rel="next" title="References" href="references.html" />
<link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
@@ -35,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,7 +35,7 @@
<div class="section" id="license">
<h1>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h1>
-<div class="highlight-default"><div class="highlight"><pre><span></span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
@@ -268,7 +255,28 @@ doc/Copyright_cmake.py.txt
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
+</ul>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
@@ -277,23 +285,24 @@ doc/Copyright_cmake.py.txt
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/license.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -302,11 +311,11 @@ doc/Copyright_cmake.py.txt
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/license.txt"
+ <a href="_sources/license.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index dfadecd6b489414ac1c71bbf09eb6963d6627076..b7382adf6aa68462f23eb9ad6e1de17c874a6cfc 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Handling All Atom Positions — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Handling All Atom Positions — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
<link rel="prev" title="Structural Data" href="structure_db.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -50,12 +36,12 @@
<div class="section" id="handling-all-atom-positions">
<h1>Handling All Atom Positions<a class="headerlink" href="#handling-all-atom-positions" title="Permalink to this headline">¶</a></h1>
<p>To represent and handle all atom loops, we provide a container
-(<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) to represent arbitrary amino acid sequences with the
-positions of all their heavy atoms and an environment (<a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) to
+(<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) to represent arbitrary amino acid sequences with the
+positions of all their heavy atoms and an environment (<a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) to
handle changes during loop modelling.</p>
<p>The example below showcases some operations on the two classes:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
<span class="c1"># load example (has res. numbering starting at 1)</span>
<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">"data/1CRN.pdb"</span><span class="p">)</span>
@@ -86,168 +72,147 @@ handle changes during loop modelling.</p>
<h2>The AllAtomEnv class<a class="headerlink" href="#the-allatomenv-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AllAtomEnv">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AllAtomEnv</code><span class="sig-paren">(</span><em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AllAtomEnv</code><span class="sig-paren">(</span><em class="sig-param">seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv" title="Permalink to this definition">¶</a></dt>
<dd><p>The all atom environment contains and handles positions of all atoms during
loop modelling. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
process with all known positions and then update the environment whenever a
new loop is being added.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
-chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
+</dd>
+</dl>
<p>Indexing to access parts of the environment:</p>
<ul class="simple">
-<li><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</li>
-<li><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
+<li><p><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</p></li>
+<li><p><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
with index <em>chain_idx</em>. <strong>The numbering starts for every chain with the
-value 1</strong>.</li>
-<li>internal residue indexing: all residues of all chains are simply
-concatenated one after each other (indexing starts at 0)</li>
+value 1</strong>.</p></li>
+<li><p>internal residue indexing: all residues of all chains are simply
+concatenated one after each other (indexing starts at 0)</p></li>
</ul>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.SetInitialEnvironment">
-<code class="descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em>env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets full environment. Existing data is cleared first.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
-order as the SEQRES items provided in constructor.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
+order as the SEQRES items provided in constructor.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
SEQRES set in constructor. This can be because of corrupt residue
-numbers or sequence mismatches.</td>
-</tr>
-</tbody>
-</table>
+numbers or sequence mismatches.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.SetEnvironment">
-<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>new_env_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">new_env_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>new_pos</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">new_pos</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
<dd><p>Add/update atom positions in environment. In the end, all residues covered
in <em>new_env_pos</em> / <em>new_pos</em> / <em>bb_list</em> will be set as defined there. This
means, that positions in the env. may be reset, newly set or cleared.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</p></li>
+<li><p><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</p></li>
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>new_pos</em> / <em>new_env_pos</em> /
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>new_pos</em> / <em>new_env_pos</em> /
<em>bb_list</em> is inconsistent with SEQRES set in constructor or when
either <em>start_resnum</em> or <em>chain_idx</em> point to invalid positions in
the SEQRES.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.ClearEnvironment">
-<code class="descname">ClearEnvironment</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ClearEnvironment</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Clears a stretch of length <em>num_residues</em> in the environment in chain
with idx <em>chain_idx</em> starting from residue number <em>start_resnum</em></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start of stretch to clear</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of stretch to clear</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to clear</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to clear</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
<em>chain_idx</em> point to invalid positions in the SEQRES.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.GetEnvironment">
-<code class="descname">GetEnvironment</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Copy of stretch of structural data in environment. Useful to store
-a loop to reset later with <a class="reference internal" href="#promod3.loop.AllAtomEnv.SetEnvironment" title="promod3.loop.AllAtomEnv.SetEnvironment"><code class="xref py py-meth docutils literal"><span class="pre">SetEnvironment()</span></code></a>.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnvPositions</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start of stretch to store</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of stretch to store</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</li>
+<code class="sig-name descname">GetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Copy of stretch of structural data in environment. Useful to store
+a loop to reset later with <a class="reference internal" href="#promod3.loop.AllAtomEnv.SetEnvironment" title="promod3.loop.AllAtomEnv.SetEnvironment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnvironment()</span></code></a>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to store</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to store</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
<em>chain_idx</em> point to invalid positions in the SEQRES.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.GetSeqres">
-<code class="descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.GetAllAtomPositions">
-<code class="descname">GetAllAtomPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetAllAtomPositions" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Reference (use with caution!) to the internal storage of all atom
+<code class="sig-name descname">GetAllAtomPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetAllAtomPositions" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Reference (use with caution!) to the internal storage of all atom
positions for the environment. All residues of all chains are
stored continuously in there. To get a copy of some positions use
-<a class="reference internal" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="promod3.loop.AllAtomEnv.GetEnvironment"><code class="xref py py-meth docutils literal"><span class="pre">GetEnvironment()</span></code></a>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="promod3.loop.AllAtomEnv.GetEnvironment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetEnvironment()</span></code></a>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -257,621 +222,557 @@ stored continuously in there. To get a copy of some positions use
<h2>The AllAtomPositions class<a class="headerlink" href="#the-allatompositions-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AllAtomPositions">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AllAtomPositions</code><a class="headerlink" href="#promod3.loop.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AllAtomPositions</code><a class="headerlink" href="#promod3.loop.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for the positions of all heavy atoms of an arbitrary amino acid sequence. This is tailored for fast operations within C++ codes. The Python export described here, is mainly meant for debugging or to initialize the object and feed it to other classes using it.</p>
<p>Indexing of positions and residues:</p>
<ul class="simple">
-<li>residue indexing is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="promod3.loop.AllAtomPositions.GetNumResidues"><code class="xref py py-meth docutils literal"><span class="pre">GetNumResidues()</span></code></a>-1] and is in the
-order of the sequence used to initialize the object</li>
-<li>indexing of single atoms is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="promod3.loop.AllAtomPositions.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>-1]. For
-each residue you can find the bounds with <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetFirstIndex" title="promod3.loop.AllAtomPositions.GetFirstIndex"><code class="xref py py-meth docutils literal"><span class="pre">GetFirstIndex()</span></code></a> and
-<a class="reference internal" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="promod3.loop.AllAtomPositions.GetLastIndex"><code class="xref py py-meth docutils literal"><span class="pre">GetLastIndex()</span></code></a> or find a single atom with <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetIndex" title="promod3.loop.AllAtomPositions.GetIndex"><code class="xref py py-meth docutils literal"><span class="pre">GetIndex()</span></code></a></li>
+<li><p>residue indexing is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="promod3.loop.AllAtomPositions.GetNumResidues"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumResidues()</span></code></a>-1] and is in the
+order of the sequence used to initialize the object</p></li>
+<li><p>indexing of single atoms is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="promod3.loop.AllAtomPositions.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>-1]. For
+each residue you can find the bounds with <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetFirstIndex" title="promod3.loop.AllAtomPositions.GetFirstIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetFirstIndex()</span></code></a> and
+<a class="reference internal" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="promod3.loop.AllAtomPositions.GetLastIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLastIndex()</span></code></a> or find a single atom with <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetIndex" title="promod3.loop.AllAtomPositions.GetIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetIndex()</span></code></a></p></li>
</ul>
<p>Each atom position is initially unset (unless a list of residues is passed
-when constructing it) and can only be set with calls to <a class="reference internal" href="#promod3.loop.AllAtomPositions.SetPos" title="promod3.loop.AllAtomPositions.SetPos"><code class="xref py py-meth docutils literal"><span class="pre">SetPos()</span></code></a> or
-<a class="reference internal" href="#promod3.loop.AllAtomPositions.SetResidue" title="promod3.loop.AllAtomPositions.SetResidue"><code class="xref py py-meth docutils literal"><span class="pre">SetResidue()</span></code></a>.</p>
+when constructing it) and can only be set with calls to <a class="reference internal" href="#promod3.loop.AllAtomPositions.SetPos" title="promod3.loop.AllAtomPositions.SetPos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetPos()</span></code></a> or
+<a class="reference internal" href="#promod3.loop.AllAtomPositions.SetResidue" title="promod3.loop.AllAtomPositions.SetResidue"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetResidue()</span></code></a>.</p>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.AllAtomPositions">
-<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a container for the given <em>sequence</em> with all positions unset.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
-code which is not one of the 20 default amino acids.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+code which is not one of the 20 default amino acids.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>residues</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a container for the given <em>residues</em>. Both sequence and positions
are extracted from the given residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if any residue has a one letter
-code which is not one of the 20 default amino acids.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>residues</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue has a one letter
+code which is not one of the 20 default amino acids.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>sequence</em>, <em>residues</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a container for the given <em>sequence</em> and extracts positions from
<em>residues</em>. The residues may be different amino acids than the given
-<em>sequence</em> (see <a class="reference internal" href="#promod3.loop.AllAtomPositions.SetResidue" title="promod3.loop.AllAtomPositions.SetResidue"><code class="xref py py-meth docutils literal"><span class="pre">SetResidue()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</li>
-<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues from which positions are extracted.</li>
+<em>sequence</em> (see <a class="reference internal" href="#promod3.loop.AllAtomPositions.SetResidue" title="promod3.loop.AllAtomPositions.SetResidue"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetResidue()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</p></li>
+<li><p><strong>residues</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues from which positions are extracted.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or if
<em>sequence</em> and <em>residues</em> are inconsistent in size.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a container for the given backbone. Both sequence and backbone
positions are extracted from the given residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Backbone list of residues</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if any residue has a one letter
-code which is not one of the 20 default amino acids.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone list of residues</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue has a one letter
+code which is not one of the 20 default amino acids.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.SetResidue">
-<code class="descname">SetResidue</code><span class="sig-paren">(</span><em>res_index</em>, <em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetResidue" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetResidue</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Set positions for residue at index <em>res_index</em> given the atoms in <em>res</em>.
For each expected heavy atom, we search for an atom of that name in <em>res</em>
and if found set the corresponding position, otherwise we unset it.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">SetResidue</code><span class="sig-paren">(</span><em>res_index</em>, <em>other</em>, <em>other_res_index</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">SetResidue</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">other</em>, <em class="sig-param">other_res_index</em><span class="sig-paren">)</span></dt>
<dd><p>Set positions for residue at index <em>res_index</em> given the positions of
residue at index <em>other_res_index</em> in <em>other</em> position container. Each
position is set or cleared according to the data in <em>other</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Position container from which we take data</li>
-<li><strong>other_res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index in <em>other</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
+<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Position container from which we take data</p></li>
+<li><p><strong>other_res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>other_res_index</em>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>other_res_index</em>
out of bounds or if residues in the two containers are inconsistent
(different amino acids).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.SetPos">
-<code class="descname">SetPos</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetPos" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Set position at that index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
+<code class="sig-name descname">SetPos</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetPos" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Set position at that index.</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ClearPos">
-<code class="descname">ClearPos</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearPos" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Unset position at that index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">ClearPos</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearPos" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Unset position at that index.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ClearResidue">
-<code class="descname">ClearResidue</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearResidue" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Unset all positions for residue at that index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">ClearResidue</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearResidue" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Unset all positions for residue at that index.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetPos">
-<code class="descname">GetPos</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPos" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom position index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetPos</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPos" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Position at given index.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.IsSet">
-<code class="descname">IsSet</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsSet" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if the position at that index is currently set.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom position index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">IsSet</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsSet" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if the position at that index is currently set.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetIndex">
-<code class="descname">GetIndex</code><span class="sig-paren">(</span><em>res_index</em>, <em>atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom position index for atom named <em>atom_name</em> (standard PDB
+<code class="sig-name descname">GetIndex</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Atom position index for atom named <em>atom_name</em> (standard PDB
naming) for residue at index <em>res_index</em>.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
+<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds or
-if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds or
+if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetFirstIndex">
-<code class="descname">GetFirstIndex</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetFirstIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">First atom position index for residue at index <em>res_index</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetFirstIndex</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetFirstIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>First atom position index for residue at index <em>res_index</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetLastIndex">
-<code class="descname">GetLastIndex</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Last atom position index for residue at index <em>res_index</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetLastIndex</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Last atom position index for residue at index <em>res_index</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetAA">
-<code class="descname">GetAA</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetAA" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetAA" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Amino acid type of residue at index <em>res_index</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.IsAnySet">
-<code class="descname">IsAnySet</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAnySet" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if any atom position of residue at index <em>res_index</em> is set.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">IsAnySet</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAnySet" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if any atom position of residue at index <em>res_index</em> is set.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.IsAllSet">
-<code class="descname">IsAllSet</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAllSet" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if all atom positions of residue at index <em>res_index</em> are set.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">IsAllSet</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAllSet" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if all atom positions of residue at index <em>res_index</em> are set.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetPhiTorsion">
-<code class="descname">GetPhiTorsion</code><span class="sig-paren">(</span><em>res_index</em>, <em>def_angle=-1.0472</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Phi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
+<code class="sig-name descname">GetPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">def_angle=-1.0472</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Phi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
if required atom positions (C-N-CA-C) are not set.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Default phi angle.</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
+<li><p><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default phi angle.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
out of bounds.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetPsiTorsion">
-<code class="descname">GetPsiTorsion</code><span class="sig-paren">(</span><em>res_index</em>, <em>def_angle=-0.7854</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Psi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
+<code class="sig-name descname">GetPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">def_angle=-0.7854</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Psi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
if required atom positions (N-CA-C-N) are not set.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Default psi angle.</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
+<li><p><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default psi angle.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>res_index</em> + 1
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>res_index</em> + 1
out of bounds.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetOmegaTorsion">
-<code class="descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em>res_index</em>, <em>def_angle=3.14159</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Omega torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
+<code class="sig-name descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">def_angle=3.14159</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Omega torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
if required atom positions (CA-C-N-CA) are not set.
Here, we use CA-C of residue <em>res_index</em> - 1 and N-CA of residue
-<em>res_index</em> (consistent with OST’s
-<code class="xref py py-meth docutils literal"><span class="pre">GetOmegaTorsion()</span></code>).</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Default omega angle.</li>
+<em>res_index</em> (consistent with OST’s
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
+<li><p><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default omega angle.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
out of bounds.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetNumAtoms">
-<code class="descname">GetNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of atom positions stored in this container.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of atom positions stored in this container.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetNumResidues">
-<code class="descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of residues stored in this container.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of residues stored in this container.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetSequence">
-<code class="descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Sequence of one letter codes of all residues stored here.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Sequence of one letter codes of all residues stored here.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.Copy">
-<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Full copy of this object.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Full copy of this object.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.Extract">
-<code class="descname">Extract</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Container with residues with indices in range [<em>from</em>, <em>to</em>-1].</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First residue index</li>
-<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – One after last residue index</li>
+<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Container with residues with indices in range [<em>from</em>, <em>to</em>-1].</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue index</p></li>
+<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – One after last residue index</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em> or if any residue
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em> or if any residue
index is out of bounds.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">Extract</code><span class="sig-paren">(</span><em>res_indices</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Container with residues with indices in <em>res_indices</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – List of residue index</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if any residue index is out of
-bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">res_indices</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Container with residues with indices in <em>res_indices</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – List of residue index</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue index is out of
+bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ExtractBackbone">
-<code class="descname">ExtractBackbone</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ExtractBackbone" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Backbone list of residues with indices in range [<em>from</em>, <em>to</em>-1].
+<code class="sig-name descname">ExtractBackbone</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ExtractBackbone" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Backbone list of residues with indices in range [<em>from</em>, <em>to</em>-1].
CB atoms are reconstructed if unset.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First residue index</li>
-<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – One after last residue index</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue index</p></li>
+<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – One after last residue index</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em>, if any residue
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em>, if any residue
index is out of bounds or if any residue has any unset backbone
atom (N, CA, C, O).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ToEntity">
-<code class="descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ToEntity" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ToEntity" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>All residues packed in a single chain as an OST entity.
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.InsertInto">
-<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>res_index</em>, <em>chain</em>, <em>res_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.InsertInto" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">InsertInto</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">chain</em>, <em class="sig-param">res_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.InsertInto" title="Permalink to this definition">¶</a></dt>
<dd><p>Insert a single residue (taken from given index) into the <em>chain</em> (with
given res. number). Existing data is replaced and atoms are (re)connected
according to the default connectivity of that amino acid. Peptide links to
neighboring residues are set according to residue numbering. To make this
function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
+<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds, if
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds, if
<em>chain</em> is invalid or if not all backbone atoms (N, C, CA) set.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -881,38 +782,32 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<h2>The AllAtomEnvPositions class<a class="headerlink" href="#the-allatomenvpositions-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AllAtomEnvPositions">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AllAtomEnvPositions</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions" title="Permalink to this definition">¶</a></dt>
-<dd><p>To link the arbitrary amino acid sequence defined in <a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>
-and the SEQRES of <a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>, we provide a helper class containing
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AllAtomEnvPositions</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions" title="Permalink to this definition">¶</a></dt>
+<dd><p>To link the arbitrary amino acid sequence defined in <a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>
+and the SEQRES of <a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>, we provide a helper class containing
structural data as well as a mapping to the internal residue indices of
-<a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>.</p>
+<a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>.</p>
<dl class="attribute">
<dt id="promod3.loop.AllAtomEnvPositions.all_pos">
-<code class="descname">all_pos</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.all_pos" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">all_pos</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.all_pos" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for the positions of all heavy atoms of some residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.AllAtomEnvPositions.res_indices">
-<code class="descname">res_indices</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.res_indices" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue indices to be used by <a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for each residue defined
+<code class="sig-name descname">res_indices</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.res_indices" title="Permalink to this definition">¶</a></dt>
+<dd><p>Residue indices to be used by <a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for each residue defined
in <em>all_pos</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -922,7 +817,7 @@ in <em>all_pos</em>.</p>
<h2>Distinguishing amino acid atoms<a class="headerlink" href="#distinguishing-amino-acid-atoms" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AminoAcidAtom">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidAtom</code><a class="headerlink" href="#promod3.loop.AminoAcidAtom" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidAtom</code><a class="headerlink" href="#promod3.loop.AminoAcidAtom" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates all heavy atoms of all amino acids. The naming scheme is TLC_AN,
where TLC is the standard three letter code of the amino acid and AN is the
atom name (standard PDB naming) of the heavy atom. Examples: <em>ALA_CB</em>,
@@ -936,13 +831,13 @@ integer in the range [0, <em>XXX_NUM_ATOMS</em>-1].</p>
<dl class="class">
<dt id="promod3.loop.AminoAcidHydrogen">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidHydrogen</code><a class="headerlink" href="#promod3.loop.AminoAcidHydrogen" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidHydrogen</code><a class="headerlink" href="#promod3.loop.AminoAcidHydrogen" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates all hydrogens of all amino acids. The naming scheme is TLC_AN,
where TLC is the standard three letter code of the amino acid and AN is the
atom name (standard PDB naming) of the hydrogen. Examples: <em>ALA_H</em>,
<em>ARG_HD3</em>, <em>ASN_HB2</em>, <em>ASP_HA</em>, <em>CYS_HB3</em>, <em>LEU_H</em>.</p>
<p>We include all hydrogens that amino acids can have including <em>H1</em> (def. PDB
-name = “H”), <em>H2</em> and (if not PRO) <em>H3</em> for charged N-terminal residues. Note
+name = “H”), <em>H2</em> and (if not PRO) <em>H3</em> for charged N-terminal residues. Note
that the H atom attached to N when peptide bound (<em>H</em>) is distinct from the N
terminal hydrogens (e.g. <em>ALA_H</em> != <em>ALA_H1</em>). For <em>HIS</em> we consider the fully
protonated state, while <em>ASP</em> and <em>GLU</em> are included in their charged state.</p>
@@ -953,343 +848,310 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dl class="class">
<dt id="promod3.loop.AminoAcidLookup">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
-hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
-<dl class="staticmethod">
+(<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and
+hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
-<em class="property">static </em><code class="descname">GetOLC</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetOLC" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">One letter code for the given amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetOLC</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetOLC" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>One letter code for the given amino acid</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetAAA">
-<em class="property">static </em><code class="descname">GetAAA</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAA" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetAAA</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAA" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="descname">GetAAA</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Heavy atom type for the given amino acid and atom.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
-<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</li>
-<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
+<em class="property">static </em><code class="sig-name descname">GetAAA</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Heavy atom type for the given amino acid and atom.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</p></li>
+<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
<em>atom_name</em> is not one of the heavy atoms of <em>aa</em>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetAAH">
-<em class="property">static </em><code class="descname">GetAAH</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAH" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetAAH</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAH" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="descname">GetAAH</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Hydrogen type for the given amino acid and atom.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
-<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</li>
-<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
+<em class="property">static </em><code class="sig-name descname">GetAAH</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Hydrogen type for the given amino acid and atom.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</p></li>
+<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
<em>atom_name</em> is not one of the hydrogens of <em>aa</em>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetIndex">
-<em class="property">static </em><code class="descname">GetIndex</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom index (in [0, GetNumAtoms(aa)-1]) for the given amino acid and
+<em class="property">static </em><code class="sig-name descname">GetIndex</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Atom index (in [0, GetNumAtoms(aa)-1]) for the given amino acid and
atom.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
-<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
heavy atoms of <em>aa</em>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetHydrogenIndex">
-<em class="property">static </em><code class="descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom index (in [0, GetNumHydrogens(aa)-1]) for the given amino acid
+<em class="property">static </em><code class="sig-name descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Atom index (in [0, GetNumHydrogens(aa)-1]) for the given amino acid
and atom.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
-<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
hydrogens of <em>aa</em>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetNumAtoms">
-<em class="property">static </em><code class="descname">GetNumAtoms</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of heavy atoms of the given amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetNumAtoms</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of heavy atoms of the given amino acid</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetMaxNumAtoms">
-<em class="property">static </em><code class="descname">GetMaxNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Max. number of heavy atoms for any amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetMaxNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Max. number of heavy atoms for any amino acid</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetNumHydrogens">
-<em class="property">static </em><code class="descname">GetNumHydrogens</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumHydrogens" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of hydrogens of the given amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetNumHydrogens</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumHydrogens" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of hydrogens of the given amino acid</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetMaxNumHydrogens">
-<em class="property">static </em><code class="descname">GetMaxNumHydrogens</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumHydrogens" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Max. number of hydrogens for any amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetMaxNumHydrogens</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumHydrogens" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Max. number of hydrogens for any amino acid</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetAA">
-<em class="property">static </em><code class="descname">GetAA</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAA" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAA" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="descname">GetAA</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</li>
-<li><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</li>
+<em class="property">static </em><code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Amino acid type of the given heavy atom type</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</p></li>
+<li><p><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetAtomName">
-<em class="property">static </em><code class="descname">GetAtomName</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomName" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetAtomName</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomName" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="descname">GetAtomName</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
+<em class="property">static </em><code class="sig-name descname">GetAtomName</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
<dt id="promod3.loop.AminoAcidLookup.GetAtomNameCharmm">
-<em class="property">static </em><code class="descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameCharmm" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameCharmm" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
+<em class="property">static </em><code class="sig-name descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
<dt id="promod3.loop.AminoAcidLookup.GetAtomNameAmber">
-<em class="property">static </em><code class="descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameAmber" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameAmber" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom name of the given heavy atom type according to PDB (default),
+<em class="property">static </em><code class="sig-name descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Atom name of the given heavy atom type according to PDB (default),
CHARMM or AMBER naming.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</li>
-<li><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</p></li>
+<li><p><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetElement">
-<em class="property">static </em><code class="descname">GetElement</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetElement" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chemical element of the given heavy atom type</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetElement</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetElement" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Chemical element of the given heavy atom type</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetAnchorAtomIndex">
-<em class="property">static </em><code class="descname">GetAnchorAtomIndex</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAnchorAtomIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Atom index (in [0, GetNumAtoms(GetAA(aah))-1]) of the anchor to
-which the given hydrogen is attached.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetAnchorAtomIndex</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAnchorAtomIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Atom index (in [0, GetNumAtoms(GetAA(aah))-1]) of the anchor to
+which the given hydrogen is attached.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetHNIndex">
-<em class="property">static </em><code class="descname">GetHNIndex</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHNIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
-when residue is peptide bound.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetHNIndex</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHNIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
+when residue is peptide bound.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetH1Index">
-<em class="property">static </em><code class="descname">GetH1Index</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH1Index" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetH1Index</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH1Index" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.AminoAcidLookup.GetH2Index">
-<em class="property">static </em><code class="descname">GetH2Index</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH2Index" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetH2Index</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH2Index" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.AminoAcidLookup.GetH3Index">
-<em class="property">static </em><code class="descname">GetH3Index</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH3Index" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
-when residue is N terminal.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetH3Index</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH3Index" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
+when residue is N terminal.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -1304,46 +1166,70 @@ when residue is N terminal.</td>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Handling All Atom Positions</a><ul>
-<li><a class="reference internal" href="#the-allatomenv-class">The AllAtomEnv class</a></li>
-<li><a class="reference internal" href="#the-allatompositions-class">The AllAtomPositions class</a></li>
-<li><a class="reference internal" href="#the-allatomenvpositions-class">The AllAtomEnvPositions class</a></li>
-<li><a class="reference internal" href="#distinguishing-amino-acid-atoms">Distinguishing amino acid atoms</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="structure_db.html" title="previous chapter">Structural Data</a></li>
- <li>Next: <a href="mm_system_creation.html" title="next chapter">Generate <code class="docutils literal"><span class="pre">ost.mol.mm</span></code> systems</a></li>
+ <li>Next: <a href="mm_system_creation.html" title="next chapter">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/loop/all_atom.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1352,11 +1238,11 @@ when residue is N terminal.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/loop/all_atom.txt"
+ <a href="../_sources/loop/all_atom.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 40d4716eb10fc56ed0ef6e7626f2ea8d3bc366f8..45a0992aa4b3a2b8aae53a1d73803f1bbcefd28a 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Representing Loops — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Representing Loops — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
<link rel="prev" title="loop - Loop Handling" href="index.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -50,12 +36,12 @@
<div class="section" id="representing-loops">
<h1>Representing Loops<a class="headerlink" href="#representing-loops" title="Permalink to this headline">¶</a></h1>
<p>The most simple representation of structural information in ProMod3 is the
-<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
+<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
residues. They provide structural manipulations, they can be manipulated and
-converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="s2">"AAAAAAAA"</span>
@@ -92,791 +78,685 @@ converted from, to, or inserted to a <a class="reference external" href="https:/
<h2>The BackboneList class<a class="headerlink" href="#the-backbonelist-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.BackboneList">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">BackboneList</code><a class="headerlink" href="#promod3.loop.BackboneList" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">BackboneList</code><a class="headerlink" href="#promod3.loop.BackboneList" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for the positions of the backbone atoms (nitrogen (N), alpha carbon
(CA), beta carbon (CB), carbon (C), oxygen (O)), the one letter codes and
amino acid types of a segment. This object allows to get, set or modify the
atom positions, etc through a set of functions (<strong>indexing to access each
residue starts at 0</strong>). To simplify algorithms, which use this structure, each
-residue has a CB position defined (i.e. even if it’s a glycine) and we only
+residue has a CB position defined (i.e. even if it’s a glycine) and we only
allow amino acid types belonging to the 20 default amino acids. Note that the
omega torsion angle defined here for residue <em>i</em> is the dihedral between CA-C
of residue <em>i</em> and N-CA of residue <em>i+1</em> (this is shifted by 1 residue
-compared to OST’s <code class="xref py py-meth docutils literal"><span class="pre">GetOmegaTorsion()</span></code>).</p>
+compared to OST’s <code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p>
<dl class="method">
<dt id="promod3.loop.BackboneList.BackboneList">
-<code class="descname">BackboneList</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.BackboneList" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.BackboneList" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates empty BackboneList</p>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a helical BackboneList from given sequence</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
-code which is not one of the 20 default amino acids.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+code which is not one of the 20 default amino acids.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em>, <em>dihedral_angles</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">dihedral_angles</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a BackboneList from given <em>sequence</em> and <em>dihedral_angles</em></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
-<li><strong>dihedral_angles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> objects defining the backbone
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p></li>
+<li><p><strong>dihedral_angles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> objects defining the backbone
dihedral angles of created BackboneList. Every
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> must either have two or three
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> must either have two or three
elements. Two elements are considered to define the
phi and psi angles, leading to an idealized omega
angle of 180 degrees. In case of three elements, all
-angles are defined.</li>
+angles are defined.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or if
<em>sequence</em> and <em>dihedral_angles</em> are inconsistent in size.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>residues</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a BackboneList with positions and sequence extracted from
<em>residues</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions and one letter codes
-are extracted.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if a residue in <em>residues</em>
+are extracted.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if a residue in <em>residues</em>
contains a one letter code which is not one of the 20 default
amino acids or when there is a residue not providing all
-required positions.</td>
-</tr>
-</tbody>
-</table>
+required positions.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em>, <em>residues</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a BackboneList from given <em>sequence</em> and positions extracted from
<em>residues</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
-<li><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
-which the backbone positions are extracted.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p></li>
+<li><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+which the backbone positions are extracted.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or if
<em>sequence</em> and <em>residues</em> are inconsistent in size or when there is
a residue not providing all necessary positions.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ToDensity">
-<code class="descname">ToDensity</code><span class="sig-paren">(</span><em>padding=10.0</em>, <em>sampling=Vec3(1.0</em>, <em>1.0</em>, <em>1.0)</em>, <em>resolution=3.0</em>, <em>high_resolution=false</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToDensity" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
-<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – </li>
-<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
-<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
+<code class="sig-name descname">ToDensity</code><span class="sig-paren">(</span><em class="sig-param">padding=10.0</em>, <em class="sig-param">sampling=Vec3(1.0</em>, <em class="sig-param">1.0</em>, <em class="sig-param">1.0)</em>, <em class="sig-param">resolution=3.0</em>, <em class="sig-param">high_resolution=false</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToDensity" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The whole backbone list converted to a density map.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
+<li><p><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </p></li>
+<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
+<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ToEntity">
-<code class="descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToEntity" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToEntity" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The whole backbone list converted to an OST entity.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.InsertInto">
-<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>chain</em>, <em>start_resnum</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.InsertInto" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">InsertInto</code><span class="sig-paren">(</span><em class="sig-param">chain</em>, <em class="sig-param">start_resnum</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.InsertInto" title="Permalink to this definition">¶</a></dt>
<dd><p>Inserts the backbone list into the <em>chain</em>. If the residues corresponding
-to the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> are already present in the entity, they will
+to the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> are already present in the entity, they will
be replaced, otherwise they will be added to the entity.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>map</em>, <em>resolution=3.0</em>, <em>high_resolution=false</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
-<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
-<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
+<code class="sig-name descname">InsertInto</code><span class="sig-paren">(</span><em class="sig-param">map</em>, <em class="sig-param">resolution=3.0</em>, <em class="sig-param">high_resolution=false</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </p></li>
+<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
+<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetBounds">
-<code class="descname">GetBounds</code><span class="sig-paren">(</span><em>all_atom=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetBounds" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetBounds</code><span class="sig-paren">(</span><em class="sig-param">all_atom=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetBounds" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p></p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetSequence">
-<code class="descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The amino acid sequence.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The amino acid sequence.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetSequence">
-<code class="descname">SetSequence</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Set amino acid sequence to this.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+<code class="sig-name descname">SetSequence</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Set amino acid sequence to this.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or size of
-<em>sequence</em> does not match.</td>
-</tr>
-</tbody>
-</table>
+<em>sequence</em> does not match.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.Extract">
-<code class="descname">Extract</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Items with indices <em>from</em>, ..., <em>to</em>-1 of this list.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Items with indices <em>from</em>, …, <em>to</em>-1 of this list.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReplaceFragment">
-<code class="descname">ReplaceFragment</code><span class="sig-paren">(</span><em>sub_fragment</em>, <em>index</em>, <em>superpose_stems</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReplaceFragment" title="Permalink to this definition">¶</a></dt>
-<dd><p>Replaces a fragment of the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> starting at position
+<code class="sig-name descname">ReplaceFragment</code><span class="sig-paren">(</span><em class="sig-param">sub_fragment</em>, <em class="sig-param">index</em>, <em class="sig-param">superpose_stems</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReplaceFragment" title="Permalink to this definition">¶</a></dt>
+<dd><p>Replaces a fragment of the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> starting at position
<em>index</em> by the <em>sub_fragment</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>sub_fragment</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The fragment to be inserted</li>
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The position at which the fragment
-replacement will begin</li>
-<li><strong>superpose_stems</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to false, the function will simply
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sub_fragment</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The fragment to be inserted</p></li>
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The position at which the fragment
+replacement will begin</p></li>
+<li><p><strong>superpose_stems</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to false, the function will simply
replace the according
-<code class="xref py py-class docutils literal"><span class="pre">Backbone</span></code> objects. If set to True,
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Backbone</span></code> objects. If set to True,
the n-terminal and c-terminal tails are superposed onto the <em>sub_fragment</em>
stems using the positions at <em>index</em> and
-<em>index</em> + len( <em>sub_fragment</em> )-1.</li>
+<em>index</em> + len( <em>sub_fragment</em> )-1.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if
<em>sub_fragment</em> does not fully fit into
actual fragment at specified <em>index</em></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetN">
-<code class="descname">GetN</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetN" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetN</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetN" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetCA">
-<code class="descname">GetCA</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCA" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetCA</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCA" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetCB">
-<code class="descname">GetCB</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCB" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetCB</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCB" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetC">
-<code class="descname">GetC</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetC" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetC</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetC" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetO">
-<code class="descname">GetO</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetO" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
-atom for residue at given index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetO</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetO" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
+atom for residue at given index.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetN">
-<code class="descname">SetN</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetN" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetN</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetN" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetCA">
-<code class="descname">SetCA</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCA" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetCA</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCA" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetCB">
-<code class="descname">SetCB</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCB" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetCB</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCB" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetC">
-<code class="descname">SetC</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetC" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetC</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetC" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetO">
-<code class="descname">SetO</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetO" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
-/ oxygen atom to this.</li>
+<code class="sig-name descname">SetO</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetO" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+/ oxygen atom to this.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetOLC">
-<code class="descname">GetOLC</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOLC" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">One letter code of the residue at given index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">char</span></code></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetOLC</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOLC" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>One letter code of the residue at given index.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetOLC">
-<code class="descname">SetOLC</code><span class="sig-paren">(</span><em>index</em>, <em>olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetOLC" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
+<code class="sig-name descname">SetOLC</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetOLC" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
+<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetAA">
-<code class="descname">GetAA</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetAA" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetAA" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Amino acid type of the residue at given index.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetAA">
-<code class="descname">SetAA</code><span class="sig-paren">(</span><em>index</em>, <em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAA" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
+<code class="sig-name descname">SetAA</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAA" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>aa</em> == ost.conop.XXX.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>aa</em> == ost.conop.XXX.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.Set">
-<code class="descname">Set</code><span class="sig-paren">(</span><em>index</em>, <em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Set" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">cb_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Set" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">Set</code><span class="sig-paren">(</span><em>index</em>, <em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">Set</code><span class="sig-paren">(</span><em>index</em>, <em>res</em>, <em>olc</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
<dd><p>Set all backbone informations. This will reconstruct CB positions if needed
and set the amino acid type according to the given one letter code.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
-<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
+<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
+<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
+<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of residues in this backbone list.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of residues in this backbone list.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.resize">
-<code class="descname">resize</code><span class="sig-paren">(</span><em>new_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.resize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>new_size</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Resize backbone list to contain this number of residues.
+<code class="sig-name descname">resize</code><span class="sig-paren">(</span><em class="sig-param">new_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.resize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>new_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Resize backbone list to contain this number of residues.
If new residues are added, their properties will not be
initialized. Existing residues are untouched unless the
-list is shrinked (in that case extra residues are deleted).</td>
-</tr>
-</tbody>
-</table>
+list is shrinked (in that case extra residues are deleted).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.empty">
-<code class="descname">empty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.empty" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True if the list is empty (i.e. size 0).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">empty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.empty" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True if the list is empty (i.e. size 0).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.append">
-<code class="descname">append</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.append" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">append</code><span class="sig-paren">(</span><em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">cb_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.append" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">append</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">append</code><span class="sig-paren">(</span><em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">append</code><span class="sig-paren">(</span><em>res</em>, <em>olc</em><span class="sig-paren">)</span></dt>
-<dd><p>Appends a new residue at the end of the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>. This will
+<code class="sig-name descname">append</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
+<dd><p>Appends a new residue at the end of the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>. This will
reconstruct CB positions if needed and set the amino acid type according
to the given one letter code.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
-<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
+<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
+<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
+<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.clear">
-<code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.clear" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.clear" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove all residues from this list.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.Copy">
-<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Creates and returns a deep copy of this <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>. This can be
+<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a deep copy of this <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>. This can be
useful, since Python uses reference assignments.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReconstructCBetaPositions">
-<code class="descname">ReconstructCBetaPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCBetaPositions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ReconstructCBetaPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCBetaPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Does a simple reconstruction of all CB positions based on the current
N, CA and C positions.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReconstructOxygenPositions">
-<code class="descname">ReconstructOxygenPositions</code><span class="sig-paren">(</span><em>last_psi=-0.78540</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructOxygenPositions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ReconstructOxygenPositions</code><span class="sig-paren">(</span><em class="sig-param">last_psi=-0.78540</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructOxygenPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Does a simple reconstruction of all oxygen positions based on the actual
N, CA and C positions. The position of the last oxygen depends on the next
residue, an additional parameter is therefore required.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>last_psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi angle of the last BackboneList residue,
-the default value corresponds to a typical alpha-helix.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>last_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of the last BackboneList residue,
+the default value corresponds to a typical alpha-helix.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReconstructCStemOxygen">
-<code class="descname">ReconstructCStemOxygen</code><span class="sig-paren">(</span><em>after_c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCStemOxygen" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ReconstructCStemOxygen</code><span class="sig-paren">(</span><em class="sig-param">after_c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCStemOxygen" title="Permalink to this definition">¶</a></dt>
<dd><p>Reconstructs the last oxygen of this backbone list. The oxygen position
depends on the residue following the C stem. The position is only
reconstructed if the residue handle is valid.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
-element of this backbone list)</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+element of this backbone list)</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ApplyTransform">
-<code class="descname">ApplyTransform</code><span class="sig-paren">(</span><em>index</em>, <em>transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ApplyTransform" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyTransform</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ApplyTransform" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies a transformation to the positions of a single residue.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">ApplyTransform</code><span class="sig-paren">(</span><em>from</em>, <em>to</em>, <em>transform</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyTransform</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em>, <em class="sig-param">transform</em><span class="sig-paren">)</span></dt>
<dd><p>Applies a transformation to the positions of the residues with indices
-<em>from</em>, ..., <em>to</em>-1 of this list.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start index.</li>
-<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<em>from</em>, …, <em>to</em>-1 of this list.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start index.</p></li>
+<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</p></li>
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">ApplyTransform</code><span class="sig-paren">(</span><em>transform</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyTransform</code><span class="sig-paren">(</span><em class="sig-param">transform</em><span class="sig-paren">)</span></dt>
<dd><p>Applies a transformation to all positions of this list.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetTransform">
-<code class="descname">GetTransform</code><span class="sig-paren">(</span><em>index</em>, <em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetTransform" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetTransform</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetTransform" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetTransform</code><span class="sig-paren">(</span><em>index</em>, <em>other</em>, <em>other_index</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Minimum RMSD transformation of residue <em>index</em> onto <em>res</em> or
+<code class="sig-name descname">GetTransform</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">other</em>, <em class="sig-param">other_index</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Minimum RMSD transformation of residue <em>index</em> onto <em>res</em> or
residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
-<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
-<li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</p></li>
+<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p></li>
+<li><p><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">GetTransform</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
-list onto CA positions of <em>other</em> backbone list.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetTransform</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Get minimum RMSD transformation of CA positions of this backbone
+list onto CA positions of <em>other</em> backbone list.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SuperposeOnto">
-<code class="descname">SuperposeOnto</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SuperposeOnto" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SuperposeOnto</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SuperposeOnto" title="Permalink to this definition">¶</a></dt>
<dd><p>Superposes this backbone list onto another one using CA positions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.RotateAroundPhiTorsion">
-<code class="descname">RotateAroundPhiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">RotateAroundPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.RotateAroundPsiTorsion">
-<code class="descname">RotateAroundPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">RotateAroundPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.RotateAroundOmegaTorsion">
-<code class="descname">RotateAroundOmegaTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>omega</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">RotateAroundOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">omega</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.RotateAroundPhiPsiTorsion">
-<code class="descname">RotateAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">RotateAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundPhiTorsion">
-<code class="descname">SetAroundPhiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetAroundPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundPsiTorsion">
-<code class="descname">SetAroundPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetAroundPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundOmegaTorsion">
-<code class="descname">SetAroundOmegaTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>omega</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetAroundOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">omega</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundPhiPsiTorsion">
-<code class="descname">SetAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dd><p>Rotates/sets the phi/psi/omega torsion angle of the backbone at position
<em>index</em> in the backbone list by/to the given angle(s).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle by which to rotate phi torsion.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle by which to rotate psi torsion.</li>
-<li><strong>omega</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle by which to rotate omega torsion.</li>
-<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate phi torsion.</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate psi torsion.</p></li>
+<li><p><strong>omega</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate omega torsion.</p></li>
+<li><p><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all
residues after the one with <em>index</em>. Otherwise, it will
be propagated in the direction where it will affect the
-least number of residues.</li>
+least number of residues.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetPhiTorsion">
-<code class="descname">GetPhiTorsion</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetPsiTorsion">
-<code class="descname">GetPsiTorsion</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetOmegaTorsion">
-<code class="descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The phi/psi/omega torsion angle for residue at given index.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The phi/psi/omega torsion angle for residue at given index.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.TransOmegaTorsions">
-<code class="descname">TransOmegaTorsions</code><span class="sig-paren">(</span><em>thresh=20/180*pi</em>, <em>allow_prepro_cis=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.TransOmegaTorsions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">TransOmegaTorsions</code><span class="sig-paren">(</span><em class="sig-param">thresh=20/180*pi</em>, <em class="sig-param">allow_prepro_cis=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.TransOmegaTorsions" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks whether this backbone list only contains trans omega torsion angles.
Usually, you would want this to be the case, but it can fail if you have any
unfavorable omega torsion angle in your backbone.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Allowed deviation from ideal trans angle (pi)</li>
-<li><strong>allow_prepro_cis</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether cis-omega torsions should be
-allowed in case of a subsequent proline.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Allowed deviation from ideal trans angle (pi)</p></li>
+<li><p><strong>allow_prepro_cis</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether cis-omega torsions should be
+allowed in case of a subsequent proline.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">whether <em>bb_list</em> only contains trans-omega torsions.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if size of this backbone list is
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>whether <em>bb_list</em> only contains trans-omega torsions.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of this backbone list is
smaller than 3.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetBackrub">
-<code class="descname">SetBackrub</code><span class="sig-paren">(</span><em>index</em>, <em>primary_rot_angle</em>, <em>flanking_rot_angle_one</em>, <em>flanking_rot_angle_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetBackrub" title="Permalink to this definition">¶</a></dt>
-<dd><p>Applies a backrub motion <a class="reference internal" href="../references.html#davis2006" id="id1">[davis2006]</a> at residue defined by <strong>index</strong>.
+<code class="sig-name descname">SetBackrub</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">primary_rot_angle</em>, <em class="sig-param">flanking_rot_angle_one</em>, <em class="sig-param">flanking_rot_angle_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetBackrub" title="Permalink to this definition">¶</a></dt>
+<dd><p>Applies a backrub motion <a class="reference internal" href="../references.html#davis2006" id="id1"><span>[davis2006]</span></a> at residue defined by <strong>index</strong>.
The first rotation axis is defined by the CA positions from residues at
<strong>index</strong> -1 and <strong>index</strong> +1. All atoms in between get rotated around this
axis by <strong>primary_rot_angle</strong>. To restore the the hydrogen bond network
@@ -887,96 +767,83 @@ position with an angle of <strong>flanking_rot_angle_one</strong>. The second ro
around the axis from the transformed central CA position to the CA position
from residue at position <strong>index</strong> +1 with an angle of
<strong>flanking_rot_angle_two</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</li>
-<li><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</li>
-<li><strong>flanking_rot_angle_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle of the first compensatory rotation
-in radians</li>
-<li><strong>flanking_rot_angle_two</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle of the second compensatory rotation
-in radians</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</p></li>
+<li><p><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</p></li>
+<li><p><strong>flanking_rot_angle_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first compensatory rotation
+in radians</p></li>
+<li><p><strong>flanking_rot_angle_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the second compensatory rotation
+in radians</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
larger size of BackboneList - 2</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">SetBackrub</code><span class="sig-paren">(</span><em>index</em>, <em>primary_rot_angle</em><span class="optional">[</span>, <em>scaling=1.0</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">SetBackrub</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">primary_rot_angle</em><span class="optional">[</span>, <em class="sig-param">scaling=1.0</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Applies the backrub motion described above but calculates the ideal angles
for the compensatory rotations in a way, that the new oxygen positions are
as close as possible to the original ones. The ideal angles can be scaled
down by <strong>scaling</strong> to make them less extreme.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</li>
-<li><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</li>
-<li><strong>scaling</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The ideal angles for the compensatory rotations will
-be scaled by this value.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</p></li>
+<li><p><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</p></li>
+<li><p><strong>scaling</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The ideal angles for the compensatory rotations will
+be scaled by this value.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
larger size of BackboneList - 2</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.MinCADistance">
-<code class="descname">MinCADistance</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.MinCADistance" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Minimal pairwise CA-distance between this and the <em>other</em>
-backbone list.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">MinCADistance</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.MinCADistance" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Minimal pairwise CA-distance between this and the <em>other</em>
+backbone list.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.RMSD">
-<code class="descname">RMSD</code><span class="sig-paren">(</span><em>other</em>, <em>superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RMSD" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">RMSD</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RMSD" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.CARMSD">
-<code class="descname">CARMSD</code><span class="sig-paren">(</span><em>other</em>, <em>superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.CARMSD" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">RMSD / C-alpha RMSD between this and the <em>other</em> backbone list.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
-<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to superpose before calculating the RMSD.</li>
+<code class="sig-name descname">CARMSD</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.CARMSD" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>RMSD / C-alpha RMSD between this and the <em>other</em> backbone list.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p></li>
+<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to superpose before calculating the RMSD.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -991,43 +858,70 @@ backbone list.</td>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Representing Loops</a><ul>
-<li><a class="reference internal" href="#the-backbonelist-class">The BackboneList class</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
<li>Next: <a href="torsion_sampler.html" title="next chapter">Sampling Dihedral Angles</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/loop/backbone.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1036,11 +930,11 @@ backbone list.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/loop/backbone.txt"
+ <a href="../_sources/loop/backbone.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 7bf3f8c338c75ba1b5d38429d398fec172c11624..3eaed6a826ff477cf623a1bcbf8fce0b5f0b61f0 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>loop - Loop Handling — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>loop - Loop Handling — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Representing Loops" href="backbone.html" />
<link rel="prev" title="Other Scoring Functions" href="../scoring/other_scoring_functions.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,12 +34,12 @@
<div class="body" role="main">
<div class="section" id="module-promod3.loop">
-<span id="loop-loop-handling"></span><h1><a class="reference internal" href="#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> - Loop Handling<a class="headerlink" href="#module-promod3.loop" title="Permalink to this headline">¶</a></h1>
+<span id="loop-loop-handling"></span><h1><a class="reference internal" href="#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> - Loop Handling<a class="headerlink" href="#module-promod3.loop" title="Permalink to this headline">¶</a></h1>
<p>Tools and algorithms for loop handling. This module provides ways for
representation of peptides and to obtain fragments to potentially use as
loops. The following example should give you an idea of what can be done:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
<span class="c1"># load an example structure</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
@@ -120,7 +106,7 @@ loops. The following example should give you an idea of what can be done:</p>
<li class="toctree-l2"><a class="reference internal" href="all_atom.html#distinguishing-amino-acid-atoms">Distinguishing amino acid atoms</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="mm_system_creation.html">Generate <code class="docutils literal"><span class="pre">ost.mol.mm</span></code> systems</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="mm_system_creation.html">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a><ul>
<li class="toctree-l2"><a class="reference internal" href="mm_system_creation.html#create-mm-systems-for-loops">Create MM systems for loops</a></li>
<li class="toctree-l2"><a class="reference internal" href="mm_system_creation.html#forcefield-lookup-for-amino-acids">Forcefield lookup for amino acids</a></li>
</ul>
@@ -136,7 +122,41 @@ loops. The following example should give you an idea of what can be done:</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
@@ -147,23 +167,24 @@ loops. The following example should give you an idea of what can be done:</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/loop/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -172,11 +193,11 @@ loops. The following example should give you an idea of what can be done:</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/loop/index.txt"
+ <a href="../_sources/loop/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index d4b5d8329d34aa539f9896870d42ff0f2b436ccf..39b2f7824021f896a9c4195dbc4d42ad7ca5c53c 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Loading Precomputed Objects — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Loading Precomputed Objects — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
<link rel="prev" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -53,118 +39,110 @@
ProMod3 offers to load precomputed instances for direct usage.</p>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSampler">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSampler</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSampler" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSampler</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id1">[solis2006]</a> that has been trained on
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id1"><span>[solis2006]</span></a> that has been trained on
non-redundant protein structures.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The torsion sampler</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSamplerCoil">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerCoil</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerCoil" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSamplerCoil</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerCoil" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id2">[solis2006]</a> that has been trained on coil
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id2"><span>[solis2006]</span></a> that has been trained on coil
residues of non-redundant protein structures.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The torsion sampler</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSamplerHelical">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerHelical</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerHelical" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSamplerHelical</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerHelical" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id3">[solis2006]</a> that has been trained on helical
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id3"><span>[solis2006]</span></a> that has been trained on helical
residues of non-redundant protein structures.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The torsion sampler</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSamplerExtended">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerExtended</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerExtended" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSamplerExtended</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerExtended" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id4">[solis2006]</a> that has been trained on extended
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id4"><span>[solis2006]</span></a> that has been trained on extended
residues of non-redundant protein structures.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The torsion sampler</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadStructureDB">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadStructureDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadStructureDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a structure db containing roughly 21000 chains form the
PDB with seqid redundancy cutoff of 60%</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure db</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The structure db</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadFragDB">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a FragDB containing fragments up to the length of 14,
therefore capable of bridging gaps up to the length of 12. The returned
-databases contains the location of fragments in the <a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>
-returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" title="promod3.loop.LoadStructureDB"><code class="xref py py-meth docutils literal"><span class="pre">LoadStructureDB()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Fragment database</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
-</tr>
-</tbody>
-</table>
+databases contains the location of fragments in the <a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>
+returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" title="promod3.loop.LoadStructureDB"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadStructureDB()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The Fragment database</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -175,36 +153,71 @@ returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" t
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
- <li>Previous: <a href="mm_system_creation.html" title="previous chapter">Generate <code class="docutils literal"><span class="pre">ost.mol.mm</span></code> systems</a></li>
- <li>Next: <a href="../core/index.html" title="next chapter"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li>Previous: <a href="mm_system_creation.html" title="previous chapter">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
+ <li>Next: <a href="../core/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/loop/load_loop_objects.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -213,11 +226,11 @@ returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" t
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/loop/load_loop_objects.txt"
+ <a href="../_sources/loop/load_loop_objects.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 2a16d4466d582ba4cbbc5a8a19f17090f2f7583d..c3a57978ee3dd7bd2f5779a36f4407a397bf2823 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Generate ost.mol.mm systems — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Generate ost.mol.mm systems — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
<link rel="prev" title="Handling All Atom Positions" href="all_atom.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,13 +34,13 @@
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
-proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal"><span class="pre">MmSystemCreator</span></code></a>) and a
-specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>).</p>
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) and a
+specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>).</p>
<p>The example below showcases the creation and use of an MM system:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
<span class="c1"># setup system creator</span>
<span class="n">ff_lookup</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">ForcefieldLookup</span><span class="o">.</span><span class="n">GetDefault</span><span class="p">()</span>
@@ -94,11 +80,11 @@ specialized forcefield lookup for amino acids (<a class="reference internal" hre
</pre></div>
</div>
<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">To simplify use when sidechains may be missing and the region of interest for
+<p class="admonition-title">Note</p>
+<p>To simplify use when sidechains may be missing and the region of interest for
the MM system has to be determined, it might be better to use the simpler
-<a class="reference internal" href="../modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.SidechainReconstructor</span></code></a> and
-<a class="reference internal" href="../modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer" title="promod3.modelling.AllAtomRelaxer"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.AllAtomRelaxer</span></code></a> classes. Even if all the sidechains
+<a class="reference internal" href="../modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.SidechainReconstructor</span></code></a> and
+<a class="reference internal" href="../modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer" title="promod3.modelling.AllAtomRelaxer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.AllAtomRelaxer</span></code></a> classes. Even if all the sidechains
are available, those classes will be helpful since the overhead to check
sidechains without reconstructing them is minimal.</p>
</div>
@@ -106,67 +92,59 @@ sidechains without reconstructing them is minimal.</p>
<h2>Create MM systems for loops<a class="headerlink" href="#create-mm-systems-for-loops" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.MmSystemCreator">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">MmSystemCreator</code><span class="sig-paren">(</span><em>ff_lookup</em>, <em>fix_surrounding_hydrogens=True</em>, <em>kill_electrostatics=False</em>, <em>nonbonded_cutoff=8</em>, <em>inaccurate_pot_energy=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">MmSystemCreator</code><span class="sig-paren">(</span><em class="sig-param">ff_lookup</em>, <em class="sig-param">fix_surrounding_hydrogens=True</em>, <em class="sig-param">kill_electrostatics=False</em>, <em class="sig-param">nonbonded_cutoff=8</em>, <em class="sig-param">inaccurate_pot_energy=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup a system creator for a specific forcefield. The constructor only stores
-the settings. Most setup work is done by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>.</p>
+the settings. Most setup work is done by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>.</p>
<p>The idea is to have a set of movable loop residues and a set of fixed
surrounding residues which interact with the loop.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_lookup</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>) – Forcefield to use with this system creator.</li>
-<li><strong>fix_surrounding_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If False, the hydrogens of the surrounding
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_lookup</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>) – Forcefield to use with this system creator.</p></li>
+<li><p><strong>fix_surrounding_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If False, the hydrogens of the surrounding
residues can move to improve H-bond building
(True by default as it only has a minor
impact on the result and a big one on
-performance).</li>
-<li><strong>kill_electrostatics</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, all charges are removed from the system.
+performance).</p></li>
+<li><p><strong>kill_electrostatics</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, all charges are removed from the system.
This is good for H-bond building, but may be bad
-if residues in the surrounding are missing (gaps).</li>
-<li><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Defines cutoff to set for non bonded interactions.
+if residues in the surrounding are missing (gaps).</p></li>
+<li><p><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Defines cutoff to set for non bonded interactions.
Recommended values: 5 if kill_electrostatics = True,
-8 otherwise. Negative value means no cutoff.</li>
-<li><strong>inaccurate_pot_energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, we do not set correct non-bonded
+8 otherwise. Negative value means no cutoff.</p></li>
+<li><p><strong>inaccurate_pot_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, we do not set correct non-bonded
interactions between fixed atoms. This leads
to inaccurate pot. energies but it is faster and
has no effect on simulation runs (e.g. ApplySD)
-otherwise.</li>
+otherwise.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetDisulfidBridges">
-<code class="descname">GetDisulfidBridges</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Pairs of indices (i,j), where res_indices[i] and res_indices[j] are
+<code class="sig-name descname">GetDisulfidBridges</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Pairs of indices (i,j), where res_indices[i] and res_indices[j] are
assumed to have a disulfid bridge (CYS-SG pairs within 2.5 A).</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</li>
-<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</p></li>
+<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.SetupSystem">
-<code class="descname">SetupSystem</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em>, <em>loop_length</em>, <em>is_n_ter</em>, <em>is_c_ter</em>, <em>disulfid_bridges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetupSystem" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetupSystem</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em>, <em class="sig-param">loop_length</em>, <em class="sig-param">is_n_ter</em>, <em class="sig-param">is_c_ter</em>, <em class="sig-param">disulfid_bridges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetupSystem" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">SetupSystem</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em>, <em>loop_start_indices</em>, <em>loop_lengths</em>, <em>is_n_ter</em>, <em>is_c_ter</em>, <em>disulfid_bridges</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">SetupSystem</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em>, <em class="sig-param">loop_start_indices</em>, <em class="sig-param">loop_lengths</em>, <em class="sig-param">is_n_ter</em>, <em class="sig-param">is_c_ter</em>, <em class="sig-param">disulfid_bridges</em><span class="sig-paren">)</span></dt>
<dd><p>Setup a new system for the loop / surrounding defined by <em>all_pos</em> and
<em>res_indices</em>. Positions are taken from <em>all_pos[res_indices[i]]</em> and each
of them must have all heavy atoms defined. Residue <em>all_pos[i]</em> is assumed
@@ -186,248 +164,217 @@ residues. Overlapping loops are merged and 0-length loops are removed.</p>
<p>If <em>loop_length</em> is given, a single loop with start index 0 and the given
loop length is defined.</p>
<p>If a system was setup previously, it is overwritten completely.</p>
-<p>If possible, this uses the “CPU” platform in OpenMM using the env. variable
-<code class="docutils literal"><span class="pre">PM3_OPENMM_CPU_THREADS</span></code> to define the number of desired threads (1 thread
+<p>If possible, this uses the “CPU” platform in OpenMM using the env. variable
+<code class="docutils literal notranslate"><span class="pre">PM3_OPENMM_CPU_THREADS</span></code> to define the number of desired threads (1 thread
is used if variable is undefined).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</li>
-<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</li>
-<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of single loop (incl. stems).</li>
-<li><strong>loop_start_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start indices of loops.</li>
-<li><strong>loop_lengths</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Lengths of loops (incl. stems).</li>
-<li><strong>is_n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_n_ter[i]</em> defines whether
-that residue is N-terminal.</li>
-<li><strong>is_c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_c_ter[i]</em> defines whether
-that residue is C-terminal.</li>
-<li><strong>disulfid_bridges</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> with two
-<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Pairs of indices (i,j), where res_indices[i] and
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</p></li>
+<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</p></li>
+<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of single loop (incl. stems).</p></li>
+<li><p><strong>loop_start_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start indices of loops.</p></li>
+<li><p><strong>loop_lengths</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Lengths of loops (incl. stems).</p></li>
+<li><p><strong>is_n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_n_ter[i]</em> defines whether
+that residue is N-terminal.</p></li>
+<li><p><strong>is_c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_c_ter[i]</em> defines whether
+that residue is C-terminal.</p></li>
+<li><p><strong>disulfid_bridges</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two
+<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Pairs of indices (i,j), where res_indices[i] and
res_indices[j] form a disulfid bridge (see
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="promod3.loop.MmSystemCreator.GetDisulfidBridges"><code class="xref py py-meth docutils literal"><span class="pre">GetDisulfidBridges()</span></code></a>)</li>
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="promod3.loop.MmSystemCreator.GetDisulfidBridges"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDisulfidBridges()</span></code></a>)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if loops out of bounds with respect
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if loops out of bounds with respect
to <em>res_indices</em>, <em>loop_start_indices</em> / <em>loop_lengths</em> or
<em>res_indices</em> / <em>is_n_ter</em> / <em>is_c_ter</em> have inconsistent lengths,
or if any <em>all_pos[res_indices[i]]</em> is invalid or has unset heavy
atoms.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.UpdatePositions">
-<code class="descname">UpdatePositions</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.UpdatePositions" title="Permalink to this definition">¶</a></dt>
-<dd><p>Updates the positions in the system. Even though <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a> is
+<code class="sig-name descname">UpdatePositions</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.UpdatePositions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Updates the positions in the system. Even though <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> is
already very fast, this can speed up resetting a simulation. The data must
-be consistent with the data used in the last <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a> call.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</li>
-<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</li>
+be consistent with the data used in the last <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</p></li>
+<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a> call (same number of residues, same AA).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call (same number of residues, same AA).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.ExtractLoopPositions">
-<code class="descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em>loop_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.ExtractLoopPositions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em class="sig-param">loop_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.ExtractLoopPositions" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em>out_pos</em>, <em>res_indices</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em class="sig-param">out_pos</em>, <em class="sig-param">res_indices</em><span class="sig-paren">)</span></dt>
<dd><p>Extracts loop positions from the current simulation. If the simulation was
-run (via <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetSimulation" title="promod3.loop.MmSystemCreator.GetSimulation"><code class="xref py py-meth docutils literal"><span class="pre">GetSimulation()</span></code></a>), we internally have new positions for the
+run (via <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetSimulation" title="promod3.loop.MmSystemCreator.GetSimulation"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetSimulation()</span></code></a>), we internally have new positions for the
residues corresponding to <em>all_pos[res_indices[i]]</em> passed in
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>. This function then extracts these positions back into a
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. This function then extracts these positions back into a
compatible output storage.</p>
<p>If <em>loop_pos</em> is passed, only the loops are stored. The loop residues are
stored contiguously and the loops are stored in the order given by
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="promod3.loop.MmSystemCreator.GetLoopStartIndices"><code class="xref py py-meth docutils literal"><span class="pre">GetLoopStartIndices()</span></code></a> / <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="promod3.loop.MmSystemCreator.GetLoopLengths"><code class="xref py py-meth docutils literal"><span class="pre">GetLoopLengths()</span></code></a>. The <em>loop_pos</em> storage
-must have at least <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetNumLoopResidues" title="promod3.loop.MmSystemCreator.GetNumLoopResidues"><code class="xref py py-meth docutils literal"><span class="pre">GetNumLoopResidues()</span></code></a> residues and must have
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="promod3.loop.MmSystemCreator.GetLoopStartIndices"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLoopStartIndices()</span></code></a> / <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="promod3.loop.MmSystemCreator.GetLoopLengths"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLoopLengths()</span></code></a>. The <em>loop_pos</em> storage
+must have at least <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetNumLoopResidues" title="promod3.loop.MmSystemCreator.GetNumLoopResidues"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumLoopResidues()</span></code></a> residues and must have
matching amino acid types with respect to the loop residues passed as
-<em>all_pos</em> of <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>.</p>
+<em>all_pos</em> of <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>.</p>
<p>If <em>out_pos</em> and <em>res_indices</em> are passed, residues must have matching amino
acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]</em> of
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>. Only loop residues with <em>i</em> in the ranges defined by
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="promod3.loop.MmSystemCreator.GetLoopStartIndices"><code class="xref py py-meth docutils literal"><span class="pre">GetLoopStartIndices()</span></code></a> / <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="promod3.loop.MmSystemCreator.GetLoopLengths"><code class="xref py py-meth docutils literal"><span class="pre">GetLoopLengths()</span></code></a> are touched.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>loop_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Reduced storage only covering loop positions.</li>
-<li><strong>out_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Storage for loop positions linked to <em>res_indices</em>.</li>
-<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue indices into <em>out_pos</em>.</li>
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. Only loop residues with <em>i</em> in the ranges defined by
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="promod3.loop.MmSystemCreator.GetLoopStartIndices"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLoopStartIndices()</span></code></a> / <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="promod3.loop.MmSystemCreator.GetLoopLengths"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLoopLengths()</span></code></a> are touched.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>loop_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Reduced storage only covering loop positions.</p></li>
+<li><p><strong>out_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Storage for loop positions linked to <em>res_indices</em>.</p></li>
+<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>out_pos</em>.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a> call (big enough and matching AA).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call (big enough and matching AA).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetSimulation">
-<code class="descname">GetSimulation</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetSimulation" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>. Use this to run
-MM simulations.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSimulation</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetSimulation" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. Use this to run
+MM simulations.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetNumResidues">
-<code class="descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumResidues" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of residues of current simulation setup.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumResidues" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of residues of current simulation setup.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetNumLoopResidues">
-<code class="descname">GetNumLoopResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumLoopResidues" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of loop residues (incl. stems) of current simulation setup.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNumLoopResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumLoopResidues" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of loop residues (incl. stems) of current simulation setup.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetLoopStartIndices">
-<code class="descname">GetLoopStartIndices</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Start indices of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetLoopStartIndices</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Start indices of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetLoopLengths">
-<code class="descname">GetLoopLengths</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Lengths of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetLoopLengths</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Lengths of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetForcefieldAminoAcids">
-<code class="descname">GetForcefieldAminoAcids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetForcefieldAminoAcids" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Forcefield-specific amino acid type for each residue of last
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a> call.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetForcefieldAminoAcids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetForcefieldAminoAcids" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Forcefield-specific amino acid type for each residue of last
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetIndexing">
-<code class="descname">GetIndexing</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetIndexing" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetIndexing</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetIndexing" title="Permalink to this definition">¶</a></dt>
<dd><p>The atoms of residue <em>i</em> are stored from <em>idx[i]</em> to <em>idx[i+1]-1</em>, where
<em>idx</em> is the list returned by this function. The atoms themselves are
-ordered according to the indexing defined by <a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Indexing to positions vector used by the simulation object.
+ordered according to the indexing defined by <a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Indexing to positions vector used by the simulation object.
The last item of the list contains the number of atoms in the
-system.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+system.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetCpuPlatformSupport">
-<code class="descname">GetCpuPlatformSupport</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if we will use OpenMM’s “CPU” platform (enabled by default
-if platform is available). False, if we use “Reference” platform.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetCpuPlatformSupport</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if we will use OpenMM’s “CPU” platform (enabled by default
+if platform is available). False, if we use “Reference” platform.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.SetCpuPlatformSupport">
-<code class="descname">SetCpuPlatformSupport</code><span class="sig-paren">(</span><em>cpu_platform_support</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
-<dd><p>Override “CPU” platform support setting. Useful to force the use of the
-OpenMM’s “Reference” platform for testing (by default we use “CPU” if it is
+<code class="sig-name descname">SetCpuPlatformSupport</code><span class="sig-paren">(</span><em class="sig-param">cpu_platform_support</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
+<dd><p>Override “CPU” platform support setting. Useful to force the use of the
+OpenMM’s “Reference” platform for testing (by default we use “CPU” if it is
available).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cpu_platform_support</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True, if “CPU” platform desired (ignored if
-platform not available). False, if “Reference”
-platform desired.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>cpu_platform_support</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if “CPU” platform desired (ignored if
+platform not available). False, if “Reference”
+platform desired.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -435,483 +382,427 @@ platform desired.</td>
</div>
<div class="section" id="forcefield-lookup-for-amino-acids">
<h2>Forcefield lookup for amino acids<a class="headerlink" href="#forcefield-lookup-for-amino-acids" title="Permalink to this headline">¶</a></h2>
-<p>The <a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a> class and its helpers define a fast way to extract
+<p>The <a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a> class and its helpers define a fast way to extract
FF specific data for amino acids in a protein. We distinguish amino acid types
(and a few variants thereof) which may all be N- and/or C-terminal.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLookup">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
-<li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
-<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
-residue is terminal)</li>
-<li>extract masses, charges and LJ-parameters for each atom (list of length <em>N</em>)</li>
-<li>extract connectivities (<a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldConnectivity</span></code></a>), which include all
-possible bonds, angles, dihedrals, impropers and LJ pairs</li>
+<li><p>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
+<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
+residue is terminal)</p></li>
+<li><p>extract masses, charges and LJ-parameters for each atom (list of length <em>N</em>)</p></li>
+<li><p>extract connectivities (<a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a>), which include all
+possible bonds, angles, dihedrals, impropers and LJ pairs</p></li>
</ul>
<p>There is functionality to adapt the lookup and store it as needed or you can
-load a predefined one with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-meth docutils literal"><span class="pre">GetDefault()</span></code></a> or <a class="reference internal" href="#promod3.loop.ForcefieldLookup.LoadCHARMM" title="promod3.loop.ForcefieldLookup.LoadCHARMM"><code class="xref py py-meth docutils literal"><span class="pre">LoadCHARMM()</span></code></a>.</p>
-<p>The atom indexing and <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetAA" title="promod3.loop.ForcefieldLookup.GetAA"><code class="xref py py-meth docutils literal"><span class="pre">GetAA()</span></code></a> are independent of the loaded file.</p>
-<dl class="staticmethod">
+load a predefined one with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDefault()</span></code></a> or <a class="reference internal" href="#promod3.loop.ForcefieldLookup.LoadCHARMM" title="promod3.loop.ForcefieldLookup.LoadCHARMM"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadCHARMM()</span></code></a>.</p>
+<p>The atom indexing and <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetAA" title="promod3.loop.ForcefieldLookup.GetAA"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetAA()</span></code></a> are independent of the loaded file.</p>
+<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetDefault">
-<em class="property">static </em><code class="descname">GetDefault</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDefault" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A default singleton instance (shared throughout the Python process)
+<em class="property">static </em><code class="sig-name descname">GetDefault</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDefault" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>A default singleton instance (shared throughout the Python process)
of this class with all data defined. Using this instance has the
-advantage that the object is only loaded once!</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a></td>
-</tr>
-</tbody>
-</table>
+advantage that the object is only loaded once!</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetDefault">
-<em class="property">static </em><code class="descname">SetDefault</code><span class="sig-paren">(</span><em>new_default</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDefault" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets default singleton instance for all future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-meth docutils literal"><span class="pre">GetDefault()</span></code></a> calls.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>new_default</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>) – Lookup object to use as the new default.</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="staticmethod">
+<em class="property">static </em><code class="sig-name descname">SetDefault</code><span class="sig-paren">(</span><em class="sig-param">new_default</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDefault" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets default singleton instance for all future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDefault()</span></code></a> calls.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>new_default</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>) – Lookup object to use as the new default.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.LoadCHARMM">
-<em class="property">static </em><code class="descname">LoadCHARMM</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadCHARMM" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Predefined lookup object extracted from a CHARMM forcefield
-(loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="staticmethod">
+<em class="property">static </em><code class="sig-name descname">LoadCHARMM</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadCHARMM" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Predefined lookup object extracted from a CHARMM forcefield
+(loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.ForcefieldLookup.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.Save" title="promod3.loop.ForcefieldLookup.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.SavePortable" title="promod3.loop.ForcefieldLookup.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.Save" title="promod3.loop.ForcefieldLookup.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.SavePortable" title="promod3.loop.ForcefieldLookup.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded lookup object</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded lookup object</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.ForcefieldLookup.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetAA">
-<code class="descname">GetAA</code><span class="sig-paren">(</span><em>ff_aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetAA" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetAA" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Amino acid type for given <em>ff_aa</em></p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetNumAtoms">
-<code class="descname">GetNumAtoms</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Number of atoms for given input.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
-<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
+<code class="sig-name descname">GetNumAtoms</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of atoms for given input.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
+<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetHeavyIndex">
-<code class="descname">GetHeavyIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHeavyIndex" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetHeavyIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHeavyIndex" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetHeavyIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal index for given heavy atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>]</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index as returned by <a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetIndex" title="promod3.loop.AminoAcidLookup.GetIndex"><code class="xref py py-meth docutils literal"><span class="pre">AminoAcidLookup.GetIndex()</span></code></a></li>
-<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
+<code class="sig-name descname">GetHeavyIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Internal index for given heavy atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>]</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index as returned by <a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetIndex" title="promod3.loop.AminoAcidLookup.GetIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AminoAcidLookup.GetIndex()</span></code></a></p></li>
+<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetHydrogenIndex">
-<code class="descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal index for given hydrogen atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>]</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index as returned by
-<a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="promod3.loop.AminoAcidLookup.GetHydrogenIndex"><code class="xref py py-meth docutils literal"><span class="pre">AminoAcidLookup.GetHydrogenIndex()</span></code></a></li>
-<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
+<code class="sig-name descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Internal index for given hydrogen atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>]</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index as returned by
+<a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="promod3.loop.AminoAcidLookup.GetHydrogenIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AminoAcidLookup.GetHydrogenIndex()</span></code></a></p></li>
+<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetOXTIndex">
-<code class="descname">GetOXTIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetOXTIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal index of OXT atom for C-terminal residue</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
+<code class="sig-name descname">GetOXTIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetOXTIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Internal index of OXT atom for C-terminal residue</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetFudgeLJ">
-<code class="descname">GetFudgeLJ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeLJ" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetFudgeLJ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeLJ" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Dampening factor for LJ 1,4 interactions (see
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetFudgeQQ">
-<code class="descname">GetFudgeQQ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeQQ" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetFudgeQQ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeQQ" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Dampening factor for electrostatic 1,4 interactions (see
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetMasses">
-<code class="descname">GetMasses</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetMasses" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
-<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
+<code class="sig-name descname">GetMasses</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetMasses" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
+<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetCharges">
-<code class="descname">GetCharges</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetCharges" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
-<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
+<code class="sig-name descname">GetCharges</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetCharges" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
+<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetSigmas">
-<code class="descname">GetSigmas</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetSigmas" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
-<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
+<code class="sig-name descname">GetSigmas</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetSigmas" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Sigma in nm for each atom
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
+<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetEpsilons">
-<code class="descname">GetEpsilons</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetEpsilons" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
-<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
+<code class="sig-name descname">GetEpsilons</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetEpsilons" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Epsilon in kJ/mol for each atom
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
+<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetInternalConnectivity">
-<code class="descname">GetInternalConnectivity</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal connectivity of a residue</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldConnectivity</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
-<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
+<code class="sig-name descname">GetInternalConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Internal connectivity of a residue</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
+<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity">
-<code class="descname">GetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em>ff_aa_one</em>, <em>ff_aa_two</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">All connectivity which include peptide bond between two residues
-(additional to <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal"><span class="pre">GetInternalConnectivity()</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldConnectivity</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ff_aa_one</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of first residue</li>
-<li><strong>ff_aa_two</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of second residue</li>
-<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if first residue is N-terminal</li>
-<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True if second residue is C-terminal</li>
+<code class="sig-name descname">GetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa_one</em>, <em class="sig-param">ff_aa_two</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>All connectivity which include peptide bond between two residues
+(additional to <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetInternalConnectivity()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ff_aa_one</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of first residue</p></li>
+<li><p><strong>ff_aa_two</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of second residue</p></li>
+<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if first residue is N-terminal</p></li>
+<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if second residue is C-terminal</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetDisulfidConnectivity">
-<code class="descname">GetDisulfidConnectivity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All connectivity which include disulfid bridge between two cysteins
-(additional to <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal"><span class="pre">GetInternalConnectivity()</span></code></a>)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldConnectivity</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetDisulfidConnectivity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>All connectivity which include disulfid bridge between two cysteins
+(additional to <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetInternalConnectivity()</span></code></a>)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetFudgeLJ">
-<code class="descname">SetFudgeLJ</code><span class="sig-paren">(</span><em>fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeLJ" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetFudgeLJ" title="promod3.loop.ForcefieldLookup.GetFudgeLJ"><code class="xref py py-meth docutils literal"><span class="pre">GetFudgeLJ()</span></code></a> calls to <em>fudge</em>.</p>
+<code class="sig-name descname">SetFudgeLJ</code><span class="sig-paren">(</span><em class="sig-param">fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeLJ" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetFudgeLJ" title="promod3.loop.ForcefieldLookup.GetFudgeLJ"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetFudgeLJ()</span></code></a> calls to <em>fudge</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetFudgeQQ">
-<code class="descname">SetFudgeQQ</code><span class="sig-paren">(</span><em>fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeQQ" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetFudgeQQ" title="promod3.loop.ForcefieldLookup.GetFudgeQQ"><code class="xref py py-meth docutils literal"><span class="pre">GetFudgeQQ()</span></code></a> calls to <em>fudge</em>.</p>
+<code class="sig-name descname">SetFudgeQQ</code><span class="sig-paren">(</span><em class="sig-param">fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeQQ" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetFudgeQQ" title="promod3.loop.ForcefieldLookup.GetFudgeQQ"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetFudgeQQ()</span></code></a> calls to <em>fudge</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetMasses">
-<code class="descname">SetMasses</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>masses</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetMasses" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetMasses" title="promod3.loop.ForcefieldLookup.GetMasses"><code class="xref py py-meth docutils literal"><span class="pre">GetMasses()</span></code></a> calls to <em>masses</em>.</p>
+<code class="sig-name descname">SetMasses</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">masses</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetMasses" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetMasses" title="promod3.loop.ForcefieldLookup.GetMasses"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetMasses()</span></code></a> calls to <em>masses</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetCharges">
-<code class="descname">SetCharges</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>charges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetCharges" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetCharges" title="promod3.loop.ForcefieldLookup.GetCharges"><code class="xref py py-meth docutils literal"><span class="pre">GetCharges()</span></code></a> calls to <em>charges</em>.</p>
+<code class="sig-name descname">SetCharges</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">charges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetCharges" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetCharges" title="promod3.loop.ForcefieldLookup.GetCharges"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetCharges()</span></code></a> calls to <em>charges</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetSigmas">
-<code class="descname">SetSigmas</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>sigmas</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetSigmas" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetSigmas" title="promod3.loop.ForcefieldLookup.GetSigmas"><code class="xref py py-meth docutils literal"><span class="pre">GetSigmas()</span></code></a> calls to <em>sigmas</em>.</p>
+<code class="sig-name descname">SetSigmas</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">sigmas</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetSigmas" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetSigmas" title="promod3.loop.ForcefieldLookup.GetSigmas"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetSigmas()</span></code></a> calls to <em>sigmas</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetEpsilons">
-<code class="descname">SetEpsilons</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>epsilons</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetEpsilons" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetEpsilons" title="promod3.loop.ForcefieldLookup.GetEpsilons"><code class="xref py py-meth docutils literal"><span class="pre">GetEpsilons()</span></code></a> calls to <em>epsilons</em>.</p>
+<code class="sig-name descname">SetEpsilons</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">epsilons</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetEpsilons" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetEpsilons" title="promod3.loop.ForcefieldLookup.GetEpsilons"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetEpsilons()</span></code></a> calls to <em>epsilons</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetInternalConnectivity">
-<code class="descname">SetInternalConnectivity</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal"><span class="pre">GetInternalConnectivity()</span></code></a> calls to
+<code class="sig-name descname">SetInternalConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetInternalConnectivity()</span></code></a> calls to
<em>connectivity</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity">
-<code class="descname">SetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em>ff_aa_one</em>, <em>ff_aa_two</em>, <em>is_nter</em>, <em>is_cter</em>, <em>connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity" title="promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity"><code class="xref py py-meth docutils literal"><span class="pre">GetPeptideBoundConnectivity()</span></code></a> calls to
+<code class="sig-name descname">SetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa_one</em>, <em class="sig-param">ff_aa_two</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity" title="promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetPeptideBoundConnectivity()</span></code></a> calls to
<em>connectivity</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetDisulfidConnectivity">
-<code class="descname">SetDisulfidConnectivity</code><span class="sig-paren">(</span><em>connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity" title="promod3.loop.ForcefieldLookup.GetDisulfidConnectivity"><code class="xref py py-meth docutils literal"><span class="pre">GetDisulfidConnectivity()</span></code></a> calls to
+<code class="sig-name descname">SetDisulfidConnectivity</code><span class="sig-paren">(</span><em class="sig-param">connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity" title="promod3.loop.ForcefieldLookup.GetDisulfidConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDisulfidConnectivity()</span></code></a> calls to
<em>connectivity</em>.</p>
</dd></dl>
@@ -919,629 +810,510 @@ for details.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldAminoAcid">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
(<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
types. The full list of values is:</p>
<blockquote>
-<div><em>FF_ALA</em>, <em>FF_ARG</em>, <em>FF_ASN</em>, <em>FF_ASP</em>, <em>FF_GLN</em>, <em>FF_GLU</em>, <em>FF_LYS</em>,
+<div><p><em>FF_ALA</em>, <em>FF_ARG</em>, <em>FF_ASN</em>, <em>FF_ASP</em>, <em>FF_GLN</em>, <em>FF_GLU</em>, <em>FF_LYS</em>,
<em>FF_SER</em>, <em>FF_CYS</em>, <em>FF_MET</em>, <em>FF_TRP</em>, <em>FF_TYR</em>, <em>FF_THR</em>, <em>FF_VAL</em>,
<em>FF_ILE</em>, <em>FF_LEU</em>, <em>FF_GLY</em>, <em>FF_PRO</em> <em>FF_HISE</em>, <em>FF_PHE</em>, <em>FF_CYS2</em>,
-<em>FF_HISD</em>, <em>FF_XXX</em></div></blockquote>
+<em>FF_HISD</em>, <em>FF_XXX</em></p>
+</div></blockquote>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldConnectivity">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldConnectivity</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldConnectivity</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity" title="Permalink to this definition">¶</a></dt>
<dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
are the combination of all bonds and 1,3 pairs of angles and are not stored
-separately). Each type of connectivity has it’s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+separately). Each type of connectivity has it’s own class (see below) storing
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
-= <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
+= <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the
second one are in [<em>N1, N1+N2-1</em>], where <em>N1</em> and <em>N2</em> are the number of atoms
of the two residues. For disulfid bridges, <em>N1</em> = <em>N2</em> = <em>GetNumAtoms(FF_CYS2,
False, False)</em>.</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.harmonic_bonds">
-<code class="descname">harmonic_bonds</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_bonds" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">harmonic_bonds</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_bonds" title="Permalink to this definition">¶</a></dt>
<dd><p>List of harmonic bonds.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldBondInfo" title="promod3.loop.ForcefieldBondInfo"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldBondInfo</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldBondInfo" title="promod3.loop.ForcefieldBondInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldBondInfo</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.harmonic_angles">
-<code class="descname">harmonic_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_angles" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">harmonic_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_angles" title="Permalink to this definition">¶</a></dt>
<dd><p>List of harmonic angles.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="promod3.loop.ForcefieldHarmonicAngleInfo"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldHarmonicAngleInfo</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="promod3.loop.ForcefieldHarmonicAngleInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldHarmonicAngleInfo</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.urey_bradley_angles">
-<code class="descname">urey_bradley_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.urey_bradley_angles" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">urey_bradley_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.urey_bradley_angles" title="Permalink to this definition">¶</a></dt>
<dd><p>List of Urey-Bradley angles.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="promod3.loop.ForcefieldUreyBradleyAngleInfo"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldUreyBradleyAngleInfo</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="promod3.loop.ForcefieldUreyBradleyAngleInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldUreyBradleyAngleInfo</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.periodic_dihedrals">
-<code class="descname">periodic_dihedrals</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_dihedrals" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">periodic_dihedrals</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_dihedrals" title="Permalink to this definition">¶</a></dt>
<dd><p>List of periodic dihedrals.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.periodic_impropers">
-<code class="descname">periodic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_impropers" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">periodic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_impropers" title="Permalink to this definition">¶</a></dt>
<dd><p>List of periodic impropers.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.harmonic_impropers">
-<code class="descname">harmonic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_impropers" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">harmonic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_impropers" title="Permalink to this definition">¶</a></dt>
<dd><p>List of harmonic impropers.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="promod3.loop.ForcefieldHarmonicImproperInfo"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldHarmonicImproperInfo</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="promod3.loop.ForcefieldHarmonicImproperInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldHarmonicImproperInfo</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.lj_pairs">
-<code class="descname">lj_pairs</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.lj_pairs" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">lj_pairs</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.lj_pairs" title="Permalink to this definition">¶</a></dt>
<dd><p>List of LJ pairs.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldLJPairInfo" title="promod3.loop.ForcefieldLJPairInfo"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLJPairInfo</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldLJPairInfo" title="promod3.loop.ForcefieldLJPairInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLJPairInfo</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
-<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_two">
-<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.bond_length">
-<code class="descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.bond_length" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.bond_length" title="Permalink to this definition">¶</a></dt>
<dd><p>Bond length in nm</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.force_constant">
-<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant in kJ/mol/nm^2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
-<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_two">
-<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_three">
-<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.angle">
-<code class="descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle in radians</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.force_constant">
-<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant in kJ/mol/radian^2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
-<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two">
-<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three">
-<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.angle">
-<code class="descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle in radians</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant">
-<code class="descname">angle_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle force constant kJ/mol/radian^2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length">
-<code class="descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length" title="Permalink to this definition">¶</a></dt>
<dd><p>Bond length in nm</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant">
-<code class="descname">bond_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">bond_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Bond force constant kJ/mol/nm^2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
-<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_two">
-<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_three">
-<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_four">
-<code class="descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_four" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_four" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 4</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity">
-<code class="descname">multiplicity</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">multiplicity</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Multiplicity</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.phase">
-<code class="descname">phase</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.phase" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">phase</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.phase" title="Permalink to this definition">¶</a></dt>
<dd><p>Phase in radians</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant">
-<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant in kJ/mol/radian^2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
-<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_two">
-<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_three">
-<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_four">
-<code class="descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_four" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_four" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 4</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.angle">
-<code class="descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.angle" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.angle" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle in radians</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.force_constant">
-<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant kJ/mol/radian^2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
-<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_two">
-<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.sigma">
-<code class="descname">sigma</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.sigma" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">sigma</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.sigma" title="Permalink to this definition">¶</a></dt>
<dd><p>Sigma in nm</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.epsilon">
-<code class="descname">epsilon</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.epsilon" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">epsilon</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.epsilon" title="Permalink to this definition">¶</a></dt>
<dd><p>Epsilon in kJ/mol</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -1556,20 +1328,45 @@ False, False)</em>.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Generate <code class="docutils literal"><span class="pre">ost.mol.mm</span></code> systems</a><ul>
-<li><a class="reference internal" href="#create-mm-systems-for-loops">Create MM systems for loops</a></li>
-<li><a class="reference internal" href="#forcefield-lookup-for-amino-acids">Forcefield lookup for amino acids</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="all_atom.html" title="previous chapter">Handling All Atom Positions</a></li>
<li>Next: <a href="load_loop_objects.html" title="next chapter">Loading Precomputed Objects</a></li>
</ul></li>
@@ -1577,23 +1374,24 @@ False, False)</em>.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/loop/mm_system_creation.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1602,11 +1400,11 @@ False, False)</em>.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/loop/mm_system_creation.txt"
+ <a href="../_sources/loop/mm_system_creation.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 5eebf7852d21dc65b572a917e016ba590eb13bc7..0d038160140c4e48f9c6fcbfab2bd0860137d21e 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Structural Data — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Structural Data — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
<link rel="prev" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -49,21 +35,21 @@
<div class="section" id="structural-data">
<h1>Structural Data<a class="headerlink" href="#structural-data" title="Permalink to this headline">¶</a></h1>
-<p>The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> serves as a container for structural backbone and
+<p>The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> serves as a container for structural backbone and
sequence data. Custom accessor objects can be implemented that relate
arbitrary features to structural data. Examples provided by ProMod3 include
-accession using matching stem geometry (see: <a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) or sequence
-features (see: <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a>).
+accession using matching stem geometry (see: <a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) or sequence
+features (see: <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a>).
Besides backbone and sequence data, derived features can
optionally be stored. E.g. sequence profiles or secondary structure information.
Optional data includes:</p>
<blockquote>
<div><ul class="simple">
-<li>The phi/psi dihedral angles</li>
-<li>The secondary structure state as defined by dssp</li>
-<li>The solvent accessibility in square Angstrom</li>
-<li>The amino acid frequencies as given by an input sequence profile</li>
-<li>The residue depth - The residue depth is defined as the minimum distance of
+<li><p>The phi/psi dihedral angles</p></li>
+<li><p>The secondary structure state as defined by dssp</p></li>
+<li><p>The solvent accessibility in square Angstrom</p></li>
+<li><p>The amino acid frequencies as given by an input sequence profile</p></li>
+<li><p>The residue depth - The residue depth is defined as the minimum distance of
a residue towards any of the exposed residues.
Distances are calculated using CB positions (artificially constructed in case
of glycine) and exposed is defined as:
@@ -72,105 +58,101 @@ to the OUTER surface. To determine whether an atom is part of that outer
surface, the full structure is placed into a 3D grid and a flood fill
algorithm is used to determine the atoms of interest.
Internal cavities are excluded by using this approach. This is a simplified
-version of the residue depth as discussed in <a class="reference internal" href="../references.html#chakravarty1999" id="id1">[chakravarty1999]</a> and gets
-directly calculated when structural information is added to the StructureDB.</li>
-<li>The amino acid frequency derived from structural alignments as described
-in <a class="reference internal" href="../references.html#zhou2005" id="id2">[zhou2005]</a> - Since the calculation of such a profile already requires a
-StructureDB, we end up in a hen and egg problem here... When adding
+version of the residue depth as discussed in <a class="reference internal" href="../references.html#chakravarty1999" id="id1"><span>[chakravarty1999]</span></a> and gets
+directly calculated when structural information is added to the StructureDB.</p></li>
+<li><p>The amino acid frequency derived from structural alignments as described
+in <a class="reference internal" href="../references.html#zhou2005" id="id2"><span>[zhou2005]</span></a> - Since the calculation of such a profile already requires a
+StructureDB, we end up in a hen and egg problem here… When adding
structural information to the StructureDB, the according memory gets
just allocated and set to zero. The usage of this information
is therefore only meaningful if you calculate these profiles
-and manually set them (or load the provided default database).</li>
+and manually set them (or load the provided default database).</p></li>
</ul>
</div></blockquote>
<div class="section" id="defining-chains-and-fragments">
<h2>Defining Chains and Fragments<a class="headerlink" href="#defining-chains-and-fragments" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.CoordInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">CoordInfo</code><a class="headerlink" href="#promod3.loop.CoordInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">CoordInfo</code><a class="headerlink" href="#promod3.loop.CoordInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>The CoordInfo gets automatically generated when new chains are added to
-a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>. It contains internal information of how a
+a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>. It contains internal information of how a
connected stretch of residues is stored in the database.</p>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.id">
-<code class="descname">id</code><a class="headerlink" href="#promod3.loop.CoordInfo.id" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">id</code><a class="headerlink" href="#promod3.loop.CoordInfo.id" title="Permalink to this definition">¶</a></dt>
<dd><p>An id string specified when adding the corresponding stretch to the
structure db</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.chain_name">
-<code class="descname">chain_name</code><a class="headerlink" href="#promod3.loop.CoordInfo.chain_name" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">chain_name</code><a class="headerlink" href="#promod3.loop.CoordInfo.chain_name" title="Permalink to this definition">¶</a></dt>
<dd><p>A chain name string specified when adding the corresponding stretch to the
structure db</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.offset">
-<code class="descname">offset</code><a class="headerlink" href="#promod3.loop.CoordInfo.offset" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">offset</code><a class="headerlink" href="#promod3.loop.CoordInfo.offset" title="Permalink to this definition">¶</a></dt>
<dd><p>All residues of the added stretch are stored in a linear memory layout.
The offset parameter tells us where it exactly starts in the global data
-structure. (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+structure. (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.size">
-<code class="descname">size</code><a class="headerlink" href="#promod3.loop.CoordInfo.size" title="Permalink to this definition">¶</a></dt>
-<dd><p>The number of residues in that stretch (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<code class="sig-name descname">size</code><a class="headerlink" href="#promod3.loop.CoordInfo.size" title="Permalink to this definition">¶</a></dt>
+<dd><p>The number of residues in that stretch (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.start_resnum">
-<code class="descname">start_resnum</code><a class="headerlink" href="#promod3.loop.CoordInfo.start_resnum" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">start_resnum</code><a class="headerlink" href="#promod3.loop.CoordInfo.start_resnum" title="Permalink to this definition">¶</a></dt>
<dd><p>Residue number of first residue in the added stretch. The residue number
is relative to the SEQRES provided in the input profile when adding the
-stuff to the structure db. (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+stuff to the structure db. (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.shift">
-<code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>Translation from original coordinates that has been applied before storing
-structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.FragmentInfo">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragmentInfo</code><span class="sig-paren">(</span><em>chain_index</em>, <em>offset</em>, <em>length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>The FragmentInfo defines any fragment in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>. If you
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">FragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">chain_index</em>, <em class="sig-param">offset</em>, <em class="sig-param">length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentInfo" title="Permalink to this definition">¶</a></dt>
+<dd><p>The FragmentInfo defines any fragment in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>. If you
implement your own accessor object, thats the information you want to store.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>chain_index</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.chain_index" title="promod3.loop.FragmentInfo.chain_index"><code class="xref py py-attr docutils literal"><span class="pre">chain_index</span></code></a></li>
-<li><strong>offset</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.offset" title="promod3.loop.FragmentInfo.offset"><code class="xref py py-attr docutils literal"><span class="pre">offset</span></code></a></li>
-<li><strong>length</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.length" title="promod3.loop.FragmentInfo.length"><code class="xref py py-attr docutils literal"><span class="pre">length</span></code></a></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>chain_index</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.chain_index" title="promod3.loop.FragmentInfo.chain_index"><code class="xref py py-attr docutils literal notranslate"><span class="pre">chain_index</span></code></a></p></li>
+<li><p><strong>offset</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.offset" title="promod3.loop.FragmentInfo.offset"><code class="xref py py-attr docutils literal notranslate"><span class="pre">offset</span></code></a></p></li>
+<li><p><strong>length</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.length" title="promod3.loop.FragmentInfo.length"><code class="xref py py-attr docutils literal notranslate"><span class="pre">length</span></code></a></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.chain_index">
-<code class="descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
-<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a>) in the
-<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> this particle belongs to. (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<code class="sig-name descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
+<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a>) in the
+<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> this particle belongs to. (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.offset">
-<code class="descname">offset</code><a class="headerlink" href="#promod3.loop.FragmentInfo.offset" title="Permalink to this definition">¶</a></dt>
-<dd><p>Index of residue in <strong>chain</strong> the fragment starts. (0-based, <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<code class="sig-name descname">offset</code><a class="headerlink" href="#promod3.loop.FragmentInfo.offset" title="Permalink to this definition">¶</a></dt>
+<dd><p>Index of residue in <strong>chain</strong> the fragment starts. (0-based, <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.length">
-<code class="descname">length</code><a class="headerlink" href="#promod3.loop.FragmentInfo.length" title="Permalink to this definition">¶</a></dt>
-<dd><p>Length of the fragment (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<code class="sig-name descname">length</code><a class="headerlink" href="#promod3.loop.FragmentInfo.length" title="Permalink to this definition">¶</a></dt>
+<dd><p>Length of the fragment (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -180,8 +162,8 @@ implement your own accessor object, thats the information you want to store.</p>
<h2>The Structure Database<a class="headerlink" href="#the-structure-database" title="Permalink to this headline">¶</a></h2>
<p>The following code example demonstrates how to create a structural database
and fill it with content.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="c1"># StructureDB where all data get extracted</span>
@@ -271,110 +253,104 @@ and fill it with content.</p>
the size of the database used as source. If you want to do this for a larger
database, you might want to consider two things:</p>
<ol class="arabic simple">
-<li>Use a database of limited size to generate the actual profiles (something
-in between 5000 and 10000 nonredundant chains is enough)</li>
-<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
-running in parallel</li>
+<li><p>Use a database of limited size to generate the actual profiles (something
+in between 5000 and 10000 nonredundant chains is enough)</p></li>
+<li><p>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+running in parallel</p></li>
</ol>
<dl class="class">
<dt id="promod3.loop.StructureDBDataType">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDBDataType</code><a class="headerlink" href="#promod3.loop.StructureDBDataType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">StructureDBDataType</code><a class="headerlink" href="#promod3.loop.StructureDBDataType" title="Permalink to this definition">¶</a></dt>
<dd><p>The StructureDBDataType enum has to be passed at initialization of a
StructureDB in order to define what data you want to store additionally
to backbone coordinates and sequence.
For the bare minimum (only backbone coordinates and sequence), use Minimal.
If you want to store all data possible, use All. If you only want a subset,
you can combine some of the datatypes with a bitwise or operation
-(see example script for <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>). One important note:
+(see example script for <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>). One important note:
If you enable AAFrequenciesStruct, the actual information is not automatically
assigned. Only the according memory is allocated and set to zero, the actual
-information must be assigned manually (see example script again...).</p>
+information must be assigned manually (see example script again…).</p>
<p>Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP,
AAFrequencies, AAFrequenciesStruct</p>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.StructureDB">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDB</code><span class="sig-paren">(</span><em>data_to_store</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Generates an empty <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> that can be filled with content
-through <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
-<em>data_to_store</em>. Have a look at the <a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>
-documentation and at the example script...</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data_to_store</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>) – Specifies what data to store in the database, several
-flags can be combined with a bitwise or operator.</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">StructureDB</code><span class="sig-paren">(</span><em class="sig-param">data_to_store</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generates an empty <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> that can be filled with content
+through <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
+<em>data_to_store</em>. Have a look at the <a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>
+documentation and at the example script…</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>data_to_store</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>) – Specifies what data to store in the database, several
+flags can be combined with a bitwise or operator.</p>
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.loop.StructureDB.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.StructureDB.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.StructureDB.Save" title="promod3.loop.StructureDB.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.loop.StructureDB.SavePortable" title="promod3.loop.StructureDB.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.StructureDB.Save" title="promod3.loop.StructureDB.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.loop.StructureDB.SavePortable" title="promod3.loop.StructureDB.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded data base</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded data base</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.StructureDB.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where the database will be saved</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where the database will be saved</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.HasData">
-<code class="descname">HasData</code><span class="sig-paren">(</span><em>data_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.HasData" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">HasData</code><span class="sig-paren">(</span><em class="sig-param">data_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.HasData" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks, whether requested data type is available in the current database.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data_type</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>) – Data type to check</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether the requested datatype is available</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>data_type</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>) – Data type to check</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether the requested datatype is available</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.AddCoordinates">
-<code class="descname">AddCoordinates</code><span class="sig-paren">(</span><em>id</em>, <em>chain_name</em>, <em>ent</em>, <em>seqres</em>, <em>prof=None</em>, <em>only_longest_stretch=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.AddCoordinates" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddCoordinates</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">chain_name</em>, <em class="sig-param">ent</em>, <em class="sig-param">seqres</em>, <em class="sig-param">prof=None</em>, <em class="sig-param">only_longest_stretch=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.AddCoordinates" title="Permalink to this definition">¶</a></dt>
<dd><p>This method takes an entity and adds coordinates and the sequence
of one of its chains to the structural database. Additionally, all
data as specified at the initialization of the database is extracted
@@ -386,11 +362,11 @@ All residues in chain with name <em>chain_name</em> must have residue numbers
that directly relate them to the <em>seqres</em> with an indexing scheme
starting from one.
If this is not the case, an error gets thrown. You might want to
-consider to use <code class="xref py py-meth docutils literal"><span class="pre">ost.seq.Renumber()</span></code> for proper numbering.
+consider to use <code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.Renumber()</span></code> for proper numbering.
Based on consecutive numbering and additionally checking for valid
peptide bonds, connected stretches are identified
and every added connected stretch gets its own entry with
-<a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a> as a descriptor.
+<a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a> as a descriptor.
To avoid cluttering the database with many small fragments, the flag:
<em>only_longest_stretch</em> can be used. Set it to False if all
connected stretches of chain with name <em>chain_name</em> should be added.
@@ -400,482 +376,429 @@ z - direction for every connected stretch is limited to 655A. This should
be sufficient for most structures, but stretches exceeding this maximum
are discarded. For storing the structural data given these restraints,
a translation is applied that gets stored as the <em>shift</em> attribute
-in the according <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a> object.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</li>
-<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
-as specified by <em>chain_name</em>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
-<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li>
-<li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
+in the according <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a> object.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</p></li>
+<li><p><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</p></li>
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
+as specified by <em>chain_name</em>.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</p></li>
+<li><p><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
connected stretch of residues are all connected
-stretches of residues</li>
+stretches of residues</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">indices of added stretches in db</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <cite>int</cite></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if the residues in chain with
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>indices of added stretches in db</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <cite>int</cite></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the residues in chain with
name <em>chain_name</em> do not match <em>seqres</em> given the
residue numbers, when AAFrequencies have to to be extracted and
the sequence in <em>prof</em> does not match the <em>seqres</em> or <em>prof</em> is
invalid.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.RemoveCoordinates">
-<code class="descname">RemoveCoordinates</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.RemoveCoordinates" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">RemoveCoordinates</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.RemoveCoordinates" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes coordinates at specified location and all its associated data. This
-has an impact on the offset values of all <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a> objects
+has an impact on the offset values of all <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a> objects
that are internally stored afterwards and on the actual coord indices
(all shifted by one). So make sure that you adapt your data access
accordingly!</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies coordinates to be removed</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> is invalid</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Specifies coordinates to be removed</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetCoordIdx">
-<code class="descname">GetCoordIdx</code><span class="sig-paren">(</span><em>id</em>, <em>chain_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordIdx" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])
+<code class="sig-name descname">GetCoordIdx</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">chain_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordIdx" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])
of all coords (connected stretches) with matching
<em>id</em> / <em>chain_name</em>.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>id</strong> – Identifier given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal"><span class="pre">AddCoordinates()</span></code></a></li>
-<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of chain given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal"><span class="pre">AddCoordinates()</span></code></a></li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id</strong> – Identifier given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a></p></li>
+<li><p><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of chain given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetCoordInfo">
-<code class="descname">GetCoordInfo</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordInfo" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Object describing the stretch of connected residues with
-index <em>idx</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetCoordInfo</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordInfo" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Object describing the stretch of connected residues with
+index <em>idx</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetNumCoords">
-<code class="descname">GetNumCoords</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetNumCoords" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of connected stretches of residues that have been added to
-the database.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNumCoords</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetNumCoords" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of connected stretches of residues that have been added to
+the database.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.PrintStatistics">
-<code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
<dd><p>Prints out some information about the db.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetBackboneList">
-<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>fragment</em>, <em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetBackboneList" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">fragment</em>, <em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetBackboneList" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>fragment</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">fragment</em>, <em class="sig-param">sequence=""</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em>, <em class="sig-param">sequence=""</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Backbone list with positions extracted from <em>fragment</em> or
+<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">coord_idx</em>, <em class="sig-param">sequence=""</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Backbone list with positions extracted from <em>fragment</em> or
full entry at <em>coord_idx</em></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract positions.</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract positions.</li>
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract positions.</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract positions.</p></li>
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
set, the original sequence at specified location in the
-database is used.</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
-superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
-superposed onto.</li>
+database is used.</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+superposed onto.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+superposed onto.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if the length of <em>sequence</em> does
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the length of <em>sequence</em> does
not match with the desired backbone list, if <em>sequence</em> contains
a character which does not belong to the 20 proteinogenic amino
acids or if <em>fragment</em> or <em>coord_idx</em> is invalid. Fragment can
be invalid when it does not fully fit into one of the connected
stretches of residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequence">
-<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequence" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequence" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence of <em>fragment</em> or full entry at <em>coord_idx</em></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence.</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence</li>
+<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The sequence of <em>fragment</em> or full entry at <em>coord_idx</em></p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence.</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if fragment or coord_idx is
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if fragment or coord_idx is
invalid. Fragment can be invalid when it does not fully fit into
one of the connected stretches of residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDSSPStates">
-<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDSSPStates" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetDSSPStates</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDSSPStates" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The dssp states of <em>fragment</em> or full entry at <em>coord_idx</em></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the states.</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dssp states</li>
+<code class="sig-name descname">GetDSSPStates</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The dssp states of <em>fragment</em> or full entry at <em>coord_idx</em></p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the states.</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dssp states</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if database does not contain dssp
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain dssp
data or if fragment/ coord_idx is invalid. Fragment can be invalid
when it does not fully fit into one of the connected stretches of
residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDihedralAngles">
-<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDihedralAngles" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetDihedralAngles</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDihedralAngles" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The phi and psi dihedral angles of every residue of <em>fragment</em>
+<code class="sig-name descname">GetDihedralAngles</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The phi and psi dihedral angles of every residue of <em>fragment</em>
or full entry at <em>coord_idx</em></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of pairs (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dihedral angles</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of pairs (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dihedral angles</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if database does not contain
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
dihedral angle data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetResidueDepths">
-<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetResidueDepths" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetResidueDepths</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetResidueDepths" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Residue depth for each residue of <em>fragment</em> or full entry
+<code class="sig-name descname">GetResidueDepths</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Residue depth for each residue of <em>fragment</em> or full entry
at <em>coord_idx</em></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
-depths</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the residue depths</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
+depths</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the residue depths</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if database does not contain
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
residue depth data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSolventAccessibilitites">
-<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSolventAccessibilitites" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSolventAccessibilitites" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Solvent accessibility for each residue of <em>fragment</em> or full entry
+<code class="sig-name descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Solvent accessibility for each residue of <em>fragment</em> or full entry
at <em>coord_idx</em> in square A as calculated by
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">Accessibility()</span></code></a> when adding the structure to
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
the database.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
-accessibilities</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the solvent
-accessibilities</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
+accessibilities</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the solvent
+accessibilities</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if database does not contain
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
solvent accessibility data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequenceProfile">
-<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequenceProfile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetSequenceProfile</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequenceProfile" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence profile for the residues defined by <em>fragment</em> or
+<code class="sig-name descname">GetSequenceProfile</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The sequence profile for the residues defined by <em>fragment</em> or
full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
-profile</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence profile</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
+profile</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence profile</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if database does not contain
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
sequence profile data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetStructureProfile">
-<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetStructureProfile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetStructureProfile" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The structure profile for the residues defined by <em>fragment</em> or
+<code class="sig-name descname">GetStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The structure profile for the residues defined by <em>fragment</em> or
full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
-profile</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the structure profile</li>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
+profile</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the structure profile</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if database does not contain
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
structure profile data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GenerateStructureProfile">
-<code class="descname">GenerateStructureProfile</code><span class="sig-paren">(</span><em>bb_list</em>, <em>residue_depths</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GenerateStructureProfile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GenerateStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">residue_depths</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GenerateStructureProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a structure profile for <em>bb_list</em> with given <em>residue_depths</em>
using the full internal data of this StructureDB.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Positions for which to calculate the structural profile</li>
-<li><strong>residue_depths</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The residue depth for each residue in <em>bb_list</em>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Positions for which to calculate the structural profile</p></li>
+<li><p><strong>residue_depths</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The residue depth for each residue in <em>bb_list</em>
as you would extract it from any StructureDB
-containing that data.</li>
+containing that data.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The structure profile for the input with the BLOSUM62
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The structure profile for the input with the BLOSUM62
probabilities as NULL model.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
<em>residue_depths</em> differ in size, when their size is 0
or when database does not contain residue depth data.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.SetStructureProfile">
-<code class="descname">SetStructureProfile</code><span class="sig-paren">(</span><em>coord_idx</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SetStructureProfile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em>, <em class="sig-param">prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SetStructureProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes the <em>prof</em> and sets the corresponding StructureProfile
frequencies in entry with <em>coord_idx</em></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
-<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
-(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</p></li>
+<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
+(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> does not match
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> does not match
any entry in the db, when the size of the <em>prof</em> does not
exactly match the size of entry at <em>coord_idx</em> or when database
does not contain aa frequency struct data.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSubDB">
-<code class="descname">GetSubDB</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSubDB" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A new database containing only the structural infos specified by
-your input. This might be useful if you’re testing stuff and want
-to make sure that you have no close homologue in the database.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Indices of chains to be added to the sub database (in [0,
-<a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if you provide an invalid index</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSubDB</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSubDB" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>A new database containing only the structural infos specified by
+your input. This might be useful if you’re testing stuff and want
+to make sure that you have no close homologue in the database.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Indices of chains to be added to the sub database (in [0,
+<a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if you provide an invalid index</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -884,15 +807,15 @@ to make sure that you have no close homologue in the database.</td>
<div class="section" id="finding-fragments-based-on-geometric-features">
<h2>Finding Fragments based on Geometric Features<a class="headerlink" href="#finding-fragments-based-on-geometric-features" title="Permalink to this headline">¶</a></h2>
<p>The fragment database allows to organize, search and access the information
-stored in a structural database (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>). In its current form it
+stored in a structural database (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>). In its current form it
groups fragments in bins according to their length (incl. stems) and the
geometry of their N-stem and C-stem (described by 4 angles and the distance
between the N-stem C atom and the C-stem N atom). It can therefore be searched
for fragments matching a certain geometry of N and C stems. The bins are
accessed through a hash table, making searching the database ultra fast.</p>
<p>This example illustrates how to create a custom FragDB based on a StructureDB:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
<span class="c1"># let's load the default structure_db </span>
<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="o">.</span><span class="n">LoadPortable</span><span class="p">(</span><span class="s2">"data/port_str_db.dat"</span><span class="p">)</span>
@@ -929,101 +852,91 @@ accessed through a hash table, making searching the database ultra fast.</p>
</div>
<dl class="class">
<dt id="promod3.loop.FragDB">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragDB</code><span class="sig-paren">(</span><em>dist_bin_size</em>, <em>angle_bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>dist_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Size of the distance parameter binning in A</li>
-<li><strong>angle_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Size of the angle parameter binning in degree</li>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">FragDB</code><span class="sig-paren">(</span><em class="sig-param">dist_bin_size</em>, <em class="sig-param">angle_bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>dist_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Size of the distance parameter binning in A</p></li>
+<li><p><strong>angle_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Size of the angle parameter binning in degree</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.loop.FragDB.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.FragDB.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FragDB.Save" title="promod3.loop.FragDB.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.loop.FragDB.SavePortable" title="promod3.loop.FragDB.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FragDB.Save" title="promod3.loop.FragDB.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.loop.FragDB.SavePortable" title="promod3.loop.FragDB.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded database</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded database</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.FragDB.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – path to the file where the database will be saved</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – path to the file where the database will be saved</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetAngularBinSize">
-<code class="descname">GetAngularBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetAngularBinSize" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetAngularBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetAngularBinSize" title="Permalink to this definition">¶</a></dt>
<dd><p>The size of the bins for the 4 angles describing the stem geometry and used
to organize the fragments in the database.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The bin size in degrees</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The bin size in degrees</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetDistBinSize">
-<code class="descname">GetDistBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetDistBinSize" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetDistBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetDistBinSize" title="Permalink to this definition">¶</a></dt>
<dd><p>The size of the bins for the distance describing the stem geometry and used
to organize the fragments in the database.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The bin size</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The bin size</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.AddFragments">
-<code class="descname">AddFragments</code><span class="sig-paren">(</span><em>fragment_length</em>, <em>rmsd_cutoff</em>, <em>structure_db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.AddFragments" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddFragments</code><span class="sig-paren">(</span><em class="sig-param">fragment_length</em>, <em class="sig-param">rmsd_cutoff</em>, <em class="sig-param">structure_db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.AddFragments" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over all fragments of length <strong>fragment_length</strong> in
<strong>structure_db</strong> and adds them to the fragment database.
Fragments will be skipped if there is already a fragment in the database
@@ -1031,135 +944,122 @@ that has an RMSD smaller than <strong>rmsd_cutoff</strong>, where RMSD is calcul
upon superposing the stem residues.
As the fragments are added they are organized in bins described by their
length and the geometry of their N and C stem.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The length of the fragments that should be added to the databse</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The minimal RMSD between two fragments in the fragment database</li>
-<li><strong>structure_db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Database delivering the structural info</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments that should be added to the databse</p></li>
+<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The minimal RMSD between two fragments in the fragment database</p></li>
+<li><p><strong>structure_db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Database delivering the structural info</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.PrintStatistics">
-<code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
<dd><p>Prints statistics about the fragment database, notably:</p>
<ol class="arabic simple">
-<li>the number of different stem groups (number of bins used to group the
-fragments according to the geometry of their stem residues)</li>
-<li>The total number of fragments in the database</li>
-<li>The minimal and maximal number of fragments found in a stem group.</li>
+<li><p>the number of different stem groups (number of bins used to group the
+fragments according to the geometry of their stem residues)</p></li>
+<li><p>The total number of fragments in the database</p></li>
+<li><p>The minimal and maximal number of fragments found in a stem group.</p></li>
</ol>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetNumStemPairs">
-<code class="descname">GetNumStemPairs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumStemPairs" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetNumStemPairs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumStemPairs" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetNumStemPairs</code><span class="sig-paren">(</span><em>loop_length</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetNumStemPairs</code><span class="sig-paren">(</span><em class="sig-param">loop_length</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the number of stem groups (number of bins used to group the
fragments according to the geometry of their stem residues) for the whole db
or for fragments of a given length.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The length of the fragments</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The number of groups</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The number of groups</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetNumFragments">
-<code class="descname">GetNumFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumFragments" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetNumFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumFragments" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">GetNumFragments</code><span class="sig-paren">(</span><em>loop_length</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetNumFragments</code><span class="sig-paren">(</span><em class="sig-param">loop_length</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the number of fragments in the database in total or for fragments of
a given length.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The length of the fragments</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Number of fragments</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Number of fragments</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.HasFragLength">
-<code class="descname">HasFragLength</code><span class="sig-paren">(</span><em>loop_length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.HasFragLength" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The length of the fragments</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">True if fragments of given length exist.</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">HasFragLength</code><span class="sig-paren">(</span><em class="sig-param">loop_length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.HasFragLength" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>True if fragments of given length exist.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.MaxFragLength">
-<code class="descname">MaxFragLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.MaxFragLength" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Maximal fragment length contained in db.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">MaxFragLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.MaxFragLength" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Maximal fragment length contained in db.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.SearchDB">
-<code class="descname">SearchDB</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>frag_size</em>, <em>extra_bins=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SearchDB" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SearchDB</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">frag_size</em>, <em class="sig-param">extra_bins=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SearchDB" title="Permalink to this definition">¶</a></dt>
<dd><p>Search the database for fragments matching the geometry of the <strong>n_stem</strong>
and <strong>c_stem</strong> and of the same length as the <strong>frag_size</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
-<li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues of the fragment</li>
-<li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</p></li>
+<li><p><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues of the fragment</p></li>
+<li><p><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
<em>extra_bins</em> additional bins surrounding the bin given by
the <em>n_stem</em> and <em>c_stem</em> geometry. If odd, we extend to
-the closer bin, otherwise symmetrically.</li>
+the closer bin, otherwise symmetrically.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A list of <a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a> objects. These objects are related
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A list of <a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a> objects. These objects are related
to the structural database with which you called the AddFragments
function.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -1167,42 +1067,42 @@ function.</p>
</div>
<div class="section" id="finding-fragments-based-on-sequence-features">
<h2>Finding Fragments based on Sequence Features<a class="headerlink" href="#finding-fragments-based-on-sequence-features" title="Permalink to this headline">¶</a></h2>
-<p>In some cases you might want to use the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> to search
+<p>In some cases you might want to use the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> to search
for fragments that possibly represent the structural conformation of interest.
-The <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> searches a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> for n fragments,
+The <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> searches a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> for n fragments,
that maximize a certain score and gathers a set of fragments with a guaranteed
-structural diversity based on an rmsd threshold. You can use the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a>
+structural diversity based on an rmsd threshold. You can use the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a>
wrapped in a full fletched pipeline implemented in
-<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a> or search for fragments from scratch
+<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a> or search for fragments from scratch
using an arbitrary linear combination of scores:</p>
<ul class="simple">
-<li><strong>SeqID</strong>:
+<li><p><strong>SeqID</strong>:
Calculates the fraction of amino acids being identical when comparing
-a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> and the target sequence</li>
-<li><strong>SeqSim</strong>:
+a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and the target sequence</p></li>
+<li><p><strong>SeqSim</strong>:
Calculates the avg. substitution matrix based sequence similarity of amino acids
-when comparing a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> and the target
-sequence</li>
-<li><strong>SSAgree</strong>:
-Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id3">[Jones1999]</a>
-and the dssp <a class="reference internal" href="../references.html#kabsch1983" id="id4">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.
-The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="../references.html#soding2005" id="id5">[soding2005]</a>.</li>
-<li><strong>TorsionProbability</strong>:
+when comparing a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and the target
+sequence</p></li>
+<li><p><strong>SSAgree</strong>:
+Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id3"><span>[Jones1999]</span></a>
+and the dssp <a class="reference internal" href="../references.html#kabsch1983" id="id4"><span>[kabsch1983]</span></a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>.
+The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="../references.html#soding2005" id="id5"><span>[soding2005]</span></a>.</p></li>
+<li><p><strong>TorsionProbability</strong>:
Calculates the avg. probability of observing the phi/psi dihedral angles of a potential
-fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> given the target sequence. The probabilities are
-extracted from the <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> class.</li>
-<li><strong>SequenceProfile</strong>:
+fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> given the target sequence. The probabilities are
+extracted from the <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> class.</p></li>
+<li><p><strong>SequenceProfile</strong>:
Calculates the avg. profile score between the amino acid frequencies of a potential
-fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
-in between them. The scores are calculated as L1 distances between the profile columns.</li>
-<li><strong>StructureProfile</strong>:
+fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
+in between them. The scores are calculated as L1 distances between the profile columns.</p></li>
+<li><p><strong>StructureProfile</strong>:
Calculates the avg. profile score between the amino acid frequencies of a potential
-fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
+fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
in between them. The scores are calculated as L1 distances between the profile columns.
-In this case, the amino acid frequencies extracted from structural alignments are used.</li>
+In this case, the amino acid frequencies extracted from structural alignments are used.</p></li>
</ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
<span class="c1"># load an example structure</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
@@ -1250,347 +1150,295 @@ In this case, the amino acid frequencies extracted from structural alignments ar
</div>
<dl class="class">
<dt id="promod3.loop.Fragger">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">Fragger</code><span class="sig-paren">(</span><em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger" title="Permalink to this definition">¶</a></dt>
-<dd><p>A Fragger object to search a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> for fragments with <strong>seq</strong>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">Fragger</code><span class="sig-paren">(</span><em class="sig-param">seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger" title="Permalink to this definition">¶</a></dt>
+<dd><p>A Fragger object to search a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> for fragments with <strong>seq</strong>
as target sequence. You need to add some score components before you can
finally call the Fill function.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of fragments to be searched</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of fragments to be searched</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.loop.Fragger.Fill">
-<code class="descname">Fill</code><span class="sig-paren">(</span><em>db</em>, <em>rmsd_thresh</em>, <em>num_fragments</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.Fill" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Fill</code><span class="sig-paren">(</span><em class="sig-param">db</em>, <em class="sig-param">rmsd_thresh</em>, <em class="sig-param">num_fragments</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.Fill" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches <strong>db</strong> for <strong>num_fragments</strong> fragments with maximal
score based on the defined score components.
There will be no pair of fragments with RMSD below <strong>rmsd_thresh</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Source of structural data</li>
-<li><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – To guarantee structural diversity</li>
-<li><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to be extracted</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Source of structural data</p></li>
+<li><p><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To guarantee structural diversity</p></li>
+<li><p><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSeqIDParameters">
-<code class="descname">AddSeqIDParameters</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqIDParameters" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddSeqIDParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqIDParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SeqID score component with linear weight <strong>w</strong></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSeqSimParameters">
-<code class="descname">AddSeqSimParameters</code><span class="sig-paren">(</span><em>w</em>, <em>subst</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqSimParameters" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddSeqSimParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">subst</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqSimParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SeqSim score component with linear weight <strong>w</strong></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>subst</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.SubstWeightMatrix</span></code>) – Substitution matrix to calculate sequence similarity</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
+<li><p><strong>subst</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SubstWeightMatrix</span></code>) – Substitution matrix to calculate sequence similarity</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSSAgreeParameters">
-<code class="descname">AddSSAgreeParameters</code><span class="sig-paren">(</span><em>w</em>, <em>psipred_prediction</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSSAgreeParameters" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddSSAgreeParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">psipred_prediction</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSSAgreeParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SSAgree score component with linear weight <strong>w</strong></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – linear weight</li>
-<li><strong>psipred_prediction</strong> (<a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code></a>) – Psipred prediction for fraggers target_sequence</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – linear weight</p></li>
+<li><p><strong>psipred_prediction</strong> (<a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a>) – Psipred prediction for fraggers target_sequence</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddTorsionProbabilityParameters">
-<code class="descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em>w</em>, <em>torsion_sampler</em>, <em>aa_before</em>, <em>aa_after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddTorsionProbabilityParameters" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">aa_before</em>, <em class="sig-param">aa_after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddTorsionProbabilityParameters" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em>w</em>, <em>torsion_sampler_list</em>, <em>aa_before</em>, <em>aa_after</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">torsion_sampler_list</em>, <em class="sig-param">aa_before</em>, <em class="sig-param">aa_after</em><span class="sig-paren">)</span></dt>
<dd><p>Add TorsionProbability component of linear weight <strong>w</strong></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – Torsion sampler to be used for all residues.</li>
-<li><strong>torsion_sampler_list</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – One torsion sampler for each residue.</li>
-<li><strong>aa_before</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue before the sequence
-linked to this object.</li>
-<li><strong>aa_after</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue after the sequence
-linked to this object.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Torsion sampler to be used for all residues.</p></li>
+<li><p><strong>torsion_sampler_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – One torsion sampler for each residue.</p></li>
+<li><p><strong>aa_before</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue before the sequence
+linked to this object.</p></li>
+<li><p><strong>aa_after</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue after the sequence
+linked to this object.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSequenceProfileParameters">
-<code class="descname">AddSequenceProfileParameters</code><span class="sig-paren">(</span><em>w</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSequenceProfileParameters" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddSequenceProfileParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSequenceProfileParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SequenceProfile component of linear weight <strong>w</strong></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddStructureProfileParameters">
-<code class="descname">AddStructureProfileParameters</code><span class="sig-paren">(</span><em>w</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddStructureProfileParameters" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddStructureProfileParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddStructureProfileParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add StructureProfile component of linear weight <strong>w</strong></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of fragments stored in fragger.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of fragments stored in fragger.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> – Item to extract</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Fragment at given position</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> – Item to extract</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Fragment at given position</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.GetFragmentInfo">
-<code class="descname">GetFragmentInfo</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of fragment</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a> of fragment at position <strong>index</strong></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetFragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a> of fragment at position <strong>index</strong></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.GetScore">
-<code class="descname">GetScore</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the final score of fragment defined by <strong>index</strong></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of fragment</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Score of fragment at position <strong>index</strong></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Score of fragment at position <strong>index</strong></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">GetScore</code><span class="sig-paren">(</span><em>parameter_index</em>, <em>index</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">parameter_index</em>, <em class="sig-param">index</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the single feature score defined by <strong>parameter_index</strong> of
fragment defined by <strong>index</strong> with parameter indexing based on the order
-you added them to the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>parameter_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of score (0-indexed in order of score
-components that were added)</li>
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of fragment</li>
+you added them to the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a></p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>parameter_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of score (0-indexed in order of score
+components that were added)</p></li>
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.FraggerMap">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FraggerMap</code><a class="headerlink" href="#promod3.loop.FraggerMap" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">FraggerMap</code><a class="headerlink" href="#promod3.loop.FraggerMap" title="Permalink to this definition">¶</a></dt>
<dd><p>A simple storable map of Fragger objects. The idea is that one can use the map
to cache fragger lists that have already been generated.</p>
-<p>You can use <a class="reference internal" href="#promod3.loop.FraggerMap.Contains" title="promod3.loop.FraggerMap.Contains"><code class="xref py py-meth docutils literal"><span class="pre">Contains()</span></code></a> to check if an item with a given key
-(<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) already exists and access items with the [] operator (see
-<a class="reference internal" href="#promod3.loop.FraggerMap.__getitem__" title="promod3.loop.FraggerMap.__getitem__"><code class="xref py py-meth docutils literal"><span class="pre">__getitem__()</span></code></a> and <a class="reference internal" href="#promod3.loop.FraggerMap.__setitem__" title="promod3.loop.FraggerMap.__setitem__"><code class="xref py py-meth docutils literal"><span class="pre">__setitem__()</span></code></a>).</p>
+<p>You can use <a class="reference internal" href="#promod3.loop.FraggerMap.Contains" title="promod3.loop.FraggerMap.Contains"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Contains()</span></code></a> to check if an item with a given key
+(<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) already exists and access items with the [] operator (see
+<a class="reference internal" href="#promod3.loop.FraggerMap.__getitem__" title="promod3.loop.FraggerMap.__getitem__"><code class="xref py py-meth docutils literal notranslate"><span class="pre">__getitem__()</span></code></a> and <a class="reference internal" href="#promod3.loop.FraggerMap.__setitem__" title="promod3.loop.FraggerMap.__setitem__"><code class="xref py py-meth docutils literal notranslate"><span class="pre">__setitem__()</span></code></a>).</p>
<p>Serialization is meant to be temporary and is not guaranteed to be portable.</p>
<dl class="method">
<dt id="promod3.loop.FraggerMap.Load">
-<code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em>, <em>db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Load" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FraggerMap.Save" title="promod3.loop.FraggerMap.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file.</li>
-<li><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Source of structural data used when filling the fragments.</li>
+<code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em>, <em class="sig-param">db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Load" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FraggerMap.Save" title="promod3.loop.FraggerMap.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p></li>
+<li><p><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Source of structural data used when filling the fragments.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The loaded map.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal"><span class="pre">FraggerMap</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded map.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerMap</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Save" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves raw binary representation of this map. Only fragment infos and scores
are stored and not the parameters for scoring. The coordinates are to be
reread from a structure db.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.LoadBB">
-<code class="descname">LoadBB</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.LoadBB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FraggerMap.SaveBB" title="promod3.loop.FraggerMap.SaveBB"><code class="xref py py-meth docutils literal"><span class="pre">SaveBB()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded map.</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal"><span class="pre">FraggerMap</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">LoadBB</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.LoadBB" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FraggerMap.SaveBB" title="promod3.loop.FraggerMap.SaveBB"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SaveBB()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded map.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerMap</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.SaveBB">
-<code class="descname">SaveBB</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.SaveBB" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SaveBB</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.SaveBB" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves raw binary representation of this map. Only fragments and scores
are stored and not the parameters for scoring. Here, we also store the
coordinates. This file will hence be much larger than the one saved with
-<a class="reference internal" href="#promod3.loop.FraggerMap.Save" title="promod3.loop.FraggerMap.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="#promod3.loop.FraggerMap.Save" title="promod3.loop.FraggerMap.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.Contains">
-<code class="descname">Contains</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff a fragger object for this id is already in the map.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, iff a fragger object for this id is already in the map.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__getitem__" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.FraggerMap.__setitem__">
-<code class="descname">__setitem__</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__setitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__setitem__</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__setitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Allow read/write access (with [<em>id</em>]) to fragger object with given ID.</p>
</dd></dl>
@@ -1601,186 +1449,157 @@ coordinates. This file will hence be much larger than the one saved with
<h2>The PsipredPrediction class<a class="headerlink" href="#the-psipredprediction-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.PsipredPrediction">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">PsipredPrediction</code><a class="headerlink" href="#promod3.loop.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
-<dd><p>A container for the secondary structure prediction by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id6">[Jones1999]</a>.</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">PsipredPrediction</code><a class="headerlink" href="#promod3.loop.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
+<dd><p>A container for the secondary structure prediction by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id6"><span>[Jones1999]</span></a>.</p>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.PsipredPrediction">
-<code class="descname">PsipredPrediction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">PsipredPrediction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs empty container</p>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">PsipredPrediction</code><span class="sig-paren">(</span><em>prediction</em>, <em>confidence</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">PsipredPrediction</code><span class="sig-paren">(</span><em class="sig-param">prediction</em>, <em class="sig-param">confidence</em><span class="sig-paren">)</span></dt>
<dd><p>Constructs container with given content</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Secondary structure prediction as element in [‘H’,’E’,’C’]</li>
-<li><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Confidence of prediction as element in [0,9]</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Secondary structure prediction as element in [‘H’,’E’,’C’]</p></li>
+<li><p><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Confidence of prediction as element in [0,9]</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if size of <strong>prediction</strong> and
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of <strong>prediction</strong> and
<strong>confidence</strong> are inconsistent or if they contain an invalid
element</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.FromHHM">
-<code class="descname">FromHHM</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHHM" title="Permalink to this definition">¶</a></dt>
-<dd><p>Static function to Load a <a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code></a> object from hhm file,
+<code class="sig-name descname">FromHHM</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHHM" title="Permalink to this definition">¶</a></dt>
+<dd><p>Static function to Load a <a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> object from hhm file,
as they are provided by the hhsearch suite</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of file</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of file</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.FromHoriz">
-<code class="descname">FromHoriz</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHoriz" title="Permalink to this definition">¶</a></dt>
-<dd><p>Static function to Load a <a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code></a> object from horiz file,
+<code class="sig-name descname">FromHoriz</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHoriz" title="Permalink to this definition">¶</a></dt>
+<dd><p>Static function to Load a <a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> object from horiz file,
as they are produced by the psipred executable</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of file</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of file</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.Add">
-<code class="descname">Add</code><span class="sig-paren">(</span><em>prediction</em>, <em>confidence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Add" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Add</code><span class="sig-paren">(</span><em class="sig-param">prediction</em>, <em class="sig-param">confidence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Add" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds and appends a single residue psipred prediction at the end</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Prediction, must be one in [‘H’,’E’,’C’]</li>
-<li><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Confidence of prediction, must be in [0,9]</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Prediction, must be one in [‘H’,’E’,’C’]</p></li>
+<li><p><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Confidence of prediction, must be in [0,9]</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if input contains invalid elements</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if input contains invalid elements</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.Extract">
-<code class="descname">Extract</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><p>Extracts content and returns a sub-<a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code></a> with range <strong>from</strong>
+<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><p>Extracts content and returns a sub-<a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> with range <strong>from</strong>
to <strong>to</strong>, not including <strong>to</strong> itself</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx to start</li>
-<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx to end</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx to start</p></li>
+<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx to end</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code></a> with the specified range</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <strong>from</strong> or <strong>to</strong> are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> with the specified range</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>from</strong> or <strong>to</strong> are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetPrediction">
-<code class="descname">GetPrediction</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPrediction" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index to get prediction from</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Psipred prediction at pos <strong>idx</strong></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetPrediction</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPrediction" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index to get prediction from</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Psipred prediction at pos <strong>idx</strong></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetConfidence">
-<code class="descname">GetConfidence</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidence" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index to get confidence from</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Psipred confidence at pos <strong>idx</strong></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetConfidence</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidence" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index to get confidence from</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Psipred confidence at pos <strong>idx</strong></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetPredictions">
-<code class="descname">GetPredictions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPredictions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetPredictions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPredictions" title="Permalink to this definition">¶</a></dt>
<dd><p>Get all the predictions in the container</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> containing all the predictions in the container</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> containing all the predictions in the container</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetConfidences">
-<code class="descname">GetConfidences</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidences" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetConfidences</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidences" title="Permalink to this definition">¶</a></dt>
<dd><p>Get all the confidences in the container</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> containing all the confidences in the container</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> containing all the confidences in the container</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of elements in container</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of elements in container</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -1795,23 +1614,45 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Structural Data</a><ul>
-<li><a class="reference internal" href="#defining-chains-and-fragments">Defining Chains and Fragments</a></li>
-<li><a class="reference internal" href="#the-structure-database">The Structure Database</a></li>
-<li><a class="reference internal" href="#finding-fragments-based-on-geometric-features">Finding Fragments based on Geometric Features</a></li>
-<li><a class="reference internal" href="#finding-fragments-based-on-sequence-features">Finding Fragments based on Sequence Features</a></li>
-<li><a class="reference internal" href="#the-psipredprediction-class">The PsipredPrediction class</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="torsion_sampler.html" title="previous chapter">Sampling Dihedral Angles</a></li>
<li>Next: <a href="all_atom.html" title="next chapter">Handling All Atom Positions</a></li>
</ul></li>
@@ -1819,23 +1660,24 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/loop/structure_db.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1844,11 +1686,11 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/loop/structure_db.txt"
+ <a href="../_sources/loop/structure_db.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index 10f3569c2434bd06e32cb854097f826418fbf733..b3013277af5c1b5549b8d9f62df8a1919d2834af 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Sampling Dihedral Angles — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Sampling Dihedral Angles — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Structural Data" href="structure_db.html" />
<link rel="prev" title="Representing Loops" href="backbone.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -62,8 +48,8 @@ most methods which need to access a specific distribution can either take 3
residue names or an index as input.</p>
<p>As a showcase example, we randomly sample from a given torsion sample and
store the resulting samples as a scatter plot:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
<span class="c1"># this requires matplotlib and numpy</span>
<span class="kn">import</span> <span class="nn">matplotlib</span>
<span class="c1"># change next line, if you wish to use a GUI-based plot-output</span>
@@ -103,10 +89,10 @@ store the resulting samples as a scatter plot:</p>
<p>Since the torsion sampler considers triplets of amino acids, we need to define
them. This is done with the so called torsion group definitions.
Three strings represent the according positions of the consecutive
-amino acids. They are combined by “-”. It is either possible to
-use the keyword “all”, or write out all allowed amino acids by their
-three letter code and separate them by ”,”. An example would be: “all-
-VAL,ILE-PRO”. There are cases where a tripeptide can match several
+amino acids. They are combined by “-“. It is either possible to
+use the keyword “all”, or write out all allowed amino acids by their
+three letter code and separate them by “,”. An example would be: “all-
+VAL,ILE-PRO”. There are cases where a tripeptide can match several
group definitions. The list of group definitions is iterated for every
combination of three consecutive amino acids and the first hit is
decisive.</p>
@@ -115,430 +101,360 @@ decisive.</p>
<h2>The Torsion Sampler Class<a class="headerlink" href="#the-torsion-sampler-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.TorsionSampler">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">TorsionSampler</code><span class="sig-paren">(</span><em>group_definitions</em>, <em>bins_per_dimension</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">TorsionSampler</code><span class="sig-paren">(</span><em class="sig-param">group_definitions</em>, <em class="sig-param">bins_per_dimension</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>Basic object used to sample the backbone torsion angles phi and psi.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid triplets</li>
-<li><strong>bins_per_dimension</strong> – Number of bins to represent the 360 degrees of each
-torsion angle</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for random number generator</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid triplets</p></li>
+<li><p><strong>bins_per_dimension</strong> – Number of bins to represent the 360 degrees of each
+torsion angle</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for random number generator</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">RuntimeException</span></code> when there is a
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeException</span></code> when there is a
possible combination of the 20 standard amino
acids not matching any of the group definitions.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.ExtractStatistics">
-<code class="descname">ExtractStatistics</code><span class="sig-paren">(</span><em>view</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.ExtractStatistics" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ExtractStatistics</code><span class="sig-paren">(</span><em class="sig-param">view</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.ExtractStatistics" title="Permalink to this definition">¶</a></dt>
<dd><p>Extracts backbone torsion angles from the structure and adds them to the appropriate histograms in the sampler.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.UpdateDistributions">
-<code class="descname">UpdateDistributions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.UpdateDistributions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">UpdateDistributions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.UpdateDistributions" title="Permalink to this definition">¶</a></dt>
<dd><p>Recalculates the probability distributions from the histograms.</p>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.loop.TorsionSampler.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.TorsionSampler.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.TorsionSampler.Save" title="promod3.loop.TorsionSampler.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.loop.TorsionSampler.SavePortable" title="promod3.loop.TorsionSampler.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.TorsionSampler.Save" title="promod3.loop.TorsionSampler.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.loop.TorsionSampler.SavePortable" title="promod3.loop.TorsionSampler.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load the sampler.</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for random number generator (not saved in file).</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the sampler.</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for random number generator (not saved in file).</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A torsion sampler</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A torsion sampler</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.TorsionSampler.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where the sampler will be saved</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where the sampler will be saved</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetHistogramIndex">
-<code class="descname">GetHistogramIndex</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<code class="sig-name descname">GetHistogramIndex</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The index of the histogram corresponding to the triplet of residues specified.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The index of the histogram corresponding to the triplet of residues specified.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetHistogramIndices">
-<code class="descname">GetHistogramIndices</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndices" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of length n from which histogram indices
-should created.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">List of length n-2 containing histogram indices of
-all consecutive amino acid triplets in <strong>sequence</strong></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <strong>sequence</strong> contains non
-standard amino acid</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetHistogramIndices</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndices" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of length n from which histogram indices
+should created.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>List of length n-2 containing histogram indices of
+all consecutive amino acid triplets in <strong>sequence</strong></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>sequence</strong> contains non
+standard amino acid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.Draw">
-<code class="descname">Draw</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Draw" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Draw</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Draw" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws a pair of dihedral angles for the <em>central</em> residue from the distribution specific for such a triplet of residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A pair of phi/psi angles</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A pair of phi/psi angles</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">Draw</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">Draw</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span></dt>
<dd><p>Draws a pair of dihedral angles from the distribution specified by the <em>index</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the distribution from which a phi/psi pair will be drawn.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A pair of phi/psi angles</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a phi/psi pair will be drawn.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A pair of phi/psi angles</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.DrawPhiGivenPsi">
-<code class="descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPhiGivenPsi" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPhiGivenPsi" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws a <em>phi</em> angle for the <em>central</em> residue from the conditional distribution P( <em>phi</em> | <em>psi</em> ) specific for such a triplet of residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>An angle</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span></dt>
<dd><p>Draws a <em>phi</em> angle from the conditional distribution P( <em>phi</em> | <em>psi</em> ) specified by the <em>index</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the distribution from which a <em>phi</em> angle will be drawn.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a <em>phi</em> angle will be drawn.</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>An angle</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.DrawPsiGivenPhi">
-<code class="descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPsiGivenPhi" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPsiGivenPhi" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws a <em>phi</em> angle for the <em>central</em> residue from the conditional distribution P( <em>psi</em> | <em>phi</em> ) specific for such a triplet of residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>An angle</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span></dt>
<dd><p>Draws a <em>phi</em> angle from the conditional distribution P( <em>psi</em> | <em>phi</em> ) specified by the <em>index</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the distribution from which a psi angle will be drawn.</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a psi angle will be drawn.</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>An angle</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetProbability">
-<code class="descname">GetProbability</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetProbability" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetProbability" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the probability of a specific pair of phi/psi angles for the central residue from the corresponding distribution.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A probability</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">GetProbability</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the probability of a specific pair of phi/psi angles calulated from the distribution specified by <em>index</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the distribution.</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A probability</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">
-<code class="descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns P( <em>phi</em> | <em>psi</em> ) for the central residue from the corresponding distribution.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A probability</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">
-<code class="descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>psi</em>, <em>phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">psi</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns P( <em>psi</em> | <em>phi</em> ) for the central residue from the corresponding distribution.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A probability</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span></dt>
<dd><p>Returns P( <em>phi</em> | <em>psi</em> ) for the central residue from the corresponding distribution.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the distribution.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A probability</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em>, <em>phi</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span></dt>
<dd><p>Returns P( <em>psi</em> | <em>phi</em> ) for the central residue from the corresponding distribution.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the distribution.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A probability</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetBinsPerDimension">
-<code class="descname">GetBinsPerDimension</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinsPerDimension" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetBinsPerDimension</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinsPerDimension" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of bins per dimension of the distributions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetBinSize">
-<code class="descname">GetBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinSize" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinSize" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the size of the bins (in radians) of the distributions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -553,20 +469,45 @@ standard amino acid</td>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Sampling Dihedral Angles</a><ul>
-<li><a class="reference internal" href="#defining-amino-acid-triplets">Defining Amino Acid triplets</a></li>
-<li><a class="reference internal" href="#the-torsion-sampler-class">The Torsion Sampler Class</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="backbone.html" title="previous chapter">Representing Loops</a></li>
<li>Next: <a href="structure_db.html" title="next chapter">Structural Data</a></li>
</ul></li>
@@ -574,23 +515,24 @@ standard amino acid</td>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/loop/torsion_sampler.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -599,11 +541,11 @@ standard amino acid</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/loop/torsion_sampler.txt"
+ <a href="../_sources/loop/torsion_sampler.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 325c8ad97e78afb0754753f0b79be1c45c687022..9e4ac5d084cf1166434dc1e7706723fa4138d6a2 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Modelling Algorithms — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Modelling Algorithms — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
<link rel="prev" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -72,119 +58,107 @@ also present in solution B. As a final result, the algorithm therefore detects
common rigid subsets of positions.</p>
<dl class="method">
<dt id="promod3.modelling.RigidBlocks">
-<code class="descclassname">promod3.modelling.</code><code class="descname">RigidBlocks</code><span class="sig-paren">(</span><em>bb_list_one</em>, <em>bb_list_two</em><span class="optional">[</span>, <em>window_length = 12</em>, <em>max_iterations=20</em>, <em>distance_thresh=3.0</em>, <em>cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RigidBlocks" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RigidBlocks</code><span class="sig-paren">(</span><em class="sig-param">bb_list_one</em>, <em class="sig-param">bb_list_two</em><span class="optional">[</span>, <em class="sig-param">window_length = 12</em>, <em class="sig-param">max_iterations=20</em>, <em class="sig-param">distance_thresh=3.0</em>, <em class="sig-param">cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RigidBlocks" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs the RigidBlock algorithm on given input</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list_one</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – First piece structural information from which CA
-positions will be extracted</li>
-<li><strong>bb_list_two</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Second piece of structural information from which CA
-positions will be extracted</li>
-<li><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</li>
-<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
-iterative superposition</li>
-<li><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>bb_list_one</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – First piece structural information from which CA
+positions will be extracted</p></li>
+<li><p><strong>bb_list_two</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Second piece of structural information from which CA
+positions will be extracted</p></li>
+<li><p><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</p></li>
+<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
+iterative superposition</p></li>
+<li><p><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
considered in the same rigid block and to select
the common subset for the next iteration of the
-iterative superposition</li>
-<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
-of the solutions</li>
+iterative superposition</p></li>
+<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
+of the solutions</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> with the first element being a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> defining the
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
indices of the common subsets (rigid blocks) relative
-to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
-and the second element being a <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
+and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descclassname">promod3.modelling.</code><code class="descname">RigidBlocks</code><span class="sig-paren">(</span><em>aln</em><span class="optional">[</span>, <em>seq_one_idx=0</em>, <em>seq_two_idx=1</em>, <em>window_length = 12</em>, <em>max_iterations=20</em>, <em>distance_thresh=3.0</em>, <em>cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RigidBlocks</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="optional">[</span>, <em class="sig-param">seq_one_idx=0</em>, <em class="sig-param">seq_two_idx=1</em>, <em class="sig-param">window_length = 12</em>, <em class="sig-param">max_iterations=20</em>, <em class="sig-param">distance_thresh=3.0</em>, <em class="sig-param">cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Performs the RigidBlock algorithm on given input</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
-objects from which the positions are extracted</li>
-<li><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
-positions will be extracted</li>
-<li><strong>seq_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The idx of the second sequence from which the CA
-positions will be extracted</li>
-<li><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</li>
-<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
-iterative superposition</li>
-<li><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
+objects from which the positions are extracted</p></li>
+<li><p><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
+positions will be extracted</p></li>
+<li><p><strong>seq_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the second sequence from which the CA
+positions will be extracted</p></li>
+<li><p><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</p></li>
+<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
+iterative superposition</p></li>
+<li><p><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
considered in the same rigid block and to select
the common subset for the next iteration of the
-iterative superposition</li>
-<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
-of the solutions</li>
+iterative superposition</p></li>
+<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
+of the solutions</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> with the first element being a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> defining the
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
-and the second element being a <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descclassname">promod3.modelling.</code><code class="descname">RigidBlocks</code><span class="sig-paren">(</span><em>pos_one</em>, <em>pos_two</em><span class="optional">[</span>, <em>window_length = 12</em>, <em>max_iterations=20</em>, <em>distance_thresh=3.0</em>, <em>cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RigidBlocks</code><span class="sig-paren">(</span><em class="sig-param">pos_one</em>, <em class="sig-param">pos_two</em><span class="optional">[</span>, <em class="sig-param">window_length = 12</em>, <em class="sig-param">max_iterations=20</em>, <em class="sig-param">distance_thresh=3.0</em>, <em class="sig-param">cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Performs the RigidBlock algorithm on given input</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>pos_one</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – First piece position information</li>
-<li><strong>pos_two</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – Second piece of position information</li>
-<li><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</li>
-<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
-iterative superposition</li>
-<li><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – First piece position information</p></li>
+<li><p><strong>pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Second piece of position information</p></li>
+<li><p><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</p></li>
+<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
+iterative superposition</p></li>
+<li><p><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
considered in the same rigid block and to select
the common subset for the next iteration of the
-iterative superposition</li>
-<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
-of the solutions</li>
+iterative superposition</p></li>
+<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
+of the solutions</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> with the first element being a
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> defining the
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
indices of the common subsets (rigid blocks) relative
-to the input <code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code> objects
-and the second element being a <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+to the input <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code> objects
+and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -196,8 +170,8 @@ as well as a convenient function to combine the functionalities into an
example pipeline.</p>
<dl class="class">
<dt id="promod3.modelling.FraggerHandle">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">FraggerHandle</code><span class="sig-paren">(</span><em>sequence</em>, <em>profile=None</em>, <em>psipred_pred=None</em>, <em>fragment_length=9</em>, <em>fragments_per_position=100</em>, <em>rmsd_thresh=0.0</em>, <em>structure_db=None</em>, <em>torsion_sampler_coil=None</em>, <em>torsion_sampler_helix=None</em>, <em>torsion_sampler_extended=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle" title="Permalink to this definition">¶</a></dt>
-<dd><p>Handler for <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects linked to a
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FraggerHandle</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">profile=None</em>, <em class="sig-param">psipred_pred=None</em>, <em class="sig-param">fragment_length=9</em>, <em class="sig-param">fragments_per_position=100</em>, <em class="sig-param">rmsd_thresh=0.0</em>, <em class="sig-param">structure_db=None</em>, <em class="sig-param">torsion_sampler_coil=None</em>, <em class="sig-param">torsion_sampler_helix=None</em>, <em class="sig-param">torsion_sampler_extended=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Handler for <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects linked to a
specific chain.</p>
<p>Tries to get the most accurate fragments given your input.
You can only provide a SEQRES, the returned fragments are
@@ -206,112 +180,107 @@ You can massively increase the accuracy of the found fragments by
providing a secondary structure prediction and / or sequence profile.</p>
<p>Following features influence the fragment search given your input:</p>
<ul class="simple">
-<li><strong>sequence</strong>:<ul>
-<li>Sequence Similarity with BLOSUM62</li>
+<li><p><strong>sequence</strong>:</p>
+<ul>
+<li><p>Sequence Similarity with BLOSUM62</p></li>
</ul>
</li>
-<li><strong>sequence</strong>, <strong>psipred_pred</strong>:<ul>
-<li>Sequence Similarity with BLOSUM62</li>
-<li>Secondary Structure Agreement</li>
-<li>Secondary Structure Dependent Torsion Probabilities</li>
+<li><p><strong>sequence</strong>, <strong>psipred_pred</strong>:</p>
+<ul>
+<li><p>Sequence Similarity with BLOSUM62</p></li>
+<li><p>Secondary Structure Agreement</p></li>
+<li><p>Secondary Structure Dependent Torsion Probabilities</p></li>
</ul>
</li>
-<li><strong>sequence</strong>, <strong>profile</strong>:<ul>
-<li>Sequence Profile Score</li>
-<li>Structure Profile Score</li>
+<li><p><strong>sequence</strong>, <strong>profile</strong>:</p>
+<ul>
+<li><p>Sequence Profile Score</p></li>
+<li><p>Structure Profile Score</p></li>
</ul>
</li>
-<li><strong>sequence</strong>, <strong>psipred_pred</strong>, <strong>profile</strong>:<ul>
-<li>Secondary Structure Agreement</li>
-<li>Secondary Structure Dependent Torsion Probabilities</li>
-<li>Sequence Profile Score</li>
-<li>Structure Profile Score</li>
+<li><p><strong>sequence</strong>, <strong>psipred_pred</strong>, <strong>profile</strong>:</p>
+<ul>
+<li><p>Secondary Structure Agreement</p></li>
+<li><p>Secondary Structure Dependent Torsion Probabilities</p></li>
+<li><p>Sequence Profile Score</p></li>
+<li><p>Structure Profile Score</p></li>
</ul>
</li>
</ul>
-<p>The FraggerHandle internally uses the <a class="reference internal" href="../loop/structure_db.html#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.FraggerMap</span></code></a> for caching. You
+<p>The FraggerHandle internally uses the <a class="reference internal" href="../loop/structure_db.html#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.FraggerMap</span></code></a> for caching. You
can therefore request fragments for a certain position several times and the
search is performed only once. This also allows to save the FraggerHandle to
disk. When loading the FraggerHandle again, you need to provide all parameters
again. These parameters must be exactly the same than the ones you used when
initially constructing the FraggerHandle, especially the structure database.
Weird things are happening otherwise.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
-<li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li>
-<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</li>
-<li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
-position.</li>
-<li><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – To guarantee structural diversity, no pair of fragments
-at a given position will have RMSD below <cite>rmsd_thresh</cite>.</li>
-<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.StructureDB</span></code></a>) – Source of structural data</li>
-<li><strong>torsion_sampler_coil</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for coil residues.</li>
-<li><strong>torsion_sampler_helix</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for helical residues.</li>
-<li><strong>torsion_sampler_extended</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for extended residues.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</p></li>
+<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</p></li>
+<li><p><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</p></li>
+<li><p><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</p></li>
+<li><p><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
+position.</p></li>
+<li><p><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To guarantee structural diversity, no pair of fragments
+at a given position will have RMSD below <cite>rmsd_thresh</cite>.</p></li>
+<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.StructureDB</span></code></a>) – Source of structural data</p></li>
+<li><p><strong>torsion_sampler_coil</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for coil residues.</p></li>
+<li><p><strong>torsion_sampler_helix</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for helical residues.</p></li>
+<li><p><strong>torsion_sampler_extended</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for extended residues.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.Get">
-<code class="descname">Get</code><span class="sig-paren">(</span><em>frag_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.Get" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">frag_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.Get" title="Permalink to this definition">¶</a></dt>
<dd><p>Get fragger for sequence at index frag_pos..frag_pos+frag_length-1.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frag_pos</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A <code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code> object.</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if index out-of-bounds.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>frag_pos</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A <code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code> object.</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code> if index out-of-bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.GetList">
-<code class="descname">GetList</code><span class="sig-paren">(</span><em>pos_start=0</em>, <em>pos_end=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.GetList" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetList</code><span class="sig-paren">(</span><em class="sig-param">pos_start=0</em>, <em class="sig-param">pos_end=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.GetList" title="Permalink to this definition">¶</a></dt>
<dd><p>Get List of fraggers covering sequence indices pos_start..pos_end.</p>
<p>This will return an empty list if range is smaller than fragment_length.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>pos_start</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</li>
-<li><strong>pos_end</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – End-index or -1 if it should go to the sequence-end.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>pos_start</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</p></li>
+<li><p><strong>pos_end</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End-index or -1 if it should go to the sequence-end.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code> objects.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> if indices out-of-bounds.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code> objects.</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code> if indices out-of-bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.LoadCached">
-<code class="descname">LoadCached</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.LoadCached" title="Permalink to this definition">¶</a></dt>
-<dd><p>Load fragger objects stored with <a class="reference internal" href="#promod3.modelling.FraggerHandle.SaveCached" title="promod3.modelling.FraggerHandle.SaveCached"><code class="xref py py-meth docutils literal"><span class="pre">SaveCached()</span></code></a>.
+<code class="sig-name descname">LoadCached</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.LoadCached" title="Permalink to this definition">¶</a></dt>
+<dd><p>Load fragger objects stored with <a class="reference internal" href="#promod3.modelling.FraggerHandle.SaveCached" title="promod3.modelling.FraggerHandle.SaveCached"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SaveCached()</span></code></a>.
Note that here we require that the same structure db is set as was
used when <cite>filename</cite> was saved.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.SaveCached">
-<code class="descname">SaveCached</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.SaveCached" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SaveCached</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.SaveCached" title="Permalink to this definition">¶</a></dt>
<dd><p>Save cached fraggers.</p>
</dd></dl>
@@ -319,50 +288,46 @@ used when <cite>filename</cite> was saved.</p>
<dl class="function">
<dt id="promod3.modelling.GenerateDeNovoTrajectories">
-<code class="descclassname">promod3.modelling.</code><code class="descname">GenerateDeNovoTrajectories</code><span class="sig-paren">(</span><em>sequence</em>, <em>num_trajectories=200</em>, <em>avg_sampling_per_position=600</em>, <em>profile=None</em>, <em>psipred_prediction=None</em>, <em>fragment_handler=None</em>, <em>scorer=None</em>, <em>scorer_env=None</em>, <em>scoring_weights=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GenerateDeNovoTrajectories" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GenerateDeNovoTrajectories</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">num_trajectories=200</em>, <em class="sig-param">avg_sampling_per_position=600</em>, <em class="sig-param">profile=None</em>, <em class="sig-param">psipred_prediction=None</em>, <em class="sig-param">fragment_handler=None</em>, <em class="sig-param">scorer=None</em>, <em class="sig-param">scorer_env=None</em>, <em class="sig-param">scoring_weights=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GenerateDeNovoTrajectories" title="Permalink to this definition">¶</a></dt>
<dd><p>Example de novo modelling pipeline based on Fragment sampling and
backbone scoring. Take this as a starting point for more advanced
de novo procedures.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence you want to sample</li>
-<li><strong>num_trajectories</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The number of sampling trajectories you
-want to generate</li>
-<li><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence you want to sample</p></li>
+<li><p><strong>num_trajectories</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The number of sampling trajectories you
+want to generate</p></li>
+<li><p><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
-len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
-fragment search performance.</li>
-<li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
-increases the fragment search performance</li>
-<li><strong>fragment_handler</strong> (<a class="reference internal" href="#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>) – You can provide already initialized fragments.
+len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></p></li>
+<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
+fragment search performance.</p></li>
+<li><p><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
+increases the fragment search performance</p></li>
+<li><p><strong>fragment_handler</strong> (<a class="reference internal" href="#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>) – You can provide already initialized fragments.
If you pass this parameter, <strong>profile</strong> and
<strong>psipred_prediction</strong> get neglected and do
not influence the fragment search, the
ones you initialized <strong>fragment_handler</strong> with
-get used instead.</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">promod3.scoring.BackboneOverallScorer</span></code></a>) – Scorer doing the backbone scoring. If not provided, a
+get used instead.</p></li>
+<li><p><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.scoring.BackboneOverallScorer</span></code></a>) – Scorer doing the backbone scoring. If not provided, a
default one gets loaded with default objects with
following keys: clash, reduced, cb_packing, hbond, cbeta,
-torsion and pairwise</li>
-<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">promod3.scoring.BackboneScoreEnv</span></code></a>) – The scoring env that relates to <strong>scorer</strong>
-This environment will be changed!</li>
-<li><strong>scoring_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a>) – Linear weights for different scores. If not provided,
+torsion and pairwise</p></li>
+<li><p><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.scoring.BackboneScoreEnv</span></code></a>) – The scoring env that relates to <strong>scorer</strong>
+This environment will be changed!</p></li>
+<li><p><strong>scoring_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a>) – Linear weights for different scores. If not provided,
the output of ScoringWeights.GetWeights() is used.
Please note, that the weights must be consistent
-with the keys of the scores in <strong>scorer</strong></li>
+with the keys of the scores in <strong>scorer</strong></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A <code class="xref py py-class docutils literal"><span class="pre">promod3.loop.LoopCandidates</span></code> object containing
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A <code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.LoopCandidates</span></code> object containing
<strong>num_trajectories</strong> elements for further processing</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -371,7 +336,7 @@ with the keys of the scores in <strong>scorer</strong></li>
<p>Distinct spatial arrangements of atoms or functional groups are key for protein
function. For their detection, ProMod3 implements the MotifFinder algorithm
which is based on geometric hashing as described by Nussinov and Wolfson
-<a class="reference internal" href="../references.html#nussinov1991" id="id1">[nussinov1991]</a>. The algorithm consists of a learning stage, a detection stage
+<a class="reference internal" href="../references.html#nussinov1991" id="id1"><span>[nussinov1991]</span></a>. The algorithm consists of a learning stage, a detection stage
and a refinement stage.</p>
<p>Learning Stage: A motif (query) is represented by a set of coordinates. Triplets
(p1, p2, p3) of coordinates are selected that define triangles. For each
@@ -381,7 +346,7 @@ v2 = norm(cross(v1,v3)))). For each coordinate not in [p1,p2,p3], we add the
identity of the query/triangle as value to a hash map.
The corresponding key consists of discretized values describing the edge lengths
of the triangle, as well as the coordinate transformed into the triangle
-specific orthogonal vector basis. That’s 6 numbers in total.</p>
+specific orthogonal vector basis. That’s 6 numbers in total.</p>
<p>Detection Stage: The goal is to identify one or several subsets of target
coordinates that resemble an input query.
We first setup an accumulator containing a counter for each triangle observed
@@ -417,14 +382,14 @@ query coordinates is larger or equal <em>refine_thresh</em>.
The larger the mapping, the more accurate the superposition. As we start with
only the three triangle vertices, <em>distance_thresh</em> is doubled for the initial
iteration.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example script that loads protein structures that contain ATP and</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Example script that loads protein structures that contain ATP and</span>
<span class="c1"># generates motif queries describing their binding pockets.</span>
<span class="c1"># In a second step, those pockets are matched against a protein </span>
<span class="c1"># structure that only contains an ATP analog. The ATP from every </span>
<span class="c1"># match is transformed and stored to disk for further processing.</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
<span class="n">files</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'data/1E2Q.pdb'</span><span class="p">,</span> <span class="s1">'data/1KO5.pdb'</span><span class="p">,</span> <span class="s1">'data/2IYW.pdb'</span><span class="p">]</span>
@@ -480,91 +445,78 @@ iteration.</p>
</div>
<dl class="class">
<dt id="promod3.modelling.MotifQuery">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifQuery</code><span class="sig-paren">(</span><em class="sig-param">positions</em>, <em class="sig-param">identifier</em>, <em class="sig-param">min_triangle_edge_length</em>, <em class="sig-param">max_triangle_edge_length</em>, <em class="sig-param">bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em>, <em>flags</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifQuery</code><span class="sig-paren">(</span><em class="sig-param">positions</em>, <em class="sig-param">identifier</em>, <em class="sig-param">min_triangle_edge_length</em>, <em class="sig-param">max_triangle_edge_length</em>, <em class="sig-param">bin_size</em>, <em class="sig-param">flags</em><span class="sig-paren">)</span></dt>
<dt>
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>query_list</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifQuery</code><span class="sig-paren">(</span><em class="sig-param">query_list</em><span class="sig-paren">)</span></dt>
<dd><p>A single query or a container of queries.
The constructor performs the learning stage of a single query or combines
several queries, so they can be searched at once.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – Coordinates of the query</li>
-<li><strong>identifier</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Descriptor of the query</li>
-<li><strong>min_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – To avoid the full O(n^3) hell, triangles
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>positions</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Coordinates of the query</p></li>
+<li><p><strong>identifier</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Descriptor of the query</p></li>
+<li><p><strong>min_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To avoid the full O(n^3) hell, triangles
with any edge length below <em>min_triangle_edge_length</em>
-are skipped</li>
-<li><strong>max_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Same as <em>min_triangle_edge_length</em> but
-upper bound</li>
-<li><strong>bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Bin size in A, relevant to generate hash map keys</li>
-<li><strong>flags</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Flag in range [0,63] for every coordinate in <em>positions</em>.
-They’re also added to the hash map keys (default: 0).
+are skipped</p></li>
+<li><p><strong>max_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Same as <em>min_triangle_edge_length</em> but
+upper bound</p></li>
+<li><p><strong>bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bin size in A, relevant to generate hash map keys</p></li>
+<li><p><strong>flags</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Flag in range [0,63] for every coordinate in <em>positions</em>.
+They’re also added to the hash map keys (default: 0).
This means that additionally to having a matching
relative position, the coordinates must also have a
matching flag in the detection/refinement stage.
If not provided (in the query and in the search),
-only coordinates matter.</li>
-<li><strong>query_list</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal"><span class="pre">MotifQuery</span></code></a>) – E pluribus unum</li>
+only coordinates matter.</p></li>
+<li><p><strong>query_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifQuery</span></code></a>) – E pluribus unum</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Save" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves the query down to disk</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – filename</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – filename</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.MotifQuery.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Load" title="Permalink to this definition">¶</a></dt>
<dd><p>Load query from disk</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – filename</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – filename</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.GetPositions">
-<code class="descname">GetPositions</code><span class="sig-paren">(</span><em>query_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetPositions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetPositions</code><span class="sig-paren">(</span><em class="sig-param">query_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns coordinates of specified query</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>query_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Query from which you want the positions</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>query_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Query from which you want the positions</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.GetIdentifiers">
-<code class="descname">GetIdentifiers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetIdentifiers" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetIdentifiers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetIdentifiers" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a list of all query identifiers.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.GetN">
-<code class="descname">GetN</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetN" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetN</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetN" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of queries</p>
</dd></dl>
@@ -572,23 +524,23 @@ only coordinates matter.</li>
<dl class="class">
<dt id="promod3.modelling.MotifMatch">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifMatch</code><a class="headerlink" href="#promod3.modelling.MotifMatch" title="Permalink to this definition">¶</a></dt>
-<dd><p>Object that holds information about a match found in <a class="reference internal" href="#promod3.modelling.FindMotifs" title="promod3.modelling.FindMotifs"><code class="xref py py-meth docutils literal"><span class="pre">FindMotifs()</span></code></a></p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifMatch</code><a class="headerlink" href="#promod3.modelling.MotifMatch" title="Permalink to this definition">¶</a></dt>
+<dd><p>Object that holds information about a match found in <a class="reference internal" href="#promod3.modelling.FindMotifs" title="promod3.modelling.FindMotifs"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FindMotifs()</span></code></a></p>
<dl class="attribute">
<dt id="promod3.modelling.MotifMatch.query_idx">
-<code class="descname">query_idx</code><a class="headerlink" href="#promod3.modelling.MotifMatch.query_idx" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">query_idx</code><a class="headerlink" href="#promod3.modelling.MotifMatch.query_idx" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of matching query</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.MotifMatch.mat">
-<code class="descname">mat</code><a class="headerlink" href="#promod3.modelling.MotifMatch.mat" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">mat</code><a class="headerlink" href="#promod3.modelling.MotifMatch.mat" title="Permalink to this definition">¶</a></dt>
<dd><p>Transformation matrix to superpose matching query onto target</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.MotifMatch.alignment">
-<code class="descname">alignment</code><a class="headerlink" href="#promod3.modelling.MotifMatch.alignment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">alignment</code><a class="headerlink" href="#promod3.modelling.MotifMatch.alignment" title="Permalink to this definition">¶</a></dt>
<dd><p>List of tuples which define matching pairs of query/target coordinates</p>
</dd></dl>
@@ -596,34 +548,30 @@ only coordinates matter.</li>
<dl class="method">
<dt id="promod3.modelling.FindMotifs">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FindMotifs</code><span class="sig-paren">(</span><em class="sig-param">query</em>, <em class="sig-param">target_positions</em>, <em class="sig-param">hash_tresh=0.4</em>, <em class="sig-param">distance_thresh=1.0</em>, <em class="sig-param">refine_thresh=0.7</em>, <em class="sig-param">flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs the detection and refinement stages of the geometric hashing
algorithm.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>query</strong> – Query to be searched</li>
-<li><strong>target_positions</strong> – Coordinates of the target</li>
-<li><strong>hash_thresh</strong> – Parameter relevant for detection stage</li>
-<li><strong>distance_thresh</strong> – Parameter relevant for refinement stage</li>
-<li><strong>refine_thresh</strong> – Parameter relevant for refinement stage</li>
-<li><strong>flags</strong> – Equivalent to <em>flags</em> in <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal"><span class="pre">MotifQuery</span></code></a>
-constructor. If you didn’t provide anything there,
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>query</strong> – Query to be searched</p></li>
+<li><p><strong>target_positions</strong> – Coordinates of the target</p></li>
+<li><p><strong>hash_thresh</strong> – Parameter relevant for detection stage</p></li>
+<li><p><strong>distance_thresh</strong> – Parameter relevant for refinement stage</p></li>
+<li><p><strong>refine_thresh</strong> – Parameter relevant for refinement stage</p></li>
+<li><p><strong>flags</strong> – Equivalent to <em>flags</em> in <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifQuery</span></code></a>
+constructor. If you didn’t provide anything there,
this can be ignored. Only the actual coordinates
-matter in this case.</li>
+matter in this case.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">All found matches</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifMatch" title="promod3.modelling.MotifMatch"><code class="xref py py-class docutils literal"><span class="pre">MotifMatch</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>All found matches</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifMatch" title="promod3.modelling.MotifMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifMatch</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -636,45 +584,70 @@ matter in this case.</li>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Modelling Algorithms</a><ul>
-<li><a class="reference internal" href="#rigid-blocks">Rigid Blocks</a></li>
-<li><a class="reference internal" href="#de-novo-modelling">De Novo Modelling</a></li>
-<li><a class="reference internal" href="#motif-finder">Motif Finder</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="sidechain_reconstruction.html" title="previous chapter">Sidechain Reconstruction</a></li>
- <li>Next: <a href="../sidechain/index.html" title="next chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ <li>Next: <a href="../sidechain/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/algorithms.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -683,11 +656,11 @@ matter in this case.</li>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/algorithms.txt"
+ <a href="../_sources/modelling/algorithms.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index ea282aa48fc8a6cb13b16a999ad42fbf8abd0f51..2fb66babc2f89ea3f53639d525dde37dbe8d04c6 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Handling Gaps — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Handling Gaps — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
<link rel="prev" title="Model Checking" href="model_checking.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -55,236 +41,210 @@ classes / functions are used within the modelling pipeline.</p>
<h2>Gap classes<a class="headerlink" href="#gap-classes" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.StructuralGap">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">StructuralGap</code><span class="sig-paren">(</span><em>before</em>, <em>after</em>, <em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">StructuralGap</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">after</em>, <em class="sig-param">seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap" title="Permalink to this definition">¶</a></dt>
<dd><p>Describes a structural gap, i.e. a loop to be modeled. The gap may either be
terminal or between two defined regions. The gap stores information of the
last residue before and the first residue after the gap as well as the
sequence of gap. Gaps at the N- and C-terminals can be defined by passing
invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
-<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal"><span class="pre">seq</span></code></a></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></p></li>
+<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seq</span></code></a></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#RuntimeError" title="(in Python v3.6)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if both residues are invalid or when both
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if both residues are invalid or when both
are valid and:</p>
-<ul class="last simple">
-<li>residues are from different chains (if both valid)</li>
-<li><cite>before</cite> is located after <cite>after</cite></li>
-<li><cite>seq</cite> has a length which is inconsistent with the gap</li>
+<ul class="simple">
+<li><p>residues are from different chains (if both valid)</p></li>
+<li><p><cite>before</cite> is located after <cite>after</cite></p></li>
+<li><p><cite>seq</cite> has a length which is inconsistent with the gap</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetChainIndex">
-<code class="descname">GetChainIndex</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainIndex" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Index of chain, the gap is belonging to</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetChainIndex</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainIndex" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Index of chain, the gap is belonging to</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetChainName">
-<code class="descname">GetChainName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainName" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Name of chain, the gap is belonging to</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetChainName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainName" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Name of chain, the gap is belonging to</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetChain">
-<code class="descname">GetChain</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChain" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetChain</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChain" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Chain, the gap is belonging to</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.IsNTerminal">
-<code class="descname">IsNTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsNTerminal" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff gap is N-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a> is invalid
-and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a> is valid)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">IsNTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsNTerminal" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, iff gap is N-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a> is invalid
+and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a> is valid)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.IsCTerminal">
-<code class="descname">IsCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsCTerminal" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff gap is C-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a> is valid
-and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a> is invalid)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">IsCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsCTerminal" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, iff gap is C-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a> is valid
+and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a> is invalid)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.IsTerminal">
-<code class="descname">IsTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsTerminal" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff gap is N- or C-terminal</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">IsTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsTerminal" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, iff gap is N- or C-terminal</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.ShiftCTerminal">
-<code class="descname">ShiftCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ShiftCTerminal" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ShiftCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ShiftCTerminal" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to shift gap by one position towards C-terminal. Only possible if new
-gap is not terminal and it doesn’t try to shift the gap past another gap.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff shift succeeded (gap is only updated in that case)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+gap is not terminal and it doesn’t try to shift the gap past another gap.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, iff shift succeeded (gap is only updated in that case)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.ExtendAtNTerm">
-<code class="descname">ExtendAtNTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtNTerm" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ExtendAtNTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtNTerm" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to extend gap at N-terminal end of gap.
-Only possible if the gap is not at N-terminal and it doesn’t try to
+Only possible if the gap is not at N-terminal and it doesn’t try to
extend the gap past another gap.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff extend succeeded (gap is only updated in that case)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, iff extend succeeded (gap is only updated in that case)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.ExtendAtCTerm">
-<code class="descname">ExtendAtCTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtCTerm" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ExtendAtCTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtCTerm" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to extend gap at C-terminal end of gap.
-Only possible if the gap is not at C-terminal and it doesn’t try to
+Only possible if the gap is not at C-terminal and it doesn’t try to
extend the gap past another gap.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff extend succeeded (gap is only updated in that case)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, iff extend succeeded (gap is only updated in that case)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetLength">
-<code class="descname">GetLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetLength" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Length of the gap.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetLength" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Length of the gap.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.Copy">
-<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Copy of the gap.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Copy of the gap.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.length">
-<code class="descname">length</code><a class="headerlink" href="#promod3.modelling.StructuralGap.length" title="Permalink to this definition">¶</a></dt>
-<dd><p>Alias for <a class="reference internal" href="#promod3.modelling.StructuralGap.GetLength" title="promod3.modelling.StructuralGap.GetLength"><code class="xref py py-meth docutils literal"><span class="pre">GetLength()</span></code></a> (read-only, <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<code class="sig-name descname">length</code><a class="headerlink" href="#promod3.modelling.StructuralGap.length" title="Permalink to this definition">¶</a></dt>
+<dd><p>Alias for <a class="reference internal" href="#promod3.modelling.StructuralGap.GetLength" title="promod3.modelling.StructuralGap.GetLength"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLength()</span></code></a> (read-only, <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.seq">
-<code class="descname">seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.seq" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sequence string for the gap (read-only, <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>)</p>
+<code class="sig-name descname">seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.seq" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sequence string for the gap (read-only, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
-<code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<code class="sig-name descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
-<code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<code class="sig-name descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.full_seq">
-<code class="descname">full_seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.full_seq" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">full_seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.full_seq" title="Permalink to this definition">¶</a></dt>
<dd><p>Full sequence, including stem residues (read-only)</p>
</dd></dl>
@@ -292,21 +252,21 @@ extend the gap past another gap.</p>
<dl class="class">
<dt id="promod3.modelling.StructuralGapList">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">StructuralGapList</code><a class="headerlink" href="#promod3.modelling.StructuralGapList" title="Permalink to this definition">¶</a></dt>
-<dd><p>Represents a <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>.</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">StructuralGapList</code><a class="headerlink" href="#promod3.modelling.StructuralGapList" title="Permalink to this definition">¶</a></dt>
+<dd><p>Represents a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.</p>
</dd></dl>
</div>
<div class="section" id="gap-extender-classes">
<h2>Gap Extender classes<a class="headerlink" href="#gap-extender-classes" title="Permalink to this headline">¶</a></h2>
-<p>The extender classes work on a given <a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a> and provide an
+<p>The extender classes work on a given <a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a> and provide an
Extend() function to propose new gaps for loop modelling. The function returns
False if no new extension possible.</p>
<dl class="class">
<dt id="promod3.modelling.GapExtender">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">GapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GapExtender</code><span class="sig-paren">(</span><em class="sig-param">gap</em>, <em class="sig-param">seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender" title="Permalink to this definition">¶</a></dt>
<dd><p>The extender cycles through the following steps:</p>
-<div class="highlight-none"><div class="highlight"><pre><span></span> -
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span> -
--
--
---
@@ -318,174 +278,150 @@ False if no new extension possible.</p>
----
</pre></div>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">An exception if a terminal gap is used to construct this.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>An exception if a terminal gap is used to construct this.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.GapExtender.Extend">
-<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to extend <em>gap</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">False, if the <em>gap</em> cannot be extended any further. This happens
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>False, if the <em>gap</em> cannot be extended any further. This happens
if it reaches a terminal or another insertion gap.
Otherwise, the <em>gap</em> passed to the constructor is changed.
The gaps are extended with ascending length and will always have
-valid termini.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+valid termini.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.FullGapExtender">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">FullGapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>seqres</em>, <em>max_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FullGapExtender</code><span class="sig-paren">(</span><em class="sig-param">gap</em>, <em class="sig-param">seqres</em>, <em class="sig-param">max_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender" title="Permalink to this definition">¶</a></dt>
<dd><p>Cycles as GapExtender, but continues even if another gap was encountered.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
-<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
-<li>If -1, all possible non-terminal gaps are returned.</li>
-<li>If >= 0, this restricts the max. gap-length
-(w/o termini) producable by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
+<li><p>If -1, all possible non-terminal gaps are returned.</p></li>
+<li><p>If >= 0, this restricts the max. gap-length
+(w/o termini) producable by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
</ul>
-</li>
+</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">An exception if a terminal gap is used to construct this.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>An exception if a terminal gap is used to construct this.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.FullGapExtender.Extend">
-<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to extend <em>gap</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">False, if the <em>gap</em> cannot be extended without exceeding <em>max_length</em>.
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>False, if the <em>gap</em> cannot be extended without exceeding <em>max_length</em>.
Otherwise, the <em>gap</em> passed to the constructor is changed.
The gaps are extended with ascending length and will always have
-valid termini.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+valid termini.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ScoringGapExtender">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScoringGapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>extension_penalty</em>, <em>penalties</em>, <em>seqres</em>, <em>max_length=-2</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScoringGapExtender</code><span class="sig-paren">(</span><em class="sig-param">gap</em>, <em class="sig-param">extension_penalty</em>, <em class="sig-param">penalties</em>, <em class="sig-param">seqres</em>, <em class="sig-param">max_length=-2</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender" title="Permalink to this definition">¶</a></dt>
<dd><p>The extender scores possible gap extensions and returns them in order of
-their score when <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a> is called.
+their score when <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a> is called.
The score is penalized according to length and according to certain (well
conserved) regions in the structure as defined by <em>penalties</em>.
score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalties</cite> [i] )
(i = resnum - 1 of residues in extension)</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for length of gap.</li>
-<li><strong>penalties</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
-<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
-<li>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a>
-(i.e. it stops at gaps and termini).</li>
-<li>If -1, all possible non-terminal gaps are returned.</li>
-<li>If >= 0, this restricts the max. gap-length (w/o termini)
-producable by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
+<li><p><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for length of gap.</p></li>
+<li><p><strong>penalties</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
+<li><p>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a>
+(i.e. it stops at gaps and termini).</p></li>
+<li><p>If -1, all possible non-terminal gaps are returned.</p></li>
+<li><p>If >= 0, this restricts the max. gap-length (w/o termini)
+producable by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
</ul>
-</li>
+</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">An exception if a terminal gap is used to construct this.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>An exception if a terminal gap is used to construct this.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.ScoringGapExtender.Extend">
-<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to extend <em>gap</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">False, if the gap cannot be extended any further.
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>False, if the gap cannot be extended any further.
Otherwise, <em>gap</em> is changed and returned in ascending score.
-The updated <em>gap</em> will always have valid termini.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+The updated <em>gap</em> will always have valid termini.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ShiftExtension">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ShiftExtension</code><span class="sig-paren">(</span><em>n_num</em>, <em>c_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension" title="Permalink to this definition">¶</a></dt>
-<dd><p>Implements the underlying extension scheme of the <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ShiftExtension</code><span class="sig-paren">(</span><em class="sig-param">n_num</em>, <em class="sig-param">c_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension" title="Permalink to this definition">¶</a></dt>
+<dd><p>Implements the underlying extension scheme of the <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
It is not associated to any structural data, it just spits out the
residue numbers according to the extension scheme described above.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_num</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – N residue number to start with</li>
-<li><strong>c_num</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – C residue number to start with</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_num</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – N residue number to start with</p></li>
+<li><p><strong>c_num</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – C residue number to start with</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.ShiftExtension.Extend">
-<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension.Extend" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The next residue numbers for n_stem and c_stem</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension.Extend" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The next residue numbers for n_stem and c_stem</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -495,114 +431,98 @@ residue numbers according to the extension scheme described above.</p>
<h2>Gap Handling Functions<a class="headerlink" href="#gap-handling-functions" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.CountEnclosedGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">CountEnclosedGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedGaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CountEnclosedGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedGaps" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.CountEnclosedInsertions">
-<code class="descclassname">promod3.modelling.</code><code class="descname">CountEnclosedInsertions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedInsertions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CountEnclosedInsertions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedInsertions" title="Permalink to this definition">¶</a></dt>
<dd><p>Counts all gaps from <cite>mhandle</cite> which are fully enclosed by given <cite>gap</cite>.
This is either all gaps or only insertions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Number of gaps.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Number of gaps.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ClearGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">ClearGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ClearGaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ClearGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ClearGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes all gaps from <cite>mhandle</cite> which are fully enclosed by given <cite>gap</cite>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Index of next gap in mhandle.gaps after removal.
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Index of next gap in mhandle.gaps after removal.
Returns -1 if last gap was removed or no gaps in <em>mhandle</em>.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#RuntimeError" title="(in Python v3.6)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if any gap in mhandle.gaps is only partially
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if any gap in mhandle.gaps is only partially
enclosed by given gap.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.InsertLoopClearGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">InsertLoopClearGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>bb_list</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoopClearGaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">InsertLoopClearGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">bb_list</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoopClearGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Insert loop into model, update scoring environments and remove all gaps from
-<em>mhandle</em> which are fully enclosed by given <em>gap</em> (see <a class="reference internal" href="pipeline.html#promod3.modelling.InsertLoop" title="promod3.modelling.InsertLoop"><code class="xref py py-meth docutils literal"><span class="pre">InsertLoop()</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ClearGaps" title="promod3.modelling.ClearGaps"><code class="xref py py-meth docutils literal"><span class="pre">ClearGaps()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</li>
-<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – Gap defining range of loop to insert (must be consistent!).</li>
+<em>mhandle</em> which are fully enclosed by given <em>gap</em> (see <a class="reference internal" href="pipeline.html#promod3.modelling.InsertLoop" title="promod3.modelling.InsertLoop"><code class="xref py py-meth docutils literal notranslate"><span class="pre">InsertLoop()</span></code></a> and
+<a class="reference internal" href="#promod3.modelling.ClearGaps" title="promod3.modelling.ClearGaps"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ClearGaps()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</p></li>
+<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range of loop to insert (must be consistent!).</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Index of next gap in mhandle.gaps after removal.
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Index of next gap in mhandle.gaps after removal.
Returns -1 if last gap was removed or no gaps in <em>mhandle</em>.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#RuntimeError" title="(in Python v3.6)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and <em>gap</em> are inconsistent or
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and <em>gap</em> are inconsistent or
if any gap in mhandle.gaps is only partially enclosed by <em>gap</em>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.MergeGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">MergeGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MergeGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Merges two gaps <cite>mhandle.gaps[index]</cite> and <cite>mhandle.gaps[index+1]</cite>.
The residues in between the gaps are removed from <cite>mhandle.model</cite> and added
to the new <cite>mhandle.gaps[index]</cite>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of gap to merge with next one.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of gap to merge with next one.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#RuntimeError" title="(in Python v3.6)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if indices out of range or if trying to merge
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if indices out of range or if trying to merge
gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -615,21 +535,45 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Handling Gaps</a><ul>
-<li><a class="reference internal" href="#gap-classes">Gap classes</a></li>
-<li><a class="reference internal" href="#gap-extender-classes">Gap Extender classes</a></li>
-<li><a class="reference internal" href="#gap-handling-functions">Gap Handling Functions</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="model_checking.html" title="previous chapter">Model Checking</a></li>
<li>Next: <a href="loop_candidates.html" title="next chapter">Handling Loop Candidates</a></li>
</ul></li>
@@ -637,23 +581,24 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/gap_handling.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -662,11 +607,11 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/gap_handling.txt"
+ <a href="../_sources/modelling/gap_handling.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index e4abbbb34bba9e7e7cd26d5fb06700be81c43a27..b0f4a3f384cf9e6df550d58a4a956a296c5bd696 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>modelling - Protein Modelling — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>modelling - Protein Modelling — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Modelling Pipeline" href="pipeline.html" />
<link rel="prev" title="Singularity" href="../container/singularity.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,7 +34,7 @@
<div class="body" role="main">
<div class="section" id="module-promod3.modelling">
-<span id="modelling-protein-modelling"></span><h1><a class="reference internal" href="#module-promod3.modelling" title="promod3.modelling: Protein Modelling"><code class="xref py py-mod docutils literal"><span class="pre">modelling</span></code></a> - Protein Modelling<a class="headerlink" href="#module-promod3.modelling" title="Permalink to this headline">¶</a></h1>
+<span id="modelling-protein-modelling"></span><h1><a class="reference internal" href="#module-promod3.modelling" title="promod3.modelling: Protein Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code></a> - Protein Modelling<a class="headerlink" href="#module-promod3.modelling" title="Permalink to this headline">¶</a></h1>
<p>High-level functionality for protein modelling. The goal is to model a given
target sequence (or list of sequences for oligomers) given some template data.
Commonly, the template does not cover the full target. This module offers
@@ -56,8 +42,8 @@ capabilities to extract useful template data for the target and to fill the
remaining structural data to create a full model of the target. In its simplest
form, you can use a target-template alignment and a template structure to create
a model fully automatically as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
<span class="c1"># get raw model</span>
<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
@@ -77,6 +63,7 @@ a model fully automatically as follows:</p>
<li class="toctree-l2"><a class="reference internal" href="pipeline.html#build-raw-modelling-handle">Build Raw Modelling Handle</a></li>
<li class="toctree-l2"><a class="reference internal" href="pipeline.html#the-default-pipeline">The Default Pipeline</a></li>
<li class="toctree-l2"><a class="reference internal" href="pipeline.html#modelling-steps">Modelling Steps</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pipeline.html#alignment-fiddling">Alignment Fiddling</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="model_checking.html">Model Checking</a><ul>
@@ -132,7 +119,41 @@ a model fully automatically as follows:</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
@@ -143,23 +164,24 @@ a model fully automatically as follows:</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -168,11 +190,11 @@ a model fully automatically as follows:</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/index.txt"
+ <a href="../_sources/modelling/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 588b25acc2afa21f28834126cc58c4755d72eff0..5f918e03198370377d2581288bc971fb02845ee3 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Handling Loop Candidates — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Handling Loop Candidates — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
<link rel="prev" title="Handling Gaps" href="gap_handling.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -49,14 +35,14 @@
<div class="section" id="handling-loop-candidates">
<h1>Handling Loop Candidates<a class="headerlink" href="#handling-loop-candidates" title="Permalink to this headline">¶</a></h1>
-<p>For convenience, we provide the <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a> class as a container of
+<p>For convenience, we provide the <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a> class as a container of
loop candidates with consistent length and sequence among them. It can either be
filled manually or generated using static filling functions using the
-functionality from the <a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a> or Monte Carlo algorithms.
+functionality from the <a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a> or Monte Carlo algorithms.
Once it contains candidates you can apply closing, scoring or clustering
algorithms on all loop candidates. Example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
<span class="c1"># let's load a crambin structure from the pdb</span>
<span class="n">crambin</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
@@ -114,174 +100,157 @@ algorithms on all loop candidates. Example:</p>
<h2>The LoopCandidates class<a class="headerlink" href="#the-loopcandidates-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.LoopCandidates">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">LoopCandidates</code><span class="sig-paren">(</span><em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">LoopCandidates</code><span class="sig-paren">(</span><em class="sig-param">seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates" title="Permalink to this definition">¶</a></dt>
<dd><p>Initializes an empty container of loop candidates.</p>
-<p>Candidates can be accessed and iterated as if it was a <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence being enforced for all candidates</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+<p>Candidates can be accessed and iterated as if it was a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence being enforced for all candidates</p>
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.modelling.LoopCandidates.FillFromDatabase">
-<em class="property">static </em><code class="descname">FillFromDatabase</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>seq</em>, <em>frag_db</em>, <em>structural_db</em>, <em>extended_search=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">FillFromDatabase</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">seq</em>, <em class="sig-param">frag_db</em>, <em class="sig-param">structural_db</em>, <em class="sig-param">extended_search=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches for loop candidates matching the length (number of residues in
<em>seq</em>) and geometry (of <em>n_stem</em> and <em>c_stem</em>) of the loop to be modelled in
a fragment database.</p>
-<p>This call also adds fragment infos (<a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal"><span class="pre">HasFragmentInfos()</span></code></a> will be True).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
-<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
-<em>n_stem</em> and <em>c_stem</em></li>
-<li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – The fragment database</li>
-<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – The according structural database</li>
-<li><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether search should be extended to fragments
+<p>This call also adds fragment infos (<a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> will be True).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</p></li>
+<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
+<em>n_stem</em> and <em>c_stem</em></p></li>
+<li><p><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – The fragment database</p></li>
+<li><p><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – The according structural database</p></li>
+<li><p><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether search should be extended to fragments
matching the geometry of the <em>n_stem</em> and <em>c_stem</em>
-a bit less precisely.</li>
+a bit less precisely.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A list of loop candidates</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A list of loop candidates</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
atoms.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler">
-<em class="property">static </em><code class="descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em>seq</em>, <em>num_loops</em>, <em>steps</em>, <em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em class="sig-param">seq</em>, <em class="sig-param">num_loops</em>, <em class="sig-param">steps</em>, <em class="sig-param">sampler</em>, <em class="sig-param">closer</em>, <em class="sig-param">scorer</em>, <em class="sig-param">cooler</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em>initial_bb</em>, <em>seq</em>, <em>num_loops</em>, <em>steps</em>, <em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>random_seed=0</em><span class="sig-paren">)</span></dt>
+<em class="property">static </em><code class="sig-name descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em class="sig-param">initial_bb</em>, <em class="sig-param">seq</em>, <em class="sig-param">num_loops</em>, <em class="sig-param">steps</em>, <em class="sig-param">sampler</em>, <em class="sig-param">closer</em>, <em class="sig-param">scorer</em>, <em class="sig-param">cooler</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span></dt>
<dd><p>Uses Monte Carlo simulated annealing to sample the loop to be modelled.
If <em>initial_bb</em> is given, every Monte Carlo run starts from that configuration.</p>
<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<p class="last">The <a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>
+<p class="admonition-title">Warning</p>
+<p>The <a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>
attached to <em>scorer</em> will be altered in the specified stretch.
You might consider the Stash / Pop mechanism of the
-<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
+<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
original state once the sampling is done.</p>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>initial_bb</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Initial configuration used for the sampling</li>
-<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence of residues to be sampled</li>
-<li><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of loop candidates to return</li>
-<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
-generated</li>
-<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Used to generate a new configuration at each MC step</li>
-<li><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Used to close the loop after each MC step</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Used to score the generated configurations at each MC step</li>
-<li><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed to feed the random number generator for
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>initial_bb</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Initial configuration used for the sampling</p></li>
+<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be sampled</p></li>
+<li><p><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to return</p></li>
+<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
+generated</p></li>
+<li><p><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Used to generate a new configuration at each MC step</p></li>
+<li><p><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Used to close the loop after each MC step</p></li>
+<li><p><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Used to score the generated configurations at each MC step</p></li>
+<li><p><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</p></li>
+<li><p><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed to feed the random number generator for
accepting/rejecting proposed monte carlo steps.
For every monte carlo run, the random number generator
-gets refreshed and this seed gets increased by 1.</li>
+gets refreshed and this seed gets increased by 1.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The resulting candidates</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code>, if <em>initial_bb</em> is not given and
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The resulting candidates</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code>, if <em>initial_bb</em> is not given and
the Monte Carlo sampler failed to initialize (i.e. stems are too
far apart) or if <em>initial_bb</em> is given and it is inconsistent with
<em>seq</em>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetSequence">
-<code class="descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Sequence</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The Sequence</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.ApplyCCD">
-<code class="descname">ApplyCCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>max_iterations=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>keep_non_converged=false</em>, <em>random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyCCD" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyCCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">max_iterations=1000</em>, <em class="sig-param">rmsd_cutoff=0.1</em>, <em class="sig-param">keep_non_converged=false</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyCCD" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">ApplyCCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>torsion_sampler</em>, <em>max_iterations=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>keep_non_converged=false</em>, <em>random_seed=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyCCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">max_iterations=1000</em>, <em class="sig-param">rmsd_cutoff=0.1</em>, <em class="sig-param">keep_non_converged=false</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">ApplyCCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>torsion_samplers</em>, <em>max_iterations=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>keep_non_converged=false</em>, <em>random_seed=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyCCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">torsion_samplers</em>, <em class="sig-param">max_iterations=1000</em>, <em class="sig-param">rmsd_cutoff=0.1</em>, <em class="sig-param">keep_non_converged=false</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span></dt>
<dd><p>Closes all loop candidates in this container using the CCD algorithm (i.e.
modifies the candidates so that its stem residues match those of <em>n_stem</em>
-and <em>c_stem</em>). CCD (cyclic coordinate descent, see <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD" title="promod3.modelling.CCD"><code class="xref py py-class docutils literal"><span class="pre">CCD</span></code></a>) is an
+and <em>c_stem</em>). CCD (cyclic coordinate descent, see <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD" title="promod3.modelling.CCD"><code class="xref py py-class docutils literal notranslate"><span class="pre">CCD</span></code></a>) is an
iterative minimization algorithm.</p>
<p>If <em>torsion_sampler</em> is given, it is used at each step of the closing to
calculate the probability of the proposed move, which is then accepted or
not depending on a metropolis criterium.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
-should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
-should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>
-of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
-of samplers (one per residue).</li>
-<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximum number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Cutoff in stem residue RMSD used to determine
-convergence</li>
-<li><strong>keep_non_converged</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to keep loop candidates for which the
-closing did not converge</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – seed for random number generator used to
-accept/reject moves in CCD algorithm</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
+of samplers (one per residue).</p></li>
+<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximum number of iterations</p></li>
+<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff in stem residue RMSD used to determine
+convergence</p></li>
+<li><p><strong>keep_non_converged</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to keep loop candidates for which the
+closing did not converge</p></li>
+<li><p><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – seed for random number generator used to
+accept/reject moves in CCD algorithm</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">An index for each kept candidate corresponding to the candidate
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>An index for each kept candidate corresponding to the candidate
index before this function was called. This is useful to keep track
of scores and other data extracted before.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.ApplyKIC">
-<code class="descname">ApplyKIC</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>pivot_one</em>, <em>pivot_two</em>, <em>pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyKIC" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyKIC</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">pivot_one</em>, <em class="sig-param">pivot_two</em>, <em class="sig-param">pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyKIC" title="Permalink to this definition">¶</a></dt>
<dd><p>Closes all loop candidates in this container (i.e. modifies the candidates
so that its stem residues match those of <em>n_stem</em> and <em>c_stem</em>, which are
the stem residues of the loop being modelled), using the KIC algorithm. This
@@ -289,357 +258,318 @@ algorithm finds analytical solutions for closing the loop by modifying the
torsion angles of just three pivot residues. Due to the underlying
mathematical formalism in KIC, up to 16 solutions can be found for every
candidate. This leads to an increase in number of loops.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
-should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
-should match</li>
-<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First pivot residue</li>
-<li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Second pivot residue</li>
-<li><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Third pivot residue</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+should match</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+should match</p></li>
+<li><p><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First pivot residue</p></li>
+<li><p><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Second pivot residue</p></li>
+<li><p><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Third pivot residue</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">An index for each added candidate corresponding to the original
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>An index for each added candidate corresponding to the original
candidate index before this function was called (each candidate can
lead to multiple or no candidates after KIC is applied). This is
useful to keep track of scores and other data extracted before.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.CalculateBackboneScores">
-<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>scorer_env</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateBackboneScores" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">scorer</em>, <em class="sig-param">scorer_env</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateBackboneScores" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>scorer_env</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">scorer</em>, <em class="sig-param">scorer_env</em>, <em class="sig-param">keys</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">keys</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt id="promod3.modelling.LoopCandidates.CalculateAllAtomScores">
-<code class="descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateAllAtomScores" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateAllAtomScores" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">keys</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
<dd><p>Calculate backbone / all-atom scores for each loop candidate.
-Note that (unless otherwise noted) a lower “score” is better!</p>
+Note that (unless otherwise noted) a lower “score” is better!</p>
<p>The computed scores are in the same same order as the candidates in here.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the given
-key names (or the ones from <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a>)</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a>) – Backbone scoring object with set environment for the
-particular loop modelling problem.</li>
-<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring environment attached to <em>scorer</em></li>
-<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle set up scoring (see
-<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultBackboneScoring()</span></code></a>
-<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>).</li>
-<li><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Keys of the desired scorers. If not given, we use the set of
-keys given by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="promod3.modelling.ScoringWeights.GetBackboneScoringKeys"><code class="xref py py-meth docutils literal"><span class="pre">ScoringWeights.GetBackboneScoringKeys()</span></code></a> /
-<a class="reference internal" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="promod3.modelling.ScoringWeights.GetAllAtomScoringKeys"><code class="xref py py-meth docutils literal"><span class="pre">ScoringWeights.GetAllAtomScoringKeys()</span></code></a>.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loops belong to.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the given
+key names (or the ones from <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a>)</p></li>
+<li><p><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a>) – Backbone scoring object with set environment for the
+particular loop modelling problem.</p></li>
+<li><p><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring environment attached to <em>scorer</em></p></li>
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle set up scoring (see
+<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a>
+<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>).</p></li>
+<li><p><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Keys of the desired scorers. If not given, we use the set of
+keys given by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="promod3.modelling.ScoringWeights.GetBackboneScoringKeys"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ScoringWeights.GetBackboneScoringKeys()</span></code></a> /
+<a class="reference internal" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="promod3.modelling.ScoringWeights.GetAllAtomScoringKeys"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ScoringWeights.GetAllAtomScoringKeys()</span></code></a>.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loops belong to.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="pipeline.html#promod3.modelling.IsAllAtomScoringSetUp" title="promod3.modelling.IsAllAtomScoringSetUp"><code class="xref py py-func docutils literal"><span class="pre">IsAllAtomScoringSetUp()</span></code></a>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="pipeline.html#promod3.modelling.IsAllAtomScoringSetUp" title="promod3.modelling.IsAllAtomScoringSetUp"><code class="xref py py-func docutils literal notranslate"><span class="pre">IsAllAtomScoringSetUp()</span></code></a>
is False, if <em>keys</em> has a key for which no scorer exists or if
anything is raised when calculating the scores.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.CalculateSequenceProfileScores">
-<code class="descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.LoopCandidates.CalculateStructureProfileScores">
-<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
details, <em>prof.null_model</em> is used for weighting).</p>
-<p>Note that for profile scores a higher “score” is better! So take care when
+<p>Note that for profile scores a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
<p>This requires that each candidate has a connected fragment info into the
-given <em>structure_db</em> (e.g. <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a> must have been called
+given <em>structure_db</em> (e.g. <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a> must have been called
with this DB).</p>
<p>The computed scores are in the same same order as the candidates in here.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
-key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
-<li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
+key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
+<li><p><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a></p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</p></li>
+<li><p><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal"><span class="pre">HasFragmentInfos()</span></code></a> is
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> is
False, if <em>structure_db</em> is incompatible with the stored fragment
infos or if <em>prof</em> has less than <em>offset+len</em> elements (len =
length of loops stored in here).</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.CalculateStemRMSDs">
-<code class="descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em>score_container</em>, <em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStemRMSDs" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStemRMSDs" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates RMSD between the given stems and the first and last residue of
the loop candidates. This first superposes the first loop residue with
-<em>n_stem</em> and then computes the RMSD between the last residue’s N, CA, C
+<em>n_stem</em> and then computes the RMSD between the last residue’s N, CA, C
positions and the corresponding atoms in <em>c_stem</em>.</p>
-<p>Note that this score is only useful before calling <a class="reference internal" href="#promod3.modelling.LoopCandidates.ApplyCCD" title="promod3.modelling.LoopCandidates.ApplyCCD"><code class="xref py py-meth docutils literal"><span class="pre">ApplyCCD()</span></code></a> or
-<a class="reference internal" href="#promod3.modelling.LoopCandidates.ApplyKIC" title="promod3.modelling.LoopCandidates.ApplyKIC"><code class="xref py py-meth docutils literal"><span class="pre">ApplyKIC()</span></code></a>.</p>
+<p>Note that this score is only useful before calling <a class="reference internal" href="#promod3.modelling.LoopCandidates.ApplyCCD" title="promod3.modelling.LoopCandidates.ApplyCCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyCCD()</span></code></a> or
+<a class="reference internal" href="#promod3.modelling.LoopCandidates.ApplyKIC" title="promod3.modelling.LoopCandidates.ApplyKIC"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyKIC()</span></code></a>.</p>
<p>The computed scores are in the same same order as the candidates in here.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
-key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
+key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
atoms.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span></dt>
<dd><p>Same as the <em>score_container</em> variant above, but here we directly return the
score vector instead of storing it in a container.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Score for each candidate (same order as candidates in here).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Score for each candidate (same order as candidates in here).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.Add">
-<code class="descname">Add</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Add" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The loop candidate to be added.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is not
-consistent with internal sequence</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Add</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Add" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The loop candidate to be added.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is not
+consistent with internal sequence</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.AddFragmentInfo">
-<code class="descname">AddFragmentInfo</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.AddFragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Adds a fragment info for the last candidate added with <a class="reference internal" href="#promod3.modelling.LoopCandidates.Add" title="promod3.modelling.LoopCandidates.Add"><code class="xref py py-meth docutils literal"><span class="pre">Add()</span></code></a>. Note
-that these infos are added automatically with <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a> and
+<code class="sig-name descname">AddFragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.AddFragmentInfo" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adds a fragment info for the last candidate added with <a class="reference internal" href="#promod3.modelling.LoopCandidates.Add" title="promod3.modelling.LoopCandidates.Add"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Add()</span></code></a>. Note
+that these infos are added automatically with <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a> and
updated whenever the candidates are copied, removed, clustered etc.. So you
will probably never need this function.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – The fragment info to add.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>fragment</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – The fragment info to add.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.Remove">
-<code class="descname">Remove</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Remove" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Remove</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Remove" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove a loop candidate from the list of candidates.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the candidate that will be removed</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>index</em> is out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the candidate that will be removed</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.HasFragmentInfos">
-<code class="descname">HasFragmentInfos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if each loop candidate has a connected fragment info.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">HasFragmentInfos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if each loop candidate has a connected fragment info.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetFragmentInfo">
-<code class="descname">GetFragmentInfo</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Fragment info connected to loop candidate at given <em>index</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the candidate.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal"><span class="pre">HasFragmentInfos()</span></code></a> is
-False or if <em>index</em> is out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetFragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Fragment info connected to loop candidate at given <em>index</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the candidate.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> is
+False or if <em>index</em> is out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.Extract">
-<code class="descname">Extract</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Container with candidates with given <em>indices</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Candidate indices to extract.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Container with candidates with given <em>indices</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Candidate indices to extract.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetClusters">
-<code class="descname">GetClusters</code><span class="sig-paren">(</span><em>max_dist</em>, <em>superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusters" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetClusters</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusters" title="Permalink to this definition">¶</a></dt>
<dd><p>Clusters the loop candidates according to their pairwise CA RMSD using an
agglomerative hierarchical clustering algorithm. Every candidate gets
assigned a unique cluster. At every clustering step, the two clusters with
shortest distance get merged, with the distance definition being the average
CA RMSD between any of the members of the two clusters.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</li>
-<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</p></li>
+<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
RMSD superposition or simply consider the current
-positions</li>
+positions</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Lists of loop candidate indices into this container</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Lists of loop candidate indices into this container</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetClusteredCandidates">
-<code class="descname">GetClusteredCandidates</code><span class="sig-paren">(</span><em>max_dist</em>, <em>neglect_size_one=True</em>, <em>superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusteredCandidates" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">List of loop candidates clustered as in <a class="reference internal" href="#promod3.modelling.LoopCandidates.GetClusters" title="promod3.modelling.LoopCandidates.GetClusters"><code class="xref py py-meth docutils literal"><span class="pre">GetClusters()</span></code></a>.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</li>
-<li><strong>neglect_size_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether clusters should be added to the returned
-list if they only contain one loop candidate</li>
-<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
+<code class="sig-name descname">GetClusteredCandidates</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">neglect_size_one=True</em>, <em class="sig-param">superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusteredCandidates" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>List of loop candidates clustered as in <a class="reference internal" href="#promod3.modelling.LoopCandidates.GetClusters" title="promod3.modelling.LoopCandidates.GetClusters"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetClusters()</span></code></a>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</p></li>
+<li><p><strong>neglect_size_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether clusters should be added to the returned
+list if they only contain one loop candidate</p></li>
+<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
RMSD superposition or simply consider the current
-positions</li>
+positions</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetLargestCluster">
-<code class="descname">GetLargestCluster</code><span class="sig-paren">(</span><em>max_dist</em>, <em>superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetLargestCluster" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetLargestCluster</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetLargestCluster" title="Permalink to this definition">¶</a></dt>
<dd><p>Instead of performing a full clustering, the algorithm simply searches for
the candidate with the most other candidates having a CA RMSD below
<strong>max_dist</strong>. This candidate then serves as centroid for the return
cluster.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal CA RMSD to cluster centroid</li>
-<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal CA RMSD to cluster centroid</p></li>
+<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
RMSD superposition or simply consider the current
-positions</li>
+positions</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Largest possible cluster with all members having a
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Largest possible cluster with all members having a
CA RMSD below <strong>max_dist</strong> to cluster centroid.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -651,178 +581,164 @@ CA RMSD below <strong>max_dist</strong> to cluster centroid.</p>
on loop candidates.</p>
<dl class="class">
<dt id="promod3.modelling.ScoreContainer">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScoreContainer</code><a class="headerlink" href="#promod3.modelling.ScoreContainer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScoreContainer</code><a class="headerlink" href="#promod3.modelling.ScoreContainer" title="Permalink to this definition">¶</a></dt>
<dd><p>Container to keep vectors of scores (one for each loop candidate) for each
scorer (one vector for each single scorer). Each score vector is guaranteed
to have the same number of values.</p>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.IsEmpty">
-<code class="descname">IsEmpty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.IsEmpty" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if no loop candidates have been scored with any scorer yet.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">IsEmpty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.IsEmpty" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if no loop candidates have been scored with any scorer yet.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Contains">
-<code class="descname">Contains</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if a score vector for this key was already added.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if a score vector for this key was already added.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Get">
-<code class="descname">Get</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Get" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Score vector for the given <em>key</em>.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired score vector.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if there are no scores for that
-<em>key</em>.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Get" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Score vector for the given <em>key</em>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired score vector.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there are no scores for that
+<em>key</em>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Set">
-<code class="descname">Set</code><span class="sig-paren">(</span><em>key</em>, <em>scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Set" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Set scores for that <em>key</em>.</li>
-<li><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Score vector to set.</li>
+<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">key</em>, <em class="sig-param">scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Set" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Set scores for that <em>key</em>.</p></li>
+<li><p><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Score vector to set.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if this container contains other
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if this container contains other
score vectors with a different number of entries.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.GetNumCandidates">
-<code class="descname">GetNumCandidates</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of loop candidates that are scored here. This is the length
-of each score vector in this container.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNumCandidates</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of loop candidates that are scored here. This is the length
+of each score vector in this container.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.LinearCombine">
-<code class="descname">LinearCombine</code><span class="sig-paren">(</span><em>linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.LinearCombine" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Weighted, linear combination of scores.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>,
-values: <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – Weights for each scorer.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a key for
-which no scores were added.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">LinearCombine</code><span class="sig-paren">(</span><em class="sig-param">linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.LinearCombine" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Weighted, linear combination of scores.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each scorer.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a key for
+which no scores were added.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Copy">
-<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Full copy of this container.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Full copy of this container.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Extract">
-<code class="descname">Extract</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Container with scores for a subset of loop candidates.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – List of loop candidate indices to pick
-(in [0, <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCandidates()</span></code></a>-1])</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Container with scores for a subset of loop candidates.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – List of loop candidate indices to pick
+(in [0, <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a>-1])</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Extend">
-<code class="descname">Extend</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Extend each score vector with the score vector of <em>other</em> (must have
matching keys).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Score container to be added to this one.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Score container to be added to this one.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ScoringWeights">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScoringWeights</code><a class="headerlink" href="#promod3.modelling.ScoringWeights" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScoringWeights</code><a class="headerlink" href="#promod3.modelling.ScoringWeights" title="Permalink to this definition">¶</a></dt>
<dd><p>Globally accessible set of weights to be used in scoring. This also defines
a consistent naming of keys used for backbone and all atom scorers as set up
-by <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> and <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>.</p>
+by <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> and <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>.</p>
<p>Different sets of weights are available. You can get general weights
that have been optimized for a non redundant set of loops with lengths [3,14]
(including stem residues). The alternative is to get weights that have only
@@ -831,167 +747,145 @@ different weights for following lengths: [0,1,2,3,4], [5,6], [7,8], [9,10],
[11,12], [13,14].</p>
<p>If you choose to modify the weights, please ensure to set consistently named
keys in here and to use consistently named scorers and scoring computations!</p>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.GetWeights">
-<em class="property">static </em><code class="descname">GetWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetWeights" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Named weights to be used when scoring loop candidates. The default
+<em class="property">static </em><code class="sig-name descname">GetWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db=False</em>, <em class="sig-param">with_aa=False</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetWeights" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Named weights to be used when scoring loop candidates. The default
weights were optimized to give the best performance when choosing
the loop candidate with the lowest combined score. Each set of
weights includes (different) backbone scoring weights, that are
optionally only trained on a subset of loops with corresponding
loop length.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True to choose a set of weights including DB specific scores
-(stem RMSD and profile scores)</li>
-<li><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True to choose a set of weights including all atom scores</li>
-<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to use general weights or their length
-length dependent counterparts.</li>
-<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of full loop. If no weights are available for
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True to choose a set of weights including DB specific scores
+(stem RMSD and profile scores)</p></li>
+<li><p><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True to choose a set of weights including all atom scores</p></li>
+<li><p><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to use general weights or their length
+length dependent counterparts.</p></li>
+<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of full loop. If no weights are available for
this length or when <em>loop_length</em> is -1, the general
-weights are returned.</li>
+weights are returned.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.SetWeights">
-<em class="property">static </em><code class="descname">SetWeights</code><span class="sig-paren">(</span><em>with_db</em>, <em>with_aa</em>, <em>weights</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetWeights" title="Permalink to this definition">¶</a></dt>
-<dd><p>Overwrite a set of weights as returned by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a>.</p>
+<em class="property">static </em><code class="sig-name descname">SetWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db</em>, <em class="sig-param">with_aa</em>, <em class="sig-param">weights</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetWeights" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overwrite a set of weights as returned by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a>.</p>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.GetBackboneWeights">
-<em class="property">static </em><code class="descname">GetBackboneWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneWeights" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a> for backbone scoring as in
-<code class="xref py py-meth docutils literal"><span class="pre">scoring.BackboneOverallScorer.CalculateLinearCombination()</span></code>.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
-<li><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
-<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
-<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
+<em class="property">static </em><code class="sig-name descname">GetBackboneWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db=False</em>, <em class="sig-param">with_aa=False</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneWeights" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a> for backbone scoring as in
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">scoring.BackboneOverallScorer.CalculateLinearCombination()</span></code>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
+<li><p><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
+<li><p><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
+<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.GetAllAtomWeights">
-<em class="property">static </em><code class="descname">GetAllAtomWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomWeights" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a> for all atom scoring as in
-<code class="xref py py-meth docutils literal"><span class="pre">scoring.AllAtomOverallScorer.CalculateLinearCombination()</span></code>.</p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
-<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
-<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
+<em class="property">static </em><code class="sig-name descname">GetAllAtomWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db=False</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomWeights" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a> for all atom scoring as in
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">scoring.AllAtomOverallScorer.CalculateLinearCombination()</span></code>.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
+<li><p><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
+<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.GetStemRMSDsKey">
-<em class="property">static </em><code class="descname">GetStemRMSDsKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetStemRMSDsKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey">
-<em class="property">static </em><code class="descname">GetSequenceProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetSequenceProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.GetStructureProfileScoresKey">
-<em class="property">static </em><code class="descname">GetStructureProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Default key for stem RMSD / sequence profile / structure profile
-scores.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetStructureProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Default key for stem RMSD / sequence profile / structure profile
+scores.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.SetStemRMSDsKey">
-<em class="property">static </em><code class="descname">SetStemRMSDsKey</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">SetStemRMSDsKey</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey">
-<em class="property">static </em><code class="descname">SetSequenceProfileScoresKey</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">SetSequenceProfileScoresKey</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.SetStructureProfileScoresKey">
-<em class="property">static </em><code class="descname">SetStructureProfileScoresKey</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New default key for stem RMSD / sequence profile / structure
-profile scores.</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">SetStructureProfileScoresKey</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New default key for stem RMSD / sequence profile / structure
+profile scores.</p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.GetBackboneScoringKeys">
-<em class="property">static </em><code class="descname">GetBackboneScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">GetBackboneScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.GetAllAtomScoringKeys">
-<em class="property">static </em><code class="descname">GetAllAtomScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">List of backbone / all-atom scorers to be computed for any set of
-weights defined in here.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">GetAllAtomScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>List of backbone / all-atom scorers to be computed for any set of
+weights defined in here.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.modelling.ScoringWeights.SetBackboneScoringKeys">
-<em class="property">static </em><code class="descname">SetBackboneScoringKeys</code><span class="sig-paren">(</span><em>keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">SetBackboneScoringKeys</code><span class="sig-paren">(</span><em class="sig-param">keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.SetAllAtomScoringKeys">
-<em class="property">static </em><code class="descname">SetAllAtomScoringKeys</code><span class="sig-paren">(</span><em>keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New list of backbone / all-atom scorers to be computed for any
-set of weights defined in here.</td>
-</tr>
-</tbody>
-</table>
+<em class="property">static </em><code class="sig-name descname">SetAllAtomScoringKeys</code><span class="sig-paren">(</span><em class="sig-param">keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New list of backbone / all-atom scorers to be computed for any
+set of weights defined in here.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -1000,12 +894,12 @@ set of weights defined in here.</td>
<div class="section" id="example-loop-scoring-in-modelling">
<h2>Example: loop scoring in modelling<a class="headerlink" href="#example-loop-scoring-in-modelling" title="Permalink to this headline">¶</a></h2>
<p>In the example below, we show how we find and choose a loop candidate to close a
-gap for a model. This shows the combined usage of <a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a> to
-keep a consistent modelling environment, <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a> with its
-scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a> for keeping track of scores and
-<a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> to combine scores:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+gap for a model. This shows the combined usage of <a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a> to
+keep a consistent modelling environment, <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a> with its
+scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a> for keeping track of scores and
+<a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> to combine scores:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
<span class="c1"># setup raw model</span>
<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
@@ -1102,21 +996,45 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Handling Loop Candidates</a><ul>
-<li><a class="reference internal" href="#the-loopcandidates-class">The LoopCandidates class</a></li>
-<li><a class="reference internal" href="#keeping-track-of-loop-candidate-scores">Keeping track of loop candidate scores</a></li>
-<li><a class="reference internal" href="#example-loop-scoring-in-modelling">Example: loop scoring in modelling</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="gap_handling.html" title="previous chapter">Handling Gaps</a></li>
<li>Next: <a href="loop_closing.html" title="next chapter">Fitting Loops Into Gaps</a></li>
</ul></li>
@@ -1124,23 +1042,24 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/loop_candidates.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1149,11 +1068,11 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/loop_candidates.txt"
+ <a href="../_sources/modelling/loop_candidates.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index 6fae0f57b785d543b4218d788c87b88ec27e5b1b..2c5c328c7c86d8d86ff0a7fced103c4cdce1947c 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Fitting Loops Into Gaps — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Fitting Loops Into Gaps — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
<link rel="prev" title="Handling Loop Candidates" href="loop_candidates.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -53,12 +39,12 @@
stem residues. ProMod3 implements two algorithms performing this task:</p>
<blockquote>
<div><ul class="simple">
-<li>Cyclic coordinate descent (CCD) <a class="reference internal" href="../references.html#canutescu2003" id="id1">[canutescu2003]</a></li>
-<li>Kinematic closure (KIC) <a class="reference internal" href="../references.html#coutsias2005" id="id2">[coutsias2005]</a></li>
+<li><p>Cyclic coordinate descent (CCD) <a class="reference internal" href="../references.html#canutescu2003" id="id1"><span>[canutescu2003]</span></a></p></li>
+<li><p>Kinematic closure (KIC) <a class="reference internal" href="../references.html#coutsias2005" id="id2"><span>[coutsias2005]</span></a></p></li>
</ul>
</div></blockquote>
<p>In case of small gaps or small issues in the loop you might also consider the
-<a class="reference internal" href="#promod3.modelling.BackboneRelaxer" title="promod3.modelling.BackboneRelaxer"><code class="xref py py-class docutils literal"><span class="pre">BackboneRelaxer</span></code></a>.</p>
+<a class="reference internal" href="#promod3.modelling.BackboneRelaxer" title="promod3.modelling.BackboneRelaxer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneRelaxer</span></code></a>.</p>
<div class="section" id="ccd">
<h2>CCD<a class="headerlink" href="#ccd" title="Permalink to this headline">¶</a></h2>
<p>The ProMod3 implementation of the cyclic coordinate descent first superposes
@@ -75,94 +61,86 @@ than a uniform random number in the range [0,1[, the proposed dihedral pair gets
rejected. Please note, that this increases the probability of non-convergence.</p>
<dl class="class">
<dt id="promod3.modelling.CCD">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CCD</code><a class="headerlink" href="#promod3.modelling.CCD" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CCD</code><a class="headerlink" href="#promod3.modelling.CCD" title="Permalink to this definition">¶</a></dt>
<dd><p>Class, that sets up everything you need to perform a particular loop closing
action.</p>
<dl class="method">
<dt id="promod3.modelling.CCD.CCD">
-<code class="descname">CCD</code><span class="sig-paren">(</span><em>sequence</em>, <em>n_stem</em>, <em>c_stem</em>, <em>torsion_sampler</em>, <em>max_steps</em>, <em>rmsd_cutoff</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.CCD" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CCD</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">max_steps</em>, <em class="sig-param">rmsd_cutoff</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.CCD" title="Permalink to this definition">¶</a></dt>
<dd><p>All runs with this CCD object will be with application of torsion samplers
to avoid moving into unfavourable regions of the backbone dihedrals.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
-If the residue before <em>n_stem</em> doesn’t exist, the
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
-and phi angle (-1.0472) to evaluate the first angle.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
-If the residue after <em>c_stem</em> doesn’t exist, the
+and phi angle (-1.0472) to evaluate the first angle.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
-psi angle (-0.7854) to evaluate the last angle.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>
-of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – To extract probabilities for the analysis of the
+psi angle (-0.7854) to evaluate the last angle.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – To extract probabilities for the analysis of the
backbone dihedrals. Either a list of torsion
samplers (one for for every residue of the loop to
-be closed) or a single one (used for all residues).</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
-be closed has RMSD below the <em>c_stem</em></li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed of random number generator to decide whether new phi/psi pair
-should be accepted.</li>
+be closed) or a single one (used for all residues).</p></li>
+<li><p><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</p></li>
+<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
+be closed has RMSD below the <em>c_stem</em></p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed of random number generator to decide whether new phi/psi pair
+should be accepted.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if a list of torsion samplers is
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if a list of torsion samplers is
given with inconsistent length regarding the sequence. Another
requirement is that all backbone atoms of the stems must be
present.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">CCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>max_steps</em>, <em>rmsd_cutoff</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">CCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">max_steps</em>, <em class="sig-param">rmsd_cutoff</em><span class="sig-paren">)</span></dt>
<dd><p>All runs with this CCD object will be without application of torsion samplers.
This is faster but might lead to weird backbone dihedral pairs.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
-be closed has RMSD below the given <em>c_stem</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</p></li>
+<li><p><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</p></li>
+<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
+be closed has RMSD below the given <em>c_stem</em></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.CCD.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.Close" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Closes given <em>bb_list</em> with the settings set at initialization.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether <em>rmsd_cutoff</em> has been reached</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if the CCD object has been
-initialized with <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> support
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether <em>rmsd_cutoff</em> has been reached</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the CCD object has been
+initialized with <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> support
and the length of the <em>bb_list</em> is not consistent with the initial
-<em>sequence</em>.</td>
-</tr>
-</tbody>
-</table>
+<em>sequence</em>.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -177,55 +155,47 @@ at these pivot residues. Due to the internal mathematical formalism, up to
16 solutions can be found for a given loop closing problem.</p>
<dl class="class">
<dt id="promod3.modelling.KIC">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">KIC</code><a class="headerlink" href="#promod3.modelling.KIC" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">KIC</code><a class="headerlink" href="#promod3.modelling.KIC" title="Permalink to this definition">¶</a></dt>
<dd><p>Class, that sets up everything you need to perform a particular loop closing
action.</p>
<dl class="method">
<dt id="promod3.modelling.KIC.KIC">
-<code class="descname">KIC</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.KIC" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">KIC</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.KIC" title="Permalink to this definition">¶</a></dt>
<dd><p>All runs of this KIC closing object will adapt the input loops to these
stem residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> – Residue describing the stem towards n_ter</li>
-<li><strong>c_stem</strong> – Residue describing the stem towards c_ter</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> – Residue describing the stem towards n_ter</p></li>
+<li><p><strong>c_stem</strong> – Residue describing the stem towards c_ter</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.KIC.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>bb_list</em>, <em>pivot_one</em>, <em>pivot_two</em>, <em>pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.Close" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">pivot_one</em>, <em class="sig-param">pivot_two</em>, <em class="sig-param">pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies KIC algorithm, so that the output loops match the given stem residues</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of first pivot residue</li>
-<li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of second pivot residue</li>
-<li><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of third pivot residue</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</p></li>
+<li><p><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of first pivot residue</p></li>
+<li><p><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of second pivot residue</p></li>
+<li><p><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of third pivot residue</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">List of closed loops (maximum of 16 entries)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> in case of invalid pivot indices.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>List of closed loops (maximum of 16 entries)</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> in case of invalid pivot indices.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -235,235 +205,198 @@ stem residues.</p>
<h2>Relaxing Backbones<a class="headerlink" href="#relaxing-backbones" title="Permalink to this headline">¶</a></h2>
<p>In many cases one wants to quickly relax a loop. This can be useful to close
small gaps in the backbone or resolve the most severe clashes. The
-<a class="reference internal" href="#promod3.modelling.BackboneRelaxer" title="promod3.modelling.BackboneRelaxer"><code class="xref py py-class docutils literal"><span class="pre">BackboneRelaxer</span></code></a> internally sets up a topology for the input loop.
+<a class="reference internal" href="#promod3.modelling.BackboneRelaxer" title="promod3.modelling.BackboneRelaxer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneRelaxer</span></code></a> internally sets up a topology for the input loop.
Once setup, every loop of the same length and sequence can be relaxed by
the relaxer.</p>
<dl class="class">
<dt id="promod3.modelling.BackboneRelaxer">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">BackboneRelaxer</code><span class="sig-paren">(</span><em>bb_list</em>, <em>ff</em>, <em>fix_nterm=True</em>, <em>fix_cterm=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BackboneRelaxer</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">ff</em>, <em class="sig-param">fix_nterm=True</em>, <em class="sig-param">fix_cterm=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up a molecular mechanics topology for given <em>bb_list</em>. Every
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> of same length and sequence can then be
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> of same length and sequence can then be
relaxed. The parametrization is taken from <em>ff</em>, simply neglecting all
interactions to non backbone atoms. The electrostatics get neglected
completely by setting all charges to 0.0.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</li>
-<li><strong>ff</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Source for parametrization</li>
-<li><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</p></li>
+<li><p><strong>ff</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Source for parametrization</p></li>
+<li><p><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
be kept rigid during relaxation
-(C and O are left to move).</li>
-<li><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
+(C and O are left to move).</p></li>
+<li><p><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
should be kept rigid during relaxation
-(N is left to move).</li>
+(N is left to move).</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="class">
<dt>
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">BackboneRelaxer</code><span class="sig-paren">(</span><em>bb_list</em>, <em>density</em>, <em>resolution</em>, <em>fix_nterm=True</em>, <em>fix_cterm=True</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</li>
-<li><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
-be kept rigid during relaxation.</li>
-<li><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
-should be kept rigid during relaxation.</li>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BackboneRelaxer</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">density</em>, <em class="sig-param">resolution</em>, <em class="sig-param">fix_nterm=True</em>, <em class="sig-param">fix_cterm=True</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</p></li>
+<li><p><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
+be kept rigid during relaxation.</p></li>
+<li><p><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
+should be kept rigid during relaxation.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if size of <em>bb_list</em> is below 2</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of <em>bb_list</em> is below 2</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.Run">
-<code class="descname">Run</code><span class="sig-paren">(</span><em>bb_list</em>, <em>steps=100</em>, <em>stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.Run" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Run</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">steps=100</em>, <em class="sig-param">stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.Run" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs steepest descent on given BackboneList. The function possibly fails
if there are particles (almost) on top of each other, resulting in NaN
positions in the OpenMM system. The positions of <strong>bb_list</strong> are not touched
in this case and the function returns an infinit potential energy.
-In Python you can check for that with float(“inf”).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – To be relaxed</li>
-<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – number of steepest descent steps</li>
-<li><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If maximum force acting on a particle
+In Python you can check for that with float(“inf”).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – To be relaxed</p></li>
+<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of steepest descent steps</p></li>
+<li><p><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If maximum force acting on a particle
falls below that threshold, the
-relaxation aborts.</li>
+relaxation aborts.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Forcefield energy upon relaxation, infinity in case of OpenMM Error</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> has not the same
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Forcefield energy upon relaxation, infinity in case of OpenMM Error</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> has not the same
size or sequence as the initial one.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddNRestraint">
-<code class="descname">AddNRestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddNRestraint" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddNRestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddNRestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for nitrogen atom at specified residue</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
-<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddCARestraint">
-<code class="descname">AddCARestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCARestraint" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddCARestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCARestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for CA atom at specified residue</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
-<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddCBRestraint">
-<code class="descname">AddCBRestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCBRestraint" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddCBRestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCBRestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for CB atom at specified residue,
-doesn’t do anything if specified residue is a glycine</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
-<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+doesn’t do anything if specified residue is a glycine</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddCRestraint">
-<code class="descname">AddCRestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCRestraint" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddCRestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCRestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for C atom at specified residue</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
-<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddORestraint">
-<code class="descname">AddORestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddORestraint" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddORestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddORestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for O atom at specified residue</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
-<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.SetNonBondedCutoff">
-<code class="descname">SetNonBondedCutoff</code><span class="sig-paren">(</span><em>nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.SetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetNonBondedCutoff</code><span class="sig-paren">(</span><em class="sig-param">nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.SetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
<dd><p>Defines cutoff to set for non bonded interactions. By default, all atom-
pairs are compared which is the fastest for small backbones (e.g. in
-<a class="reference internal" href="pipeline.html#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-meth docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>). Otherwise, a cutoff around 5 is reasonable as
+<a class="reference internal" href="pipeline.html#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>). Otherwise, a cutoff around 5 is reasonable as
we ignore electrostatics.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Cutoff to set for non bonded interactions. Negative
-means no cutoff.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to set for non bonded interactions. Negative
+means no cutoff.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.GetNonBondedCutoff">
-<code class="descname">GetNonBondedCutoff</code><span class="sig-paren">(</span><em>nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.GetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Cutoff for non bonded interactions.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNonBondedCutoff</code><span class="sig-paren">(</span><em class="sig-param">nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.GetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Cutoff for non bonded interactions.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -472,12 +405,12 @@ means no cutoff.</td>
<div class="section" id="relaxing-all-atom-loops">
<h2>Relaxing All Atom Loops<a class="headerlink" href="#relaxing-all-atom-loops" title="Permalink to this headline">¶</a></h2>
<p>After the reconstruction of loop sidechains with the
-<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor.Reconstruct" title="promod3.modelling.SidechainReconstructor.Reconstruct"><code class="xref py py-meth docutils literal"><span class="pre">Reconstruct()</span></code></a> method of
-<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a>, it may be desired to
-quickly relax the loop. The <a class="reference internal" href="#promod3.modelling.AllAtomRelaxer" title="promod3.modelling.AllAtomRelaxer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomRelaxer</span></code></a> class takes care of that.</p>
+<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor.Reconstruct" title="promod3.modelling.SidechainReconstructor.Reconstruct"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Reconstruct()</span></code></a> method of
+<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a>, it may be desired to
+quickly relax the loop. The <a class="reference internal" href="#promod3.modelling.AllAtomRelaxer" title="promod3.modelling.AllAtomRelaxer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomRelaxer</span></code></a> class takes care of that.</p>
<p>Example usage:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
<span class="c1"># load example (has res. numbering starting at 1)</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
@@ -507,89 +440,77 @@ quickly relax the loop. The <a class="reference internal" href="#promod3.modelli
</div>
<dl class="class">
<dt id="promod3.modelling.AllAtomRelaxer">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">AllAtomRelaxer</code><span class="sig-paren">(</span><em>sc_data</em>, <em>mm_system_creator</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">AllAtomRelaxer</code><span class="sig-paren">(</span><em class="sig-param">sc_data</em>, <em class="sig-param">mm_system_creator</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup relaxer for a given sidechain reconstruction result and a given MM
system creator, which takes care of generating a simulation object.</p>
<p>N/C stems of loop are fixed if they are non-terminal.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result</li>
-<li><strong>mm_system_creator</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal"><span class="pre">MmSystemCreator</span></code></a>) – System creator to be used here</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result</p></li>
+<li><p><strong>mm_system_creator</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) – System creator to be used here</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.AllAtomRelaxer.Run">
-<code class="descname">Run</code><span class="sig-paren">(</span><em>sc_data</em>, <em>steps=100</em>, <em>stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.Run" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Run</code><span class="sig-paren">(</span><em class="sig-param">sc_data</em>, <em class="sig-param">steps=100</em>, <em class="sig-param">stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.Run" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs steepest descent for this system and writes updated positions into
<em>sc_data.env_pos.all_pos</em>. The function possibly fails
if there are particles (almost) on top of each other, resulting in NaN
positions in the OpenMM system. The positions of <em>sc_data.env_pos.all_pos</em>
are not touched in this case and the function returns an infinit potential
-energy. In Python you can check for that with float(“inf”).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result to be updated</li>
-<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of steepest descent steps</li>
-<li><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If maximum force acting on a particle falls below
-that threshold, the relaxation aborts.</li>
+energy. In Python you can check for that with float(“inf”).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result to be updated</p></li>
+<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of steepest descent steps</p></li>
+<li><p><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If maximum force acting on a particle falls below
+that threshold, the relaxation aborts.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Potential energy after relaxation, infinity in case of OpenMM Error</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Potential energy after relaxation, infinity in case of OpenMM Error</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
the one given in the constructor.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.AllAtomRelaxer.UpdatePositions">
-<code class="descname">UpdatePositions</code><span class="sig-paren">(</span><em>sc_data</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.UpdatePositions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">UpdatePositions</code><span class="sig-paren">(</span><em class="sig-param">sc_data</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.UpdatePositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Resets simulation positions to a new set of positions. It is assumed that
this <em>sc_data</em> object has the same amino acids as loops and surrounding and
the same disulfid bridges as the one given in the constructor.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructionData</span></code></a>) – Get new positions from <em>sc_data.env_pos.all_pos</em></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
-the one given in the constructor.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Get new positions from <em>sc_data.env_pos.all_pos</em></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
+the one given in the constructor.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.AllAtomRelaxer.GetSystemCreator">
-<code class="descname">GetSystemCreator</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.GetSystemCreator" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MM system creator passed in the constructor</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal"><span class="pre">MmSystemCreator</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSystemCreator</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.GetSystemCreator" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>MM system creator passed in the constructor</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -604,22 +525,45 @@ the one given in the constructor.</td>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Fitting Loops Into Gaps</a><ul>
-<li><a class="reference internal" href="#ccd">CCD</a></li>
-<li><a class="reference internal" href="#kic">KIC</a></li>
-<li><a class="reference internal" href="#relaxing-backbones">Relaxing Backbones</a></li>
-<li><a class="reference internal" href="#relaxing-all-atom-loops">Relaxing All Atom Loops</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="loop_candidates.html" title="previous chapter">Handling Loop Candidates</a></li>
<li>Next: <a href="monte_carlo.html" title="next chapter">Generating Loops De Novo</a></li>
</ul></li>
@@ -627,23 +571,24 @@ the one given in the constructor.</td>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/loop_closing.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -652,11 +597,11 @@ the one given in the constructor.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/loop_closing.txt"
+ <a href="../_sources/modelling/loop_closing.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 28d34a0c6af03e6c228515eb3f4d8c45b79cef45..9905519bfada6b68f7a73066a1f215f45ff3591a 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Model Checking — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Model Checking — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Gaps" href="gap_handling.html" />
<link rel="prev" title="Modelling Pipeline" href="pipeline.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -55,101 +41,87 @@ functionality is used within the modelling pipeline.</p>
<h2>Detecting Ring Punches<a class="headerlink" href="#detecting-ring-punches" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.GetRings">
-<code class="descclassname">promod3.modelling.</code><code class="descname">GetRings</code><span class="sig-paren">(</span><em>ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRings" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GetRings</code><span class="sig-paren">(</span><em class="sig-param">ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRings" title="Permalink to this definition">¶</a></dt>
<dd><p>Get rings for a protein structure.
A ring is only added if all ring-atoms exist or if it is a proline and
three of the atoms exist (center and radii are estimated then).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
tuple with:
-center (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
-radius (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
-</tr>
-</tbody>
-</table>
+center (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
+radius (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>),
+residue (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.GetRingPunches">
-<code class="descclassname">promod3.modelling.</code><code class="descname">GetRingPunches</code><span class="sig-paren">(</span><em>rings</em>, <em>ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRingPunches" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GetRingPunches</code><span class="sig-paren">(</span><em class="sig-param">rings</em>, <em class="sig-param">ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRingPunches" title="Permalink to this definition">¶</a></dt>
<dd><p>Get list of residues with rings that are punched by the given structure.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.HasRingPunches">
-<code class="descclassname">promod3.modelling.</code><code class="descname">HasRingPunches</code><span class="sig-paren">(</span><em>rings</em>, <em>ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.HasRingPunches" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">HasRingPunches</code><span class="sig-paren">(</span><em class="sig-param">rings</em>, <em class="sig-param">ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.HasRingPunches" title="Permalink to this definition">¶</a></dt>
<dd><p>Check if any ring is punched by the given structure.
-This check is faster than using <a class="reference internal" href="#promod3.modelling.GetRingPunches" title="promod3.modelling.GetRingPunches"><code class="xref py py-func docutils literal"><span class="pre">GetRingPunches()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+This check is faster than using <a class="reference internal" href="#promod3.modelling.GetRingPunches" title="promod3.modelling.GetRingPunches"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRingPunches()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">True, iff any ring is punched</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>True, iff any ring is punched</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FilterCandidates">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FilterCandidates</code><span class="sig-paren">(</span><em>candidates</em>, <em>model</em>, <em>gap</em>, <em>orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidates" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FilterCandidates</code><span class="sig-paren">(</span><em class="sig-param">candidates</em>, <em class="sig-param">model</em>, <em class="sig-param">gap</em>, <em class="sig-param">orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidates" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove loop candidates if they cause ring punches.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>candidates</strong> (<code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
-Offending candidates are removed from this list.</li>
-<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
-<li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li>
-<li><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
-must have as many elements as <em>candidates</em>.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>candidates</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
+Offending candidates are removed from this list.</p></li>
+<li><p><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</p></li>
+<li><p><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</p></li>
+<li><p><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
+must have as many elements as <em>candidates</em>.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FilterCandidatesWithSC">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FilterCandidatesWithSC</code><span class="sig-paren">(</span><em>candidates</em>, <em>model</em>, <em>gap</em>, <em>orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidatesWithSC" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FilterCandidatesWithSC</code><span class="sig-paren">(</span><em class="sig-param">candidates</em>, <em class="sig-param">model</em>, <em class="sig-param">gap</em>, <em class="sig-param">orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidatesWithSC" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove loop candidates if they (with sidechain) cause ring punches.
-See <a class="reference internal" href="#promod3.modelling.FilterCandidates" title="promod3.modelling.FilterCandidates"><code class="xref py py-func docutils literal"><span class="pre">FilterCandidates()</span></code></a>.</p>
+See <a class="reference internal" href="#promod3.modelling.FilterCandidates" title="promod3.modelling.FilterCandidates"><code class="xref py py-func docutils literal notranslate"><span class="pre">FilterCandidates()</span></code></a>.</p>
</dd></dl>
</div>
@@ -157,10 +129,10 @@ See <a class="reference internal" href="#promod3.modelling.FilterCandidates" tit
<h2>Model Checking With MolProbity<a class="headerlink" href="#model-checking-with-molprobity" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.RunMolProbity">
-<code class="descclassname">promod3.modelling.</code><code class="descname">RunMolProbity</code><span class="sig-paren">(</span><em>target_pdb</em>, <em>molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbity" title="Permalink to this definition">¶</a></dt>
-<dd><p>Run <code class="docutils literal"><span class="pre">MolProbity</span></code> from <code class="docutils literal"><span class="pre">Phenix</span></code> on a given PDB file.</p>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RunMolProbity</code><span class="sig-paren">(</span><em class="sig-param">target_pdb</em>, <em class="sig-param">molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbity" title="Permalink to this definition">¶</a></dt>
+<dd><p>Run <code class="docutils literal notranslate"><span class="pre">MolProbity</span></code> from <code class="docutils literal notranslate"><span class="pre">Phenix</span></code> on a given PDB file.</p>
<p>MolProbity score computation: (formula from molprobity source code)</p>
-<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">clashscore</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Clashscore"</span><span class="p">]</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">clashscore</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Clashscore"</span><span class="p">]</span>
<span class="n">rota_out</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Rotamer outliers"</span><span class="p">]</span>
<span class="n">rama_iffy</span> <span class="o">=</span> <span class="mf">100.</span> <span class="o">-</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Ramachandran favored"</span><span class="p">]</span>
<span class="n">mpscore</span> <span class="o">=</span> <span class="p">((</span> <span class="mf">0.426</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">clashscore</span><span class="p">)</span> <span class="p">)</span> <span class="o">+</span>
@@ -168,72 +140,62 @@ See <a class="reference internal" href="#promod3.modelling.FilterCandidates" tit
<span class="p">(</span> <span class="mf">0.25</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">rama_iffy</span> <span class="o">-</span> <span class="mi">2</span><span class="p">))</span> <span class="p">))</span> <span class="o">+</span> <span class="mf">0.5</span>
</pre></div>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>target_pdb</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to PDB file on which to do analysis.</li>
-<li><strong>molprobity_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to <code class="docutils literal"><span class="pre">phenix.molprobity</span></code> executable. If None, it
-searches for it in the <code class="docutils literal"><span class="pre">PATH</span></code> or (if set) in the
-env. variable <code class="docutils literal"><span class="pre">MOLPROBITY_EXECUTABLE</span></code>.
-The function was tested with <code class="docutils literal"><span class="pre">Phenix</span> <span class="pre">1.9-1692</span></code> and
-with <code class="docutils literal"><span class="pre">MolProbity</span> <span class="pre">4.2</span></code> which also includes it.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>target_pdb</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to PDB file on which to do analysis.</p></li>
+<li><p><strong>molprobity_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to <code class="docutils literal notranslate"><span class="pre">phenix.molprobity</span></code> executable. If None, it
+searches for it in the <code class="docutils literal notranslate"><span class="pre">PATH</span></code> or (if set) in the
+env. variable <code class="docutils literal notranslate"><span class="pre">MOLPROBITY_EXECUTABLE</span></code>.
+The function was tested with <code class="docutils literal notranslate"><span class="pre">Phenix</span> <span class="pre">1.9-1692</span></code> and
+with <code class="docutils literal notranslate"><span class="pre">MolProbity</span> <span class="pre">4.2</span></code> which also includes it.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><p>Dictionary with scores produced by MolProbity. Entries:</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><p>Dictionary with scores produced by MolProbity. Entries:</p>
<ul class="simple">
-<li>“Ramachandran outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</li>
-<li>“Ramachandran favored” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</li>
-<li>“Rotamer outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</li>
-<li>“C-beta deviations” (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</li>
-<li>“Clashscore” (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</li>
-<li>“MolProbity score” (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</li>
-<li>“RMS(bonds)” (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</li>
-<li>“RMS(angles)” (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</li>
+<li><p>”Ramachandran outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
+<li><p>”Ramachandran favored” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
+<li><p>”Rotamer outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
+<li><p>”C-beta deviations” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p></li>
+<li><p>”Clashscore” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
+<li><p>”MolProbity score” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
+<li><p>”RMS(bonds)” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
+<li><p>”RMS(angles)” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
</ul>
</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.0/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.RunMolProbityEntity">
-<code class="descclassname">promod3.modelling.</code><code class="descname">RunMolProbityEntity</code><span class="sig-paren">(</span><em>ost_ent</em>, <em>molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbityEntity" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RunMolProbityEntity</code><span class="sig-paren">(</span><em class="sig-param">ost_ent</em>, <em class="sig-param">molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbityEntity" title="Permalink to this definition">¶</a></dt>
<dd><p>Run molprobity from phenix on given OST entity.</p>
-<p>See <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal"><span class="pre">RunMolProbity()</span></code></a> for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
-</tr>
-</tbody>
-</table>
+<p>See <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal notranslate"><span class="pre">RunMolProbity()</span></code></a> for details.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ReportMolProbityScores">
-<code class="descclassname">promod3.modelling.</code><code class="descname">ReportMolProbityScores</code><span class="sig-paren">(</span><em>scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReportMolProbityScores" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ReportMolProbityScores</code><span class="sig-paren">(</span><em class="sig-param">scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReportMolProbityScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Print MolProbity score and its components to LogInfo.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a>) – MolProbity scores as generated by <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal"><span class="pre">RunMolProbity()</span></code></a>.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a>) – MolProbity scores as generated by <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal notranslate"><span class="pre">RunMolProbity()</span></code></a>.</p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -246,20 +208,45 @@ executable is not found.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Model Checking</a><ul>
-<li><a class="reference internal" href="#detecting-ring-punches">Detecting Ring Punches</a></li>
-<li><a class="reference internal" href="#model-checking-with-molprobity">Model Checking With MolProbity</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="pipeline.html" title="previous chapter">Modelling Pipeline</a></li>
<li>Next: <a href="gap_handling.html" title="next chapter">Handling Gaps</a></li>
</ul></li>
@@ -267,23 +254,24 @@ executable is not found.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/model_checking.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -292,11 +280,11 @@ executable is not found.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/model_checking.txt"
+ <a href="../_sources/modelling/model_checking.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 7a4734c542646cad0aa35eb4e8c02393fd6c6056..f33b8de0ad23d5621a34f0dd3bae0adf0f4ec7ce 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Generating Loops De Novo — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Generating Loops De Novo — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
<link rel="prev" title="Fitting Loops Into Gaps" href="loop_closing.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -54,18 +40,18 @@ novo structure candidates for loops or N-/C-Termini. Every iteration of the
sampling process consists basically of four steps and we define objects for
each step:</p>
<ul class="simple">
-<li><a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>: Propose new conformation</li>
-<li><a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>: Adapt new conformation to the environment</li>
-<li><a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>: Score the new conformation</li>
-<li><a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>: Accept/Reject new conformation based on the score and
-a temperature controlled Metropolis criterion</li>
+<li><p><a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>: Propose new conformation</p></li>
+<li><p><a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>: Adapt new conformation to the environment</p></li>
+<li><p><a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>: Score the new conformation</p></li>
+<li><p><a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>: Accept/Reject new conformation based on the score and
+a temperature controlled Metropolis criterion</p></li>
</ul>
<p>These steps can be arbitrarily combined to generate custom Monte Carlo sampling
pipelines. This combination either happens manually or by using the convenient
-<a class="reference internal" href="#promod3.modelling.SampleMonteCarlo" title="promod3.modelling.SampleMonteCarlo"><code class="xref py py-func docutils literal"><span class="pre">SampleMonteCarlo()</span></code></a> function. For example, here we show how to apply Monte
+<a class="reference internal" href="#promod3.modelling.SampleMonteCarlo" title="promod3.modelling.SampleMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">SampleMonteCarlo()</span></code></a> function. For example, here we show how to apply Monte
Carlo sampling to the N-terminal part of crambin:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="c1"># setup protein</span>
@@ -119,7 +105,7 @@ Carlo sampling to the N-terminal part of crambin:</p>
</div>
<dl class="function">
<dt id="promod3.modelling.SampleMonteCarlo">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>steps</em>, <em>bb_list</em>, <em>initialize</em>, <em>seed=0</em>, <em>lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em class="sig-param">sampler</em>, <em class="sig-param">closer</em>, <em class="sig-param">scorer</em>, <em class="sig-param">cooler</em>, <em class="sig-param">steps</em>, <em class="sig-param">bb_list</em>, <em class="sig-param">initialize</em>, <em class="sig-param">seed=0</em>, <em class="sig-param">lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
<dd><p>A convenient function to perform Monte Carlo sampling using a simulated
annealing scheme. In every iteration, a new loop conformation gets proposed
by the provided <em>sampler</em> and closed by the <em>closer</em>. Upon scoring, this new
@@ -129,32 +115,28 @@ the temperature given by the <em>cooler</em>
The result is stored in <em>bb_list</em> (passed by reference, so NO return value)
and is either the lowest energy conformation ever encountered or the last
accepted proposal.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Sampler object capable of initializing and altering
-conformations.</li>
-<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Closer object to adapt a new conformation to
-the environment.</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Scorer object to score new loop conformations.</li>
-<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Cooler object to control the temperature of the
-Monte Carlo trajectory.</li>
-<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo iterations to be performed.</li>
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The chosen conformation gets stored here.</li>
-<li><strong>initialize</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether a new bb_list should be generated as starting
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Sampler object capable of initializing and altering
+conformations.</p></li>
+<li><p><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Closer object to adapt a new conformation to
+the environment.</p></li>
+<li><p><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Scorer object to score new loop conformations.</p></li>
+<li><p><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Cooler object to control the temperature of the
+Monte Carlo trajectory.</p></li>
+<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo iterations to be performed.</p></li>
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The chosen conformation gets stored here.</p></li>
+<li><p><strong>initialize</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether a new bb_list should be generated as starting
point, based on the samplers Initialize function.
-The input <em>bb_list</em> gets used otherwise.</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random number generator.</li>
-<li><strong>lowest_energy_conformation</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, we choose the lowest scoring
+The input <em>bb_list</em> gets used otherwise.</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator.</p></li>
+<li><p><strong>lowest_energy_conformation</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, we choose the lowest scoring
conformation of the trajectory.
-Otherwise, the last accepted proposal.</li>
+Otherwise, the last accepted proposal.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<div class="section" id="sampler-object">
@@ -163,199 +145,175 @@ Otherwise, the last accepted proposal.</li>
propose new conformations for a sequence of interest. They build the basis
for any Monte Carlo sampling pipeline. You can either use one of the
provided samplers or any object that implements the functionality of
-<a class="reference internal" href="#promod3.modelling.SamplerBase" title="promod3.modelling.SamplerBase"><code class="xref py py-class docutils literal"><span class="pre">SamplerBase</span></code></a>.</p>
+<a class="reference internal" href="#promod3.modelling.SamplerBase" title="promod3.modelling.SamplerBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">SamplerBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.SamplerBase">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SamplerBase</code><a class="headerlink" href="#promod3.modelling.SamplerBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SamplerBase</code><a class="headerlink" href="#promod3.modelling.SamplerBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
sampler.</p>
<dl class="method">
<dt id="promod3.modelling.SamplerBase.Initialize">
-<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.Initialize" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.Initialize" title="Permalink to this definition">¶</a></dt>
<dd><p>Supposed to initialize structural information from scratch. The sequence
-of the generated <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is taken from <em>bb_list</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to this
-parameter. Sequence / length stay the same.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">None</td>
-</tr>
-</tbody>
-</table>
+of the generated <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is taken from <em>bb_list</em>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to this
+parameter. Sequence / length stay the same.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>None</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.SamplerBase.ProposeStep">
-<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">proposed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes current positions and proposes a new conformation. There is no
guarantee on maintining any special RT state. The <a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>
is supposed to sort that out.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
-function.</li>
-<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
-this parameter.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
+function.</p></li>
+<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
+this parameter.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>None</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.PhiPsiSampler">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">PhiPsiSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>torsion_sampler</em>, <em>n_stem_phi=-1.0472</em>, <em>c_stem_psi=-0.78540</em>, <em>prev_aa='A'</em>, <em>next_aa='A'</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">PhiPsiSampler</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">n_stem_phi=-1.0472</em>, <em class="sig-param">c_stem_psi=-0.78540</em>, <em class="sig-param">prev_aa='A'</em>, <em class="sig-param">next_aa='A'</em>, <em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>The PhiPsiSampler randomly draws and sets phi/psi dihedral angles from
a distribution provided by the <em>torsion_sampler</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence that should be sampled</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi pairs are drawn. It
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence that should be sampled</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi pairs are drawn. It
is also possible to pass a list of samplers with same
size as the sequence to assign a specific sampler per
-residue.</li>
-<li><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
+residue.</p></li>
+<li><p><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
the sampling region. If the first residue gets selected
for changing the dihedral angles, it draws a psi angle
-given <em>n_stem_phi</em>.</li>
-<li><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
+given <em>n_stem_phi</em>.</p></li>
+<li><p><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
the sampling region. If the last residue gets selected
for changing the dihedral angles, it draws a phi angle
-given <em>c_stem_psi</em>.</li>
-<li><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+given <em>c_stem_psi</em>.</p></li>
+<li><p><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the first residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</li>
-<li><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+always considers triplets)</p></li>
+<li><p><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the last residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</li>
+always considers triplets)</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.PhiPsiSampler.Initialize">
-<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.Initialize" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> by randomly drawing
+<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.Initialize" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> by randomly drawing
phi/psi dihedral angles.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.PhiPsiSampler.ProposeStep">
-<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>Randomly selects one of the residues and resets its phi/psi values
according to a random draw from the internal torsion samplers.
In case of the first residue, only a psi given phi is drawn. Same
principle also applies for the last residue.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</li>
-<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</p></li>
+<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
is not consistent with the internal sequence. Note, that the
-sequence itself doesn’t get checked for efficiency reasons.</p>
-</td>
-</tr>
-</tbody>
-</table>
+sequence itself doesn’t get checked for efficiency reasons.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.SoftSampler">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SoftSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>torsion_sampler</em>, <em>max_dev</em>, <em>n_stem_phi=-1.0472</em>, <em>c_stem_psi=-0.78540</em>, <em>prev_aa='A'</em>, <em>next_aa='A'</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SoftSampler</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">max_dev</em>, <em class="sig-param">n_stem_phi=-1.0472</em>, <em class="sig-param">c_stem_psi=-0.78540</em>, <em class="sig-param">prev_aa='A'</em>, <em class="sig-param">next_aa='A'</em>, <em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>Instead of drawing completely new values for a residues phi/psi angles,
only one angle gets altered by a maximum value of <em>max_dev</em> in the
SoftSampler.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence that should be sampled</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi probablities are
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence that should be sampled</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi probablities are
extracted. It is also possible to pass a list of
samplers with same size as the sequence to assign
-a specific sampler per residue.</li>
-<li><strong>max_dev</strong> – Maximal deviation of dihedral angle from its original
-value per sampling step.</li>
-<li><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
+a specific sampler per residue.</p></li>
+<li><p><strong>max_dev</strong> – Maximal deviation of dihedral angle from its original
+value per sampling step.</p></li>
+<li><p><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
the sampling region. If the psi angle of the first
residue gets selected to be changed, <em>n_stem_phi</em> is
used to calculate the phi/psi probability to estimate
-the acceptance probability.</li>
-<li><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
+the acceptance probability.</p></li>
+<li><p><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
the sampling region. If the phi angle of the last
residue gets selected to be changed, <em>c_stem_psi</em> is
used to calculate the phi/psi probability to estimate
-the acceptance probability.</li>
-<li><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+the acceptance probability.</p></li>
+<li><p><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the first residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</li>
-<li><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+always considers triplets)</p></li>
+<li><p><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the last residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</li>
+always considers triplets)</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.SoftSampler.Initialize">
-<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.Initialize" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> by randomly drawing
+<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.Initialize" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> by randomly drawing
phi/psi dihedral angles.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.SoftSampler.ProposeStep">
-<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>In an iterative process, the SoftSampler randomly selects one of the
possible dihedral angles in a conformation and changes it by a random value
in [-<em>max_dev</em>, <em>max_dev</em>]. The acceptance probability of this change is
@@ -363,93 +321,78 @@ the fraction of the phi/psi probability before and after changing the
single angle in the particular residue. There is a maximum of 100
iterations. It is therefore theoretically possible, that nothing happens
when a new step should be proposed</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</li>
-<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</p></li>
+<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
is not consistent with the internal sequence. Note, that the
-sequence itself doesn’t get checked for efficiency reasons.</p>
-</td>
-</tr>
-</tbody>
-</table>
+sequence itself doesn’t get checked for efficiency reasons.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.FragmentSampler">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">FragmentSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>fraggers</em>, <em>init_bb_list=BackboneList(sequence)</em>, <em>sampling_start_index=0</em>, <em>init_fragments=3</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FragmentSampler</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">fraggers</em>, <em class="sig-param">init_bb_list=BackboneList(sequence)</em>, <em class="sig-param">sampling_start_index=0</em>, <em class="sig-param">init_fragments=3</em>, <em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>The FragmentSampler samples by replacing full fragments originating from a
-list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects. The region, that actually gets
+list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects. The region, that actually gets
sampled is determined by <em>sampling_start_index</em> and number of
-<a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects being available. All parts not covered
+<a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects being available. All parts not covered
by any fragger remain rigid.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Overall sequence</li>
-<li><strong>fraggers</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects. The first
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Overall sequence</p></li>
+<li><p><strong>fraggers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects. The first
fragger covers the region starting at the letter
<em>sampling_start_index</em> of the <em>sequence</em> and so on.
-All fraggers must contain fragments of equal size.</li>
-<li><strong>init_bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Initial conformation, that serves as a starting point for
+All fraggers must contain fragments of equal size.</p></li>
+<li><p><strong>init_bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Initial conformation, that serves as a starting point for
sampling. The default gets constructed using the default
-constructor of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> and
-results in a helix.</li>
-<li><strong>sampling_start_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Defines the beginning of the region, that actually
-gets sampled.</li>
-<li><strong>init_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – When calling the Initialize function, the positions get set
+constructor of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> and
+results in a helix.</p></li>
+<li><p><strong>sampling_start_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Defines the beginning of the region, that actually
+gets sampled.</p></li>
+<li><p><strong>init_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – When calling the Initialize function, the positions get set
to the ones of <em>init_bb_list</em>. This is the number of
-fragments that gets randomly selected and inserted.</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for the internal random number generators</li>
+fragments that gets randomly selected and inserted.</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.FragmentSampler.Initialize">
-<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.Initialize" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> by setting the setting
+<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.Initialize" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> by setting the setting
bb_list = <em>init_bb_list</em> and randomly replace n fragments
with n = <em>init_fragments</em></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.FragmentSampler.ProposeStep">
-<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_step</em>, <em>proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_step</em>, <em class="sig-param">proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>Randomly selects a position and selects a random fragment from the according
fragger object to alter the conformation.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</li>
-<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</p></li>
+<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -463,262 +406,220 @@ fit to a given environment. This can either be structural changes, that
the stems of the sampled conformation overlap with given stem residues or
or simple stem superposition in case of terminal sampling. You can either
use any of the provided closers or any object that implements the
-functionality of <a class="reference internal" href="#promod3.modelling.CloserBase" title="promod3.modelling.CloserBase"><code class="xref py py-class docutils literal"><span class="pre">CloserBase</span></code></a>.</p>
+functionality of <a class="reference internal" href="#promod3.modelling.CloserBase" title="promod3.modelling.CloserBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">CloserBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.CloserBase">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CloserBase</code><a class="headerlink" href="#promod3.modelling.CloserBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloserBase</code><a class="headerlink" href="#promod3.modelling.CloserBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
closer.</p>
<dl class="method">
<dt id="promod3.modelling.CloserBase.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloserBase.Close" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloserBase.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes current positions and proposes a new conformation that fits to a
given environment.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
-function.</li>
-<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
-this parameter.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
+function.</p></li>
+<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
+this parameter.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Whether closing procedure was successful</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether closing procedure was successful</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.CCDCloser">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>sequence</em>, <em>torsion_sampler</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CCDCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">sequence</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The CCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
the stems given by the closer. The <em>torsion_sampler</em> is used to
avoid moving into unfavourable phi/psi ranges.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>
-of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – To enforce valid phi/psi ranges. Alternatively, you
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – To enforce valid phi/psi ranges. Alternatively, you
can also pass a list of sampler objects to assign a
unique torsion sampler to every residue of the
-conformation to be closed.</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
+conformation to be closed.</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.CCDCloser.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</li>
-<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</li>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</p></li>
+<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether CCD converged</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether CCD converged</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.DirtyCCDCloser">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DirtyCCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">DirtyCCDCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The DirtyCCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
the stems given by the closer. There is no check for reasonable backbone
-dihedral angles as it is the case for the <a class="reference internal" href="#promod3.modelling.CCDCloser" title="promod3.modelling.CCDCloser"><code class="xref py py-class docutils literal"><span class="pre">CCDCloser</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt.</li>
+dihedral angles as it is the case for the <a class="reference internal" href="#promod3.modelling.CCDCloser" title="promod3.modelling.CCDCloser"><code class="xref py py-class docutils literal notranslate"><span class="pre">CCDCloser</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.DirtyCCDCloser.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</li>
-<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</li>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</p></li>
+<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether CCD converged</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether CCD converged</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.KICCloser">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">KICCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">KICCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The KIC closer randomly picks three pivot residues in the conformation
to be closed and applies the KIC algorithm. KIC gives up to 16 possible
solutions. The KICCloser simply picks the first one.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</p></li>
+<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.KICCloser.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</li>
-<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</li>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</p></li>
+<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether KIC found a solution</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether KIC found a solution</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.NTerminalCloser">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">NTerminalCloser</code><span class="sig-paren">(</span><em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser" title="Permalink to this definition">¶</a></dt>
-<dd><p>The <a class="reference internal" href="#promod3.modelling.NTerminalCloser" title="promod3.modelling.NTerminalCloser"><code class="xref py py-class docutils literal"><span class="pre">NTerminalCloser</span></code></a> simply takes the conformation and closes by
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">NTerminalCloser</code><span class="sig-paren">(</span><em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser" title="Permalink to this definition">¶</a></dt>
+<dd><p>The <a class="reference internal" href="#promod3.modelling.NTerminalCloser" title="promod3.modelling.NTerminalCloser"><code class="xref py py-class docutils literal notranslate"><span class="pre">NTerminalCloser</span></code></a> simply takes the conformation and closes by
superposing the c_stem with the desired positions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.NTerminalCloser.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
-transformed in space).</li>
-<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
-here.</li>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
+transformed in space).</p></li>
+<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
+here.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether closing was successful</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.CTerminalCloser">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CTerminalCloser</code><span class="sig-paren">(</span><em>n_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser" title="Permalink to this definition">¶</a></dt>
-<dd><p>The <a class="reference internal" href="#promod3.modelling.CTerminalCloser" title="promod3.modelling.CTerminalCloser"><code class="xref py py-class docutils literal"><span class="pre">CTerminalCloser</span></code></a> simply takes the conformation and closes by
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CTerminalCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser" title="Permalink to this definition">¶</a></dt>
+<dd><p>The <a class="reference internal" href="#promod3.modelling.CTerminalCloser" title="promod3.modelling.CTerminalCloser"><code class="xref py py-class docutils literal notranslate"><span class="pre">CTerminalCloser</span></code></a> simply takes the conformation and closes by
superposing the n_stem with the desired positions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.CTerminalCloser.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
-transformed in space).</li>
-<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
-here.</li>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
+transformed in space).</p></li>
+<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
+here.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Whether closing was successful</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.DeNovoCloser">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DeNovoCloser</code><a class="headerlink" href="#promod3.modelling.DeNovoCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">DeNovoCloser</code><a class="headerlink" href="#promod3.modelling.DeNovoCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>In case of sampling a full stretch, you dont have external constraints. The
closer has a rather boring job in this case.</p>
<dl class="method">
<dt id="promod3.modelling.DeNovoCloser.Close">
-<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeNovoCloser.Close" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeNovoCloser.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Does absolutely nothing, except copying over the coordinates from
<em>actual_positions</em> to <em>closed_positions</em> and return true.</p>
</dd></dl>
@@ -730,85 +631,79 @@ closer has a rather boring job in this case.</p>
<span id="mc-scorer-object"></span><h2>Scorer Object<a class="headerlink" href="#scorer-object" title="Permalink to this headline">¶</a></h2>
<p>The scorer asses a proposed conformation and are intended to return a pseudo
energy, the lower the better. You can either use the provided scorer or any
-object implementing the functionality defined in <a class="reference internal" href="#promod3.modelling.ScorerBase" title="promod3.modelling.ScorerBase"><code class="xref py py-class docutils literal"><span class="pre">ScorerBase</span></code></a>.</p>
+object implementing the functionality defined in <a class="reference internal" href="#promod3.modelling.ScorerBase" title="promod3.modelling.ScorerBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScorerBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.ScorerBase">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScorerBase</code><a class="headerlink" href="#promod3.modelling.ScorerBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScorerBase</code><a class="headerlink" href="#promod3.modelling.ScorerBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
scorer.</p>
<dl class="method">
<dt id="promod3.modelling.ScorerBase.GetScore">
-<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScorerBase.GetScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScorerBase.GetScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes coordinates and spits out a score given some internal structural
environment.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Coordinates to be scored</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The score</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Coordinates to be scored</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The score</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.LinearScorer">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">LinearScorer</code><span class="sig-paren">(</span><em>scorer</em>, <em>scorer_env</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em>, <em>linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">LinearScorer</code><span class="sig-paren">(</span><em class="sig-param">scorer</em>, <em class="sig-param">scorer_env</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em>, <em class="sig-param">linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>The LinearScorer allows to combine the scores available from
-<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a> in a linear manner. See
-<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination"><code class="xref py py-meth docutils literal"><span class="pre">CalculateLinearCombination()</span></code></a> for a
+<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a> in a linear manner. See
+<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateLinearCombination()</span></code></a> for a
detailed description of the arguments.</p>
<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<p class="last">The provided <em>scorer_env</em> will be altered in every
-<a class="reference internal" href="#promod3.modelling.LinearScorer.GetScore" title="promod3.modelling.LinearScorer.GetScore"><code class="xref py py-func docutils literal"><span class="pre">GetScore()</span></code></a> call.
+<p class="admonition-title">Warning</p>
+<p>The provided <em>scorer_env</em> will be altered in every
+<a class="reference internal" href="#promod3.modelling.LinearScorer.GetScore" title="promod3.modelling.LinearScorer.GetScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetScore()</span></code></a> call.
You might consider the Stash / Pop mechanism of the
-<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
+<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
original state once the sampling is done.</p>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a>) – Scorer Object with set environment for the particular loop
-modelling problem.</li>
-<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>) – The environment that is linked to the <em>scorer</em></li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues to score</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belong to.</li>
-<li><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>,
-values: <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – Weights for each desired scorer.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a>) – Scorer Object with set environment for the particular loop
+modelling problem.</p></li>
+<li><p><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The environment that is linked to the <em>scorer</em></p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues to score</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belong to.</p></li>
+<li><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each desired scorer.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
which no scorer exists</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.LinearScorer.GetScore">
-<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer.GetScore" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop to be scored.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A linear combination of the scores</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer.GetScore" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be scored.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A linear combination of the scores</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -817,33 +712,31 @@ which no scorer exists</p>
<div class="section" id="cooler-object">
<span id="mc-cooler-object"></span><h2>Cooler Object<a class="headerlink" href="#cooler-object" title="Permalink to this headline">¶</a></h2>
<p>The cooler objects control the temperature of the Monte Carlo trajectory.
-They’re intended to deliver steadily decreasing temperatures with calls
+They’re intended to deliver steadily decreasing temperatures with calls
to their GetTemperature function. You can either use the provided cooler
or any object implementing the functionality defined in
-<a class="reference internal" href="#promod3.modelling.CoolerBase" title="promod3.modelling.CoolerBase"><code class="xref py py-class docutils literal"><span class="pre">CoolerBase</span></code></a>.</p>
+<a class="reference internal" href="#promod3.modelling.CoolerBase" title="promod3.modelling.CoolerBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoolerBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.CoolerBase">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CoolerBase</code><a class="headerlink" href="#promod3.modelling.CoolerBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CoolerBase</code><a class="headerlink" href="#promod3.modelling.CoolerBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
cooler.</p>
<dl class="method">
<dt id="promod3.modelling.CoolerBase.GetTemperature">
-<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.GetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Temperature</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The Temperature</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.CoolerBase.Reset">
-<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.Reset" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.Reset" title="Permalink to this definition">¶</a></dt>
<dd><p>Resets to original state, so a new Monte Carlo trajectory can be generated</p>
</dd></dl>
@@ -851,40 +744,33 @@ cooler.</p>
<dl class="class">
<dt id="promod3.modelling.ExponentialCooler">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ExponentialCooler</code><span class="sig-paren">(</span><em>change_frequency</em>, <em>start_temperature</em>, <em>cooling_factor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ExponentialCooler</code><span class="sig-paren">(</span><em class="sig-param">change_frequency</em>, <em class="sig-param">start_temperature</em>, <em class="sig-param">cooling_factor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler" title="Permalink to this definition">¶</a></dt>
<dd><p>The exponential cooler starts with a given <em>start_temperature</em> and counts the
-calls to its <a class="reference internal" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="promod3.modelling.ExponentialCooler.GetTemperature"><code class="xref py py-meth docutils literal"><span class="pre">GetTemperature()</span></code></a> function. According to the
+calls to its <a class="reference internal" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="promod3.modelling.ExponentialCooler.GetTemperature"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetTemperature()</span></code></a> function. According to the
<em>change_frequency</em>, the returned temperature gets multiplied by the
<em>cooling_factor</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Frequency to change temperature</li>
-<li><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – temperature to start with</li>
-<li><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Factor to decrease temperature</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Frequency to change temperature</p></li>
+<li><p><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – temperature to start with</p></li>
+<li><p><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor to decrease temperature</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.ExponentialCooler.GetTemperature">
-<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">current temperature</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>current temperature</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ExponentialCooler.Reset">
-<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.Reset" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.Reset" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets current temperature back to <em>start_temperature</em> and the
internal counter to 0</p>
</dd></dl>
@@ -901,22 +787,45 @@ internal counter to 0</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Generating Loops De Novo</a><ul>
-<li><a class="reference internal" href="#sampler-object">Sampler Object</a></li>
-<li><a class="reference internal" href="#closer-object">Closer Object</a></li>
-<li><a class="reference internal" href="#scorer-object">Scorer Object</a></li>
-<li><a class="reference internal" href="#cooler-object">Cooler Object</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="loop_closing.html" title="previous chapter">Fitting Loops Into Gaps</a></li>
<li>Next: <a href="sidechain_reconstruction.html" title="next chapter">Sidechain Reconstruction</a></li>
</ul></li>
@@ -924,23 +833,24 @@ internal counter to 0</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/monte_carlo.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -949,11 +859,11 @@ internal counter to 0</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/monte_carlo.txt"
+ <a href="../_sources/modelling/monte_carlo.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index bfbdbc05f16216a2a746c306103be168615c37b6..c513f54c9fa73d280c0c92df96811a6d15ea6434 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Modelling Pipeline — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Modelling Pipeline — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Model Checking" href="model_checking.html" />
<link rel="prev" title="modelling - Protein Modelling" href="index.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -51,23 +37,23 @@
<h1>Modelling Pipeline<a class="headerlink" href="#modelling-pipeline" title="Permalink to this headline">¶</a></h1>
<p>A protein homology modelling pipeline has the following main steps:</p>
<ul class="simple">
-<li>Build a raw model from the template (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a> function)</li>
-<li>Perform loop modelling to close (or remove) all gaps (see functions
-<a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>, <a class="reference internal" href="#promod3.modelling.RemoveTerminalGaps" title="promod3.modelling.RemoveTerminalGaps"><code class="xref py py-func docutils literal"><span class="pre">RemoveTerminalGaps()</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal"><span class="pre">MergeGapsByDistance()</span></code></a>, <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>, <a class="reference internal" href="#promod3.modelling.CloseLargeDeletions" title="promod3.modelling.CloseLargeDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseLargeDeletions()</span></code></a> or
-<a class="reference internal" href="#promod3.modelling.CloseGaps" title="promod3.modelling.CloseGaps"><code class="xref py py-func docutils literal"><span class="pre">CloseGaps()</span></code></a> that calls all these functions using predefined
-heuristics)</li>
-<li>Build sidechains (see <a class="reference internal" href="#promod3.modelling.BuildSidechains" title="promod3.modelling.BuildSidechains"><code class="xref py py-func docutils literal"><span class="pre">BuildSidechains()</span></code></a> function)</li>
-<li>Minimize energy of final model using molecular mechanics
-(see <a class="reference internal" href="#promod3.modelling.MinimizeModelEnergy" title="promod3.modelling.MinimizeModelEnergy"><code class="xref py py-func docutils literal"><span class="pre">MinimizeModelEnergy()</span></code></a> function)</li>
+<li><p>Build a raw model from the template (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a> function)</p></li>
+<li><p>Perform loop modelling to close (or remove) all gaps (see functions
+<a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>, <a class="reference internal" href="#promod3.modelling.RemoveTerminalGaps" title="promod3.modelling.RemoveTerminalGaps"><code class="xref py py-func docutils literal notranslate"><span class="pre">RemoveTerminalGaps()</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal notranslate"><span class="pre">MergeGapsByDistance()</span></code></a>, <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>, <a class="reference internal" href="#promod3.modelling.CloseLargeDeletions" title="promod3.modelling.CloseLargeDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseLargeDeletions()</span></code></a> or
+<a class="reference internal" href="#promod3.modelling.CloseGaps" title="promod3.modelling.CloseGaps"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseGaps()</span></code></a> that calls all these functions using predefined
+heuristics)</p></li>
+<li><p>Build sidechains (see <a class="reference internal" href="#promod3.modelling.BuildSidechains" title="promod3.modelling.BuildSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildSidechains()</span></code></a> function)</p></li>
+<li><p>Minimize energy of final model using molecular mechanics
+(see <a class="reference internal" href="#promod3.modelling.MinimizeModelEnergy" title="promod3.modelling.MinimizeModelEnergy"><code class="xref py py-func docutils literal notranslate"><span class="pre">MinimizeModelEnergy()</span></code></a> function)</p></li>
</ul>
<p>The last steps to go from a raw model to a final model can easily be executed
-with the <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a> function. If you want to run and tweak the
+with the <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a> function. If you want to run and tweak the
internal steps, you can start with the following code and adapt it to your
purposes:</p>
-<div class="highlight-default" id="modelling-steps-example"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default notranslate" id="modelling-steps-example"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
<span class="c1"># setup</span>
<span class="n">merge_distance</span> <span class="o">=</span> <span class="mi">4</span>
@@ -107,260 +93,221 @@ purposes:</p>
<h2>Build Raw Modelling Handle<a class="headerlink" href="#build-raw-modelling-handle" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.ModellingHandle">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ModellingHandle</code><a class="headerlink" href="#promod3.modelling.ModellingHandle" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ModellingHandle</code><a class="headerlink" href="#promod3.modelling.ModellingHandle" title="Permalink to this definition">¶</a></dt>
<dd><p>Handles the result for structure model building and provides high-level methods
-to turn an initial raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a>)
+to turn an initial raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a>)
into a complete protein model by removing any existing gaps.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.model">
-<code class="descname">model</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.model" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">model</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.model" title="Permalink to this definition">¶</a></dt>
<dd><p>The resulting model. This includes one chain per target chain (in the same
-order as the sequences in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>) and (if they were included) a
-chain named ‘_’ for ligands. You can therefore access <cite>model.chains</cite> items
-and <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a> items with the same indexing and the optional ligand
+order as the sequences in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>) and (if they were included) a
+chain named ‘_’ for ligands. You can therefore access <cite>model.chains</cite> items
+and <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a> items with the same indexing and the optional ligand
chain follows afterwards.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.gaps">
-<code class="descname">gaps</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.gaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">gaps</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.gaps" title="Permalink to this definition">¶</a></dt>
<dd><p>List of gaps in the model that could not be copied from the template. These
gaps may be the result of insertions/deletions in the alignment or due to
missing or incomplete backbone coordinates in the template structure.
Gaps of different chains are appended one after another.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGapList" title="promod3.modelling.StructuralGapList"><code class="xref py py-class docutils literal"><span class="pre">StructuralGapList</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGapList" title="promod3.modelling.StructuralGapList"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGapList</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
-<code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
+<code class="sig-name descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
-<code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
-the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>). Please note, that this
-attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>. You have
+<code class="sig-name descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please note, that this
+attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have
to fill it manually or even better by the convenient function
-<a class="reference internal" href="#promod3.modelling.SetSequenceProfiles" title="promod3.modelling.SetSequenceProfiles"><code class="xref py py-func docutils literal"><span class="pre">SetSequenceProfiles()</span></code></a>, to ensure consistency with the seqres.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="#promod3.modelling.SetSequenceProfiles" title="promod3.modelling.SetSequenceProfiles"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetSequenceProfiles()</span></code></a>, to ensure consistency with the seqres.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.psipred_predictions">
-<code class="descname">psipred_predictions</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.psipred_predictions" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of predictions with one <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a> for
-each chain of the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>). Please
-note, that this attribute won’t be set by simply calling
-<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>. You have to fill it manually or even better by
-the convenient function <a class="reference internal" href="#promod3.modelling.SetPsipredPredictions" title="promod3.modelling.SetPsipredPredictions"><code class="xref py py-func docutils literal"><span class="pre">SetPsipredPredictions()</span></code></a>, to ensure
+<code class="sig-name descname">psipred_predictions</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.psipred_predictions" title="Permalink to this definition">¶</a></dt>
+<dd><p>List of predictions with one <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a> for
+each chain of the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please
+note, that this attribute won’t be set by simply calling
+<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have to fill it manually or even better by
+the convenient function <a class="reference internal" href="#promod3.modelling.SetPsipredPredictions" title="promod3.modelling.SetPsipredPredictions"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetPsipredPredictions()</span></code></a>, to ensure
consistency with the seqres.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.backbone_scorer_env">
-<code class="descname">backbone_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">backbone_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="Permalink to this definition">¶</a></dt>
<dd><p>Backbone score environment attached to this handle. A default environment is
-set with <a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> when needed. Additional
+set with <a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> when needed. Additional
information can be added to the environment before running the pipeline
steps.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.backbone_scorer">
-<code class="descname">backbone_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">backbone_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Backbone scorer container attached to this handle. A default set of scorers
-is initialized with <a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> when needed.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+is initialized with <a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> when needed.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.all_atom_scorer_env">
-<code class="descname">all_atom_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">all_atom_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="Permalink to this definition">¶</a></dt>
<dd><p>All atom environment attached to this handle for scoring. A default
-environment is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when needed. This
+environment is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when needed. This
environment is for temporary work only and is only updated to score loops.
It is not to be updated when loops are chosen and added to the final model.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.all_atom_scorer">
-<code class="descname">all_atom_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">all_atom_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="Permalink to this definition">¶</a></dt>
<dd><p>All atom scorer container attached to this handle. A default set of scorers
-is initialized with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when needed.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomOverallScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+is initialized with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when needed.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomOverallScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.all_atom_sidechain_env">
-<code class="descname">all_atom_sidechain_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">all_atom_sidechain_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="Permalink to this definition">¶</a></dt>
<dd><p>All atom environment attached to this handle for sidechain reconstruction. A
-default environment is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when
+default environment is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when
needed.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.sidechain_reconstructor">
-<code class="descname">sidechain_reconstructor</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">sidechain_reconstructor</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>A sidechain reconstructor to add sidechains to loops prior to all atom
-scoring. A default one is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when
+scoring. A default one is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when
needed.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.fragger_handles">
-<code class="descname">fragger_handles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.fragger_handles" title="Permalink to this definition">¶</a></dt>
-<dd><p>Optional attribute which is set in <a class="reference internal" href="#promod3.modelling.SetFraggerHandles" title="promod3.modelling.SetFraggerHandles"><code class="xref py py-meth docutils literal"><span class="pre">SetFraggerHandles()</span></code></a>. Use
-<code class="xref py py-meth docutils literal"><span class="pre">hasattr()</span></code> to check if it’s available. If it’s set, it is used in
-<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">fragger_handles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.fragger_handles" title="Permalink to this definition">¶</a></dt>
+<dd><p>Optional attribute which is set in <a class="reference internal" href="#promod3.modelling.SetFraggerHandles" title="promod3.modelling.SetFraggerHandles"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetFraggerHandles()</span></code></a>. Use
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">hasattr()</span></code> to check if it’s available. If it’s set, it is used in
+<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.modelling_issues">
-<code class="descname">modelling_issues</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.modelling_issues" title="Permalink to this definition">¶</a></dt>
-<dd><p>Optional attribute which is set in <a class="reference internal" href="#promod3.modelling.AddModellingIssue" title="promod3.modelling.AddModellingIssue"><code class="xref py py-meth docutils literal"><span class="pre">AddModellingIssue()</span></code></a>. Use
-<code class="xref py py-meth docutils literal"><span class="pre">hasattr()</span></code> to check if it’s available. If it’s set, it can be used to
-check issues which occurred in <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a> (see
-<a class="reference internal" href="#promod3.modelling.MinimizeModelEnergy" title="promod3.modelling.MinimizeModelEnergy"><code class="xref py py-meth docutils literal"><span class="pre">MinimizeModelEnergy()</span></code></a> and <a class="reference internal" href="#promod3.modelling.CheckFinalModel" title="promod3.modelling.CheckFinalModel"><code class="xref py py-meth docutils literal"><span class="pre">CheckFinalModel()</span></code></a> for details).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ModellingIssue" title="promod3.modelling.ModellingIssue"><code class="xref py py-class docutils literal"><span class="pre">ModellingIssue</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">modelling_issues</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.modelling_issues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Optional attribute which is set in <a class="reference internal" href="#promod3.modelling.AddModellingIssue" title="promod3.modelling.AddModellingIssue"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddModellingIssue()</span></code></a>. Use
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">hasattr()</span></code> to check if it’s available. If it’s set, it can be used to
+check issues which occurred in <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a> (see
+<a class="reference internal" href="#promod3.modelling.MinimizeModelEnergy" title="promod3.modelling.MinimizeModelEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">MinimizeModelEnergy()</span></code></a> and <a class="reference internal" href="#promod3.modelling.CheckFinalModel" title="promod3.modelling.CheckFinalModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CheckFinalModel()</span></code></a> for details).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ModellingIssue" title="promod3.modelling.ModellingIssue"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingIssue</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ModellingHandle.Copy">
-<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingHandle.Copy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingHandle.Copy" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates a deep copy. Everything will be copied over to the returned
-<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>, except the potentially set scoring members
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal"><span class="pre">backbone_scorer</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal"><span class="pre">backbone_scorer_env</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_scorer_env</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_scorer</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_sidechain_env</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal"><span class="pre">sidechain_reconstructor</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A deep copy of the current handle</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>, except the potentially set scoring members
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer_env</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_sidechain_env</span></code></a> and
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>A deep copy of the current handle</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.BuildRawModel">
-<code class="descclassname">promod3.modelling.</code><code class="descname">BuildRawModel</code><span class="sig-paren">(</span><em>aln</em>, <em>include_ligands=False</em>, <em>chain_names= "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz"</em>, <em>spdbv_style=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildRawModel" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BuildRawModel</code><span class="sig-paren">(</span><em class="sig-param">aln</em>, <em class="sig-param">chain_names=None</em>, <em class="sig-param">include_ligands=False</em>, <em class="sig-param">spdbv_style=False</em>, <em class="sig-param">aln_preprocessing='default'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildRawModel" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds a raw (pseudo) model from the alignment. Can either take a single
alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
<p>Each alignment handle must contain exactly two sequences and the second
-sequence is considered the template sequence, which must have a
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
+sequence is considered the template sequence, which must have a
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
+<p>Before extracting the coordinates, the alignments are pre-processed
+according to <em>aln_preprocessing</em>.</p>
<p>This is a basic protein core modelling algorithm that copies backbone
coordinates based on the sequence alignment. For matching residues, the
side chain coordinates are also copied. Gaps are ignored. Hydrogen an
@@ -369,9 +316,9 @@ deuterium atoms are not copied into the model.</p>
residues are treated as follows:</p>
<blockquote>
<div><ul class="simple">
-<li>Selenium methionine residues are converted to methionine</li>
-<li>Side chains which contain all atoms of the parent amino acid, e.g.
-phosphoserine are copied as a whole with the modifications stripped off.</li>
+<li><p>Selenium methionine residues are converted to methionine</p></li>
+<li><p>Side chains which contain all atoms of the parent amino acid, e.g.
+phosphoserine are copied as a whole with the modifications stripped off.</p></li>
</ul>
</div></blockquote>
<p>Residues with missing backbone atoms and D-peptides are generally skipped and
@@ -381,48 +328,57 @@ return an empty model.</p>
<p>Residue numbers are set such that missing residue in gaps are honoured and
subsequent loop modelling can insert new residues without having to renumber.
<strong>The numbering of residues starts for every chain with the value 1</strong>.</p>
-<p>The returned <a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a> stores the obtained raw model as well
+<p>The returned <a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a> stores the obtained raw model as well
as information about insertions and deletions in the gaps list.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
-list of alignment handles for raw model with multiple chains.</li>
-<li><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+list of alignment handles for raw model with multiple chains.</p></li>
+<li><p><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
searches for ligands in all OST handles of the views
attached to the alignments. Ligands are identified
with the <cite>ligand</cite> property in the handle (set by OST
-based on HET records) or by the chain name ‘_’ (as set
+based on HET records) or by the chain name ‘_’ (as set
in SMTL). All ligands are added to a new chain named
-‘_’.</li>
-<li><strong>chain_names</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Chains are named by a single chanacter taken from this.</li>
-<li><strong>spdbv_style</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True, if we need a model in the old SPDBV style.</li>
+‘_’.</p></li>
+<li><p><strong>chain_names</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – If set, this overrides the default chain naming
+(chains are consecutively named according to
+characters in
+‘ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz’).
+If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>,
+<em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>.
+If <em>aln</em> is of type <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentList</span></code>,
+<em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> of same size as <em>aln</em> or a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>.
+For the latter case, chains will consecutively named
+according to characters in <em>chain_names</em>.</p></li>
+<li><p><strong>spdbv_style</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we need a model in the old SPDBV style.</p></li>
+<li><p><strong>aln_preprocessing</strong> – Calls <a class="reference internal" href="#promod3.modelling.PullTerminalDeletions" title="promod3.modelling.PullTerminalDeletions"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.modelling.PullTerminalDeletions()</span></code></a>
+if set to ‘default’. Can be disabled when set
+to False.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Raw (pseudo) model from the alignment.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#RuntimeError" title="(in Python v3.6)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> when:</p>
-<ul class="last simple">
-<li>the alignments do not have two sequences</li>
-<li>the second sequence does not have an attached structure</li>
-<li>the residues of the template structure do not match with the
-alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
-template sequence (but not for the target))</li>
-<li>the target sequence has a non-zero offset (cannot be honored as
-the resulting model will always start its residue numbering at 1)</li>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Raw (pseudo) model from the alignment.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> when:</p>
+<ul class="simple">
+<li><p>the alignments do not have two sequences</p></li>
+<li><p>the second sequence does not have an attached structure</p></li>
+<li><p>the residues of the template structure do not match with the
+alignment sequence (note that you can set an “offset” (see
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+template sequence (but not for the target))</p></li>
+<li><p>the target sequence has a non-zero offset (cannot be honored as
+the resulting model will always start its residue numbering at 1)</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -430,8 +386,8 @@ the resulting model will always start its residue numbering at 1)</li>
<h2>The Default Pipeline<a class="headerlink" href="#the-default-pipeline" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.BuildFromRawModel">
-<code class="descclassname">promod3.modelling.</code><code class="descname">BuildFromRawModel</code><span class="sig-paren">(</span><em>mhandle</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em>, <em>model_termini=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildFromRawModel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Build a model starting with a raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a>).</p>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BuildFromRawModel</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">use_amber_ff=False</em>, <em class="sig-param">extra_force_fields=[]</em>, <em class="sig-param">model_termini=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildFromRawModel" title="Permalink to this definition">¶</a></dt>
+<dd><p>Build a model starting with a raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a>).</p>
<p>This function implements a recommended pipeline to generate complete models
from a raw model. The steps are shown in detail in the code example
<a class="reference internal" href="#modelling-steps-example"><span class="std std-ref">above</span></a>. If you wish to use your own
@@ -439,36 +395,34 @@ pipeline, you can use that code as a starting point for your own custom
modelling pipeline. For reproducibility, we recommend that you keep copies
of custom pipelines.</p>
<p>To adapt the scoring used during loop closing, you can call
-<a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> and <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>
+<a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> and <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>
and adapt the default scoring members. Alternatively, you can setup the
scoring manually, but you must ensure consistency yourself!</p>
<p>By default, a simple backbone dihedral sampling is performed when entering
-Monte Carlo. If <em>mhandle</em> has a list of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a> objects
-attached as “fragger_handles” attribute, the sampling will be performed with
+Monte Carlo. If <em>mhandle</em> has a list of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a> objects
+attached as “fragger_handles” attribute, the sampling will be performed with
structural fragments. To ensure consistency, the fragger handles should be
-attached using <a class="reference internal" href="#promod3.modelling.SetFraggerHandles" title="promod3.modelling.SetFraggerHandles"><code class="xref py py-meth docutils literal"><span class="pre">SetFraggerHandles()</span></code></a>.
+attached using <a class="reference internal" href="#promod3.modelling.SetFraggerHandles" title="promod3.modelling.SetFraggerHandles"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetFraggerHandles()</span></code></a>.
But be aware of increased runtime due to the fragment search step.</p>
<p>If the function fails to close all gaps, it will produce a warning and
return an incomplete model.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
-alignment.</li>
-<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
+alignment.</p></li>
+<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
-with the optional force fields in <cite>extra_force_fields</cite>.</li>
-<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
+with the optional force fields in <cite>extra_force_fields</cite>.</p></li>
+<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
-existing parametrization are skipped.</li>
-<li><strong>model_termini</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – The default modelling pipeline in ProMod3 is optimized
+existing parametrization are skipped.</p></li>
+<li><p><strong>model_termini</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – The default modelling pipeline in ProMod3 is optimized
to generate a gap-free model of the region in the
target sequence(s) that is covered with template
information. Terminal extensions without template
@@ -477,18 +431,16 @@ You can activate this flag to enforce a model of the
full target sequence(s). The terminal parts will be
modelled with a crude Monte Carlo approach. Be aware
that the accuracy of those termini is likely to be
-limited. Termini of length 1 won’t be modelled.</li>
+limited. Termini of length 1 won’t be modelled.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Delivers the model as an OST entity.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -496,141 +448,128 @@ limited. Termini of length 1 won’t be modelled.</li>
<h2>Modelling Steps<a class="headerlink" href="#modelling-steps" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.SetupDefaultBackboneScoring">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SetupDefaultBackboneScoring</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultBackboneScoring" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetupDefaultBackboneScoring</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultBackboneScoring" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup scorers and environment for meddling with backbones.
This one is already tailored towards a certain modelling job.
The scorers added (with their respective keys) are:</p>
<ul class="simple">
-<li>“cb_packing”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">CBPackingScorer</span></code></a></li>
-<li>“cbeta”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal"><span class="pre">CBetaScorer</span></code></a></li>
-<li>“reduced”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal"><span class="pre">ReducedScorer</span></code></a></li>
-<li>“clash”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ClashScorer" title="promod3.scoring.ClashScorer"><code class="xref py py-class docutils literal"><span class="pre">ClashScorer</span></code></a></li>
-<li>“hbond”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal"><span class="pre">HBondScorer</span></code></a></li>
-<li>“torsion”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal"><span class="pre">TorsionScorer</span></code></a></li>
-<li>“pairwise”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal"><span class="pre">PairwiseScorer</span></code></a></li>
+<li><p>“cb_packing”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></p></li>
+<li><p>“cbeta”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></p></li>
+<li><p>“reduced”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></p></li>
+<li><p>“clash”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ClashScorer" title="promod3.scoring.ClashScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ClashScorer</span></code></a></p></li>
+<li><p>“hbond”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></p></li>
+<li><p>“torsion”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></p></li>
+<li><p>“pairwise”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseScorer</span></code></a></p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal"><span class="pre">backbone_scorer</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite>.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer</span></code></a> and
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.IsBackboneScoringSetUp">
-<code class="descclassname">promod3.modelling.</code><code class="descname">IsBackboneScoringSetUp</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsBackboneScoringSetUp" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal"><span class="pre">backbone_scorer</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite> are set.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">IsBackboneScoringSetUp</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsBackboneScoringSetUp" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer</span></code></a> and
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite> are set.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetupDefaultAllAtomScoring">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SetupDefaultAllAtomScoring</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetupDefaultAllAtomScoring</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup scorers and environment to perform all atom scoring.
This one is already tailored towards a certain modelling job, where we
reconstruct sidechains for loop candidates and score them.
The scorers added (with their respective keys) are:</p>
<ul class="simple">
-<li>“aa_interaction”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomInteractionScorer</span></code></a></li>
-<li>“aa_packing”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPackingScorer</span></code></a></li>
-<li>“aa_clash”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer" title="promod3.scoring.AllAtomClashScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomClashScorer</span></code></a></li>
+<li><p>“aa_interaction”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></p></li>
+<li><p>“aa_packing”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></p></li>
+<li><p>“aa_clash”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer" title="promod3.scoring.AllAtomClashScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomClashScorer</span></code></a></p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_scorer_env</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_scorer</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_sidechain_env</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal"><span class="pre">sidechain_reconstructor</span></code></a>.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_sidechain_env</span></code></a> and
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.IsAllAtomScoringSetUp">
-<code class="descclassname">promod3.modelling.</code><code class="descname">IsAllAtomScoringSetUp</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsAllAtomScoringSetUp" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_scorer_env</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_scorer</span></code></a>,
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_sidechain_env</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal"><span class="pre">sidechain_reconstructor</span></code></a> of <cite>mhandle</cite> are set.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">IsAllAtomScoringSetUp</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsAllAtomScoringSetUp" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer</span></code></a>,
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_sidechain_env</span></code></a> and
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a> of <cite>mhandle</cite> are set.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.InsertLoop">
-<code class="descclassname">promod3.modelling.</code><code class="descname">InsertLoop</code><span class="sig-paren">(</span><em>mhandle</em>, <em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoop" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">InsertLoop</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">bb_list</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoop" title="Permalink to this definition">¶</a></dt>
<dd><p>Insert loop into model and ensure consistent updating of scoring environments.
-Note that we do not update <a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal"><span class="pre">all_atom_scorer_env</span></code></a> as
+Note that we do not update <a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a> as
that one is meant to be updated only while scoring. To clear a gap while
-inserting a loop, use the simpler <a class="reference internal" href="gap_handling.html#promod3.modelling.InsertLoopClearGaps" title="promod3.modelling.InsertLoopClearGaps"><code class="xref py py-meth docutils literal"><span class="pre">InsertLoopClearGaps()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to.</li>
+inserting a loop, use the simpler <a class="reference internal" href="gap_handling.html#promod3.modelling.InsertLoopClearGaps" title="promod3.modelling.InsertLoopClearGaps"><code class="xref py py-meth docutils literal notranslate"><span class="pre">InsertLoopClearGaps()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.RemoveTerminalGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">RemoveTerminalGaps</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RemoveTerminalGaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RemoveTerminalGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RemoveTerminalGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes terminal gaps without modelling them (just removes them from the list
of gaps). This is useful for pipelines which lack the possibility to properly
model loops at the termini.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Number of gaps which were removed.</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Number of gaps which were removed.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ReorderGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">ReorderGaps</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReorderGaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ReorderGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReorderGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Reorders all gaps to ensure sequential order by performing lexicographical
comparison on the sequence formed by chain index of the gap and
start residue number.</p>
@@ -638,7 +577,7 @@ start residue number.</p>
<dl class="function">
<dt id="promod3.modelling.MergeMHandle">
-<code class="descclassname">promod3.modelling.</code><code class="descname">MergeMHandle</code><span class="sig-paren">(</span><em>source_mhandle</em>, <em>target_mhandle</em>, <em>source_chain_idx</em>, <em>target_chain_idx</em>, <em>start_resnum</em>, <em>end_resnum</em>, <em>transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeMHandle" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MergeMHandle</code><span class="sig-paren">(</span><em class="sig-param">source_mhandle</em>, <em class="sig-param">target_mhandle</em>, <em class="sig-param">source_chain_idx</em>, <em class="sig-param">target_chain_idx</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">end_resnum</em>, <em class="sig-param">transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeMHandle" title="Permalink to this definition">¶</a></dt>
<dd><p>Merges the specified stretch of <strong>source_mhandle</strong> into <strong>target_mhandle</strong> by
replacing all structural information and gaps in the stretch
<strong>start_resnum</strong> and <strong>end_resnum</strong> (inclusive). The residues specified by
@@ -648,178 +587,158 @@ i.e. not be enclosed by a gap. If a gap encloses <strong>start_resnum</strong> o
shortened version not including the part overlapping with the defined stretch.
If there is any scoring set up (backbone or all atom), the according
environments get updated in <strong>target_mhandle</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>source_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Source of structural information and gaps</li>
-<li><strong>target_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Structural information and gaps will be copied in here</li>
-<li><strong>source_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – This is the chain where the info comes from</li>
-<li><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First residue of the copied stretch</li>
-<li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
-they’re copied over</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>source_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Source of structural information and gaps</p></li>
+<li><p><strong>target_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Structural information and gaps will be copied in here</p></li>
+<li><p><strong>source_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info comes from</p></li>
+<li><p><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue of the copied stretch</p></li>
+<li><p><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</p></li>
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+they’re copied over</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#RuntimeError" title="(in Python v3.6)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> when:</p>
-<ul class="last simple">
-<li>the chain indices are invalid</li>
-<li>the SEQRES of the specified chains do not match</li>
-<li>the start and end residue numbers are invalid or when the residues
-at the specified positions in the <strong>source_mhandle</strong> do not exist</li>
-<li>a gap in the <strong>source_mhandle</strong> encloses the residues specified by
-<strong>start_resnum</strong> and <strong>end_resnum</strong></li>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> when:</p>
+<ul class="simple">
+<li><p>the chain indices are invalid</p></li>
+<li><p>the SEQRES of the specified chains do not match</p></li>
+<li><p>the start and end residue numbers are invalid or when the residues
+at the specified positions in the <strong>source_mhandle</strong> do not exist</p></li>
+<li><p>a gap in the <strong>source_mhandle</strong> encloses the residues specified by
+<strong>start_resnum</strong> and <strong>end_resnum</strong></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetSequenceProfiles">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SetSequenceProfiles</code><span class="sig-paren">(</span><em>mhandle</em>, <em>profiles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetSequenceProfiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets the <a class="reference internal" href="#promod3.modelling.ModellingHandle.profiles" title="promod3.modelling.ModellingHandle.profiles"><code class="xref py py-attr docutils literal"><span class="pre">sequence</span> <span class="pre">profiles</span></code></a> of <strong>mhandle</strong>
-while ensuring consistency with the <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</li>
-<li><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetSequenceProfiles</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">profiles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetSequenceProfiles" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets the <a class="reference internal" href="#promod3.modelling.ModellingHandle.profiles" title="promod3.modelling.ModellingHandle.profiles"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sequence</span> <span class="pre">profiles</span></code></a> of <strong>mhandle</strong>
+while ensuring consistency with the <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</p></li>
+<li><p><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#ValueError" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">ValueError</span></code></a> when the given <strong>profiles</strong> are not consistent
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <strong>profiles</strong> are not consistent
with seqres in <strong>mhandle</strong></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetPsipredPredictions">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SetPsipredPredictions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>predictions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetPsipredPredictions" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets the <a class="reference internal" href="#promod3.modelling.ModellingHandle.psipred_predictions" title="promod3.modelling.ModellingHandle.psipred_predictions"><code class="xref py py-attr docutils literal"><span class="pre">predictions</span></code></a> of
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetPsipredPredictions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">predictions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetPsipredPredictions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets the <a class="reference internal" href="#promod3.modelling.ModellingHandle.psipred_predictions" title="promod3.modelling.ModellingHandle.psipred_predictions"><code class="xref py py-attr docutils literal notranslate"><span class="pre">predictions</span></code></a> of
<strong>mhandle</strong> while ensuring consistency with the
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Will have the predictions attached afterwards</li>
-<li><strong>predictions</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code></a>) – The predictions to attach</li>
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the predictions attached afterwards</p></li>
+<li><p><strong>predictions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a>) – The predictions to attach</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#ValueError" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">ValueError</span></code></a> when the given <strong>predictions</strong> are not consistent
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <strong>predictions</strong> are not consistent
with seqres in <strong>mhandle</strong></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetFraggerHandles">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SetFraggerHandles</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragger_handles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetFraggerHandles" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets <a class="reference internal" href="#promod3.modelling.ModellingHandle.fragger_handles" title="promod3.modelling.ModellingHandle.fragger_handles"><code class="xref py py-attr docutils literal"><span class="pre">fragger_handles</span></code></a> in <em>mhandle</em> while
-ensuring consistency with the <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">ModellingHandle.seqres</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Will have the fragger handles attached afterwards</li>
-<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a>) – The fragger handles to attach</li>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetFraggerHandles</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">fragger_handles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetFraggerHandles" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets <a class="reference internal" href="#promod3.modelling.ModellingHandle.fragger_handles" title="promod3.modelling.ModellingHandle.fragger_handles"><code class="xref py py-attr docutils literal notranslate"><span class="pre">fragger_handles</span></code></a> in <em>mhandle</em> while
+ensuring consistency with the <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingHandle.seqres</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the fragger handles attached afterwards</p></li>
+<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – The fragger handles to attach</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/exceptions.html#ValueError" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">ValueError</span></code></a> when the given <em>fragger_handles</em> are not
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <em>fragger_handles</em> are not
consistent with seqres in <em>mhandle</em></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CloseGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">CloseGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseGaps" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloseGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">merge_distance=4</em>, <em class="sig-param">fragment_db=None</em>, <em class="sig-param">structure_db=None</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">fragger_handles=None</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to close all gaps in a model, except termini. It will go through
following steps:</p>
<ul class="simple">
-<li>Try to close small deletions by relaxing them
-(see <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>)</li>
-<li>Iteratively merge gaps up to a distance <strong>merge_distance</strong>
-(see <a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal"><span class="pre">MergeGapsByDistance()</span></code></a>) and try to fill them with a database
-approach (see <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>)</li>
-<li>Try to fill remaining gaps using a Monte Carlo approach
-(see <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>)</li>
-<li>Large deletions get closed using a last resort approach
-(see <a class="reference internal" href="#promod3.modelling.CloseLargeDeletions" title="promod3.modelling.CloseLargeDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseLargeDeletions()</span></code></a>)</li>
+<li><p>Try to close small deletions by relaxing them
+(see <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>)</p></li>
+<li><p>Iteratively merge gaps up to a distance <strong>merge_distance</strong>
+(see <a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal notranslate"><span class="pre">MergeGapsByDistance()</span></code></a>) and try to fill them with a database
+approach (see <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>)</p></li>
+<li><p>Try to fill remaining gaps using a Monte Carlo approach
+(see <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>)</p></li>
+<li><p>Large deletions get closed using a last resort approach
+(see <a class="reference internal" href="#promod3.modelling.CloseLargeDeletions" title="promod3.modelling.CloseLargeDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseLargeDeletions()</span></code></a>)</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. merge distance when performing the database
-approach</li>
-<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – Database for searching fragments in database
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. merge distance when performing the database
+approach</p></li>
+<li><p><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – Database for searching fragments in database
approach, must be consistent with provided
-<strong>structure_db</strong>. A default is loaded if None.</li>
-<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Structure db from which the <strong>fragment_db</strong> gets
-it’s structural information. A default is loaded
-if None.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>
-and <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByMonteCarlo()</span></code></a> A default one is
-loaded if None.</li>
-<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>
+<strong>structure_db</strong>. A default is loaded if None.</p></li>
+<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structure db from which the <strong>fragment_db</strong> gets
+it’s structural information. A default is loaded
+if None.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
+and <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a> A default one is
+loaded if None.</p></li>
+<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>
objects for each chain in <strong>mhandle</strong>.
If provided, fragments will be used for
-sampling when the <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>
-gets executed.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</li>
-<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed.</li>
-<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> provides different sets
+sampling when the <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>
+gets executed.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</p></li>
+<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed.</p></li>
+<li><p><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
of weights that have been trained on different
loop subsets. If this flag is true, the length
dependent weights are used to close loops with
-database / Monte Carlo.</li>
+database / Monte Carlo.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CloseSmallDeletions">
-<code class="descclassname">promod3.modelling.</code><code class="descname">CloseSmallDeletions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_extension=9</em>, <em>clash_thresh=1.0</em>, <em>e_thresh=200</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>ff_lookup=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseSmallDeletions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloseSmallDeletions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">max_extension=9</em>, <em class="sig-param">clash_thresh=1.0</em>, <em class="sig-param">e_thresh=200</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">ff_lookup=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseSmallDeletions" title="Permalink to this definition">¶</a></dt>
<dd><p>Close small deletions by relaxing neighbouring residues.</p>
<p>Small deletions in the template from the target-template alignment have a
good chance to be bridged just by relaxing neighbours around a tiny gap.
Before diving into the more demanding tasks in modeling, those may be closed
already in the raw-model. After closure some checks are done to see if the
solution is stereochemically sensible.</p>
-<p>Closed gaps are removed from <code class="xref py py-attr docutils literal"><span class="pre">mhandle.gaps</span></code>.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<p>Closed gaps are removed from <code class="xref py py-attr docutils literal notranslate"><span class="pre">mhandle.gaps</span></code>.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
<span class="c1"># setup</span>
<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/gly.pdb'</span><span class="p">)</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="s1">'GGG-GGG'</span><span class="p">),</span>
- <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="s1">'GGGAGGG'</span><span class="p">))</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="s1">'GGGG-GGGG'</span><span class="p">),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="s1">'GGGGAGGGG'</span><span class="p">))</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
<span class="c1"># close small deletion</span>
@@ -828,51 +747,47 @@ solution is stereochemically sensible.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
-(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>)</li>
-<li><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Threshold for the backbone clash score. Acceptance
-means being lower than this.</li>
-<li><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Potential energy should be lower than this.</li>
-<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal"><span class="pre">ScoringGapExtender</span></code></a> instead
-of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
+(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>)</p></li>
+<li><p><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold for the backbone clash score. Acceptance
+means being lower than this.</p></li>
+<li><p><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Potential energy should be lower than this.</p></li>
+<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
The gap is penalized according as
0.8*length + sum(helices) + sum(sheets).
For the scondary-structure-penalty to work,
the model-template must have the appropriate
-information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a> is
+information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a> is
called (e.g. with
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
-<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
-of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>. Also works in combination
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</p></li>
+<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>. Also works in combination
with <cite>use_scoring_extender</cite>. This allows the gap
extender to skip neighboring gaps and to correctly
-handle gaps close to termini.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</li>
-<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed.</li>
-<li><strong>ff_lookup</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Forcefield to parametrize
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> in
-<a class="reference internal" href="loop_closing.html#promod3.modelling.BackboneRelaxer" title="promod3.modelling.BackboneRelaxer"><code class="xref py py-class docutils literal"><span class="pre">promod3.modelling.BackboneRelaxer</span></code></a>.
+handle gaps close to termini.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</p></li>
+<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed.</p></li>
+<li><p><strong>ff_lookup</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Forcefield to parametrize
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> in
+<a class="reference internal" href="loop_closing.html#promod3.modelling.BackboneRelaxer" title="promod3.modelling.BackboneRelaxer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.BackboneRelaxer</span></code></a>.
If set to None, the one returned by
-<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-func docutils literal"><span class="pre">promod3.loop.ForcefieldLookup.GetDefault()</span></code></a>
-gets used.</li>
+<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup.GetDefault()</span></code></a>
+gets used.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.MergeGapsByDistance">
-<code class="descclassname">promod3.modelling.</code><code class="descname">MergeGapsByDistance</code><span class="sig-paren">(</span><em>mhandle</em>, <em>distance</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGapsByDistance" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MergeGapsByDistance</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">distance</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGapsByDistance" title="Permalink to this definition">¶</a></dt>
<dd><p>Merge 2 neighbouring gaps by deleting residues in-between.</p>
<p>Check if two neighbouring gaps are at max. <em>distance</em> residues apart from
each other. Then delete the residues and store a new gap spanning the whole
@@ -880,8 +795,8 @@ stretch of original gaps and the deleted region. Original gaps will be
removed. Stem residues count to the gap, so <strong>A-A-A</strong> has a distance of 0.</p>
<p>IMPORTANT: we assume here that <em>mhandle</em> stores gaps sequentially.
Non-sequential gaps are ignored!</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
<span class="c1"># setup</span>
<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
@@ -897,35 +812,31 @@ Non-sequential gaps are ignored!</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The max. no. of residues between two gaps up to which
-merge happens.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</li>
-<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, two gaps only get merged if they’re
-both in this resnum range.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The max. no. of residues between two gaps up to which
+merge happens.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</p></li>
+<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, two gaps only get merged if they’re
+both in this resnum range.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByDatabase">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragment_db</em>, <em>structure_db</em>, <em>torsion_sampler=None</em>, <em>max_loops_to_search=40</em>, <em>min_loops_required=4</em>, <em>max_res_extension=-1</em>, <em>extended_search=True</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>max_num_all_atom=0</em>, <em>clash_thresh=-1</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">fragment_db</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">max_loops_to_search=40</em>, <em class="sig-param">min_loops_required=4</em>, <em class="sig-param">max_res_extension=-1</em>, <em class="sig-param">extended_search=True</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">score_variant=0</em>, <em class="sig-param">ring_punch_detection=1</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">max_num_all_atom=0</em>, <em class="sig-param">clash_thresh=-1</em>, <em class="sig-param">length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops from a structural database.</p>
<p>Usually this will extend the gaps a bit to match candidates from the
database. Do not expect a gap being filled in between its actual stem
residues.
This function cannot fill gaps at C- or N-terminal.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
<span class="c1"># setup</span>
<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
@@ -943,96 +854,92 @@ This function cannot fill gaps at C- or N-terminal.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – A fragment database coupled to the <em>structure_db</em>.</li>
-<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Backbone/profile data.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
-loaded if None.</li>
-<li><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – A fragment database coupled to the <em>structure_db</em>.</p></li>
+<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Backbone/profile data.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
+loaded if None.</p></li>
+<li><p><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
evaluated per loop. The actual found candidates
-may be more (if we found ‘enough’) or less (if
-not enough candidates exist) of this number.</li>
-<li><strong>min_loops_required</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Define how many candidates we require to close
+may be more (if we found ‘enough’) or less (if
+not enough candidates exist) of this number.</p></li>
+<li><p><strong>min_loops_required</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates we require to close
the loop. If we did not find at least this number
of candidates for a gap, we skip it without
-closing. Can be set to <code class="docutils literal"><span class="pre">max_loops_to_search</span></code>
+closing. Can be set to <code class="docutils literal notranslate"><span class="pre">max_loops_to_search</span></code>
(or equivalently to -1) to enforce that we only
-close gaps for which we found enough candidates.</li>
-<li><strong>max_res_extension</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Only allow this number of residues to be added to
+close gaps for which we found enough candidates.</p></li>
+<li><p><strong>max_res_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Only allow this number of residues to be added to
the gaps when extending. If set to <strong>-1</strong>, any
number of residues can be added (as long as the
-<cite>fragment_db</cite> allows it).</li>
-<li><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = more loop candidates are considered.
+<cite>fragment_db</cite> allows it).</p></li>
+<li><p><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = more loop candidates are considered.
The candidate search is done less precisely (see
-<a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a>).
+<a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a>).
The candidates are still scored and evaluated the
-same though (only more of them considered).</li>
-<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal"><span class="pre">ScoringGapExtender</span></code></a> instead
-of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
-<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
-<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
-<li><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <p>How to score loop candidates. Options:</p>
+same though (only more of them considered).</p></li>
+<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
+<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
+<li><p><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <p>How to score loop candidates. Options:</p>
<ul>
-<li><strong>0</strong>: put frame of backbone residues enclosing all
-candidates and score frame. This will also “score”
-non-modelled residues!</li>
-<li><strong>1</strong>: score candidates directly</li>
-<li><strong>2</strong>: like <strong>1</strong> but penalize length of candidate</li>
+<li><p><strong>0</strong>: put frame of backbone residues enclosing all
+candidates and score frame. This will also “score”
+non-modelled residues!</p></li>
+<li><p><strong>1</strong>: score candidates directly</p></li>
+<li><p><strong>2</strong>: like <strong>1</strong> but penalize length of candidate</p></li>
</ul>
-</li>
-<li><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <p>How to deal with ring punchings. Options:</p>
+</p></li>
+<li><p><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <p>How to deal with ring punchings. Options:</p>
<ul>
-<li><strong>0</strong>: not at all (fastest)</li>
-<li><strong>1</strong>: check for punchings with existing rings</li>
-<li><strong>2</strong>: check incl. sidechain for loop cand.</li>
+<li><p><strong>0</strong>: not at all (fastest)</p></li>
+<li><p><strong>1</strong>: check for punchings with existing rings</p></li>
+<li><p><strong>2</strong>: check incl. sidechain for loop cand.</p></li>
</ul>
-</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</li>
-<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed</li>
-<li><strong>max_num_all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If > 0, we prefilter loop candidates based on
+</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</p></li>
+<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed</p></li>
+<li><p><strong>max_num_all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If > 0, we prefilter loop candidates based on
non-all-atom-scores and apply all atom scoring to
the best <em>max_num_all_atom</em> candidates. If desired,
<em>5</em> is a good value here (larger values give only
numerical improvement). With <em>5</em>, this will be
approx. 2x slower than without and will give a
-slight improvement in loop selection.</li>
-<li><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If > 0, we only keep loop candidates which have a
-backbone clash score lower than this.</li>
-<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> provides different sets
+slight improvement in loop selection.</p></li>
+<li><p><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If > 0, we only keep loop candidates which have a
+backbone clash score lower than this.</p></li>
+<li><p><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
of weights that have been trained on different
loop subsets. If this flag is true, the length
dependent weights are used to select the final
-loops.</li>
+loops.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByMonteCarlo">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler=None</em>, <em>max_loops_to_search=6</em>, <em>max_extension=30</em>, <em>mc_num_loops=2</em>, <em>mc_steps=5000</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">max_loops_to_search=6</em>, <em class="sig-param">max_extension=30</em>, <em class="sig-param">mc_num_loops=2</em>, <em class="sig-param">mc_steps=5000</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">score_variant=0</em>, <em class="sig-param">ring_punch_detection=1</em>, <em class="sig-param">fragger_handles=None</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops with Monte Carlo sampling.</p>
-<p>This is meant as a “last-resort” approach when it is not possible to fill
-the loops from the database with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>.
+<p>This is meant as a “last-resort” approach when it is not possible to fill
+the loops from the database with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.
This will extend the gaps (up to <em>max_extension</em> times) a bit to allow for
more loop candidates to be found.</p>
<p>The loops are modelled by either sampling the dihedral angles or (if
-<em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> lists. The latter
+<em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> lists. The latter
is only used if the gap length is >= the length of fragments stored.</p>
<p>This function cannot fill gaps at C- or N-terminal.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
<span class="c1"># setup</span>
<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
@@ -1049,99 +956,91 @@ is only used if the gap length is >= the length of fragments stored.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
-loaded if None.</li>
-<li><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
-evaluated per loop.</li>
-<li><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
-(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>)</li>
-<li><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each extended gap
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
-<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
-<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal"><span class="pre">ScoringGapExtender</span></code></a> instead
-of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
-<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
-<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
-<li><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – How to score loop candidates (AllAtom not supported).
-See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>.</li>
-<li><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – How to deal with ring punchings.
-See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>.</li>
-<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
-fragger handle for each chain in <em>mhandle</em>.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</li>
-<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed</li>
-<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> provides different sets
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
+loaded if None.</p></li>
+<li><p><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
+evaluated per loop.</p></li>
+<li><p><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
+(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>)</p></li>
+<li><p><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each extended gap
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
+<li><p><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
+<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
+<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
+<li><p><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – How to score loop candidates (AllAtom not supported).
+See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.</p></li>
+<li><p><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – How to deal with ring punchings.
+See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.</p></li>
+<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
+fragger handle for each chain in <em>mhandle</em>.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</p></li>
+<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed</p></li>
+<li><p><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
of weights that have been trained on different
loop subsets. If this flag is true, the length
dependent weights are used to select the final
-loops.</li>
+loops.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CloseLargeDeletions">
-<code class="descclassname">promod3.modelling.</code><code class="descname">CloseLargeDeletions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>structure_db</em>, <em>linker_length=8</em>, <em>num_fragments=500</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseLargeDeletions" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloseLargeDeletions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">linker_length=8</em>, <em class="sig-param">num_fragments=500</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseLargeDeletions" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to close large deletions.</p>
-<p>This is meant as a “last-resort” approach. In some cases you cannot
+<p>This is meant as a “last-resort” approach. In some cases you cannot
close very large deletions simply because the two parts separated
by a deletion are too far apart. The idea is to sample a linker region
and always move the whole chain towards the n-terminus.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – The database from which to extract fragments for
-the linker region.</li>
-<li><strong>linker_length</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Desired length (in residues w/o stems) for the
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – The database from which to extract fragments for
+the linker region.</p></li>
+<li><p><strong>linker_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired length (in residues w/o stems) for the
linker. This may be shorter if extender cannot
-extend further.</li>
-<li><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to sample the linker.</li>
-<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal"><span class="pre">ScoringGapExtender</span></code></a> instead
-of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
-<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
-<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</li>
-<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed</li>
+extend further.</p></li>
+<li><p><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to sample the linker.</p></li>
+<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
+<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</p></li>
+<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ModelTermini">
-<code class="descclassname">promod3.modelling.</code><code class="descname">ModelTermini</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler</em>, <em>fragger_handles=None</em>, <em>mc_num_loops=20</em>, <em>mc_steps=5000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModelTermini" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ModelTermini</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">fragger_handles=None</em>, <em class="sig-param">mc_num_loops=20</em>, <em class="sig-param">mc_steps=5000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModelTermini" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to model termini with Monte Carlo sampling.</p>
<p>Use with care! This is an experimental feature which will increase coverage
but we do not assume that the resulting termini are of high quality!</p>
<p>The termini are modelled by either sampling the dihedral angles or (if
-<em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> lists. The latter
+<em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> lists. The latter
is only used if the gap length is >= the length of fragments stored.</p>
<p>Terminal gaps of length 1 are ignored by this function!</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
<span class="c1"># setup</span>
<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/gly.pdb'</span><span class="p">)</span>
@@ -1158,210 +1057,182 @@ is only used if the gap length is >= the length of fragments stored.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles.</li>
-<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
-fragger handle for each chain in <em>mhandle</em>.</li>
-<li><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each terminal gap
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
-<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles.</p></li>
+<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
+fragger handle for each chain in <em>mhandle</em>.</p></li>
+<li><p><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each terminal gap
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
+<li><p><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.BuildSidechains">
-<code class="descclassname">promod3.modelling.</code><code class="descname">BuildSidechains</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>rotamer_library=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BuildSidechains</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">merge_distance=4</em>, <em class="sig-param">fragment_db=None</em>, <em class="sig-param">structure_db=None</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">rotamer_library=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
<dd><p>Build sidechains for model.</p>
-<p>This is a wrapper for <a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>,
+<p>This is a wrapper for <a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>,
followed by a check for ring punches. If ring punches are found it
introduces gaps for the residues with punched rings and tries to fill them
-with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a> with <em>ring_punch_detection=2</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal"><span class="pre">MergeGapsByDistance()</span></code></a>
-if ring punches are found.</li>
-<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>
+with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a> with <em>ring_punch_detection=2</em>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal notranslate"><span class="pre">MergeGapsByDistance()</span></code></a>
+if ring punches are found.</p></li>
+<li><p><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
if ring punches are found. A default one is loaded
-if None.</li>
-<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>
+if None.</p></li>
+<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
if ring punches are found. A default one is loaded
-if None.</li>
-<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>
+if None.</p></li>
+<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
if ring punches are found. A default one is loaded
-if None.</li>
-<li><strong>rotamer_library</strong> (<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a> or
-<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Used as parameter for
-<code class="xref py py-func docutils literal"><span class="pre">modelling.ReconstructSidechains()</span></code>, a default
-one is loaded if None.</li>
+if None.</p></li>
+<li><p><strong>rotamer_library</strong> (<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a> or
+<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>) – Used as parameter for
+<code class="xref py py-func docutils literal notranslate"><span class="pre">modelling.ReconstructSidechains()</span></code>, a default
+one is loaded if None.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.MinimizeModelEnergy">
-<code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">max_iterations=12</em>, <em class="sig-param">max_iter_sd=20</em>, <em class="sig-param">max_iter_lbfgs=10</em>, <em class="sig-param">use_amber_ff=False</em>, <em class="sig-param">extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
-<li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
-<li>run up to <em>max_iter_lbfgs</em> minimization iter. of a Limited-memory
-Broyden-Fletcher-Goldfarb-Shanno method</li>
-<li>abort if no stereochemical problems found</li>
+<li><p>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</p></li>
+<li><p>run up to <em>max_iter_lbfgs</em> minimization iter. of a Limited-memory
+Broyden-Fletcher-Goldfarb-Shanno method</p></li>
+<li><p>abort if no stereochemical problems found</p></li>
</ul>
-<p>The idea is that we don’t want to minimize “too much”. So, we iteratively
+<p>The idea is that we don’t want to minimize “too much”. So, we iteratively
minimize until there are no stereochemical problems and not more.</p>
<p>To speed things up, this can run on multiple CPU threads by setting the
-env. variable <code class="docutils literal"><span class="pre">PM3_OPENMM_CPU_THREADS</span></code> to the number of desired threads.
+env. variable <code class="docutils literal notranslate"><span class="pre">PM3_OPENMM_CPU_THREADS</span></code> to the number of desired threads.
If the variable is not set, 1 thread will be used by default.</p>
<p>If the starting model is so bad that the energy is NaN or Inf from the start
(happens if atoms are on top of each other or almost), the energy
minimization is aborted. This issue is logged and added as a major issue to
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal"><span class="pre">modelling_issues</span></code></a> of <em>mhandle</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
-<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. number of iterations for SD+LBFGS</li>
-<li><strong>max_iter_sd</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. number of iterations within SD method</li>
-<li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</li>
-<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
-<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
-<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a> of <em>mhandle</em>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
+<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations for SD+LBFGS</p></li>
+<li><p><strong>max_iter_sd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within SD method</p></li>
+<li><p><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</p></li>
+<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
+CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
+<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The model including all oxygens as used in the minimizer.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CheckFinalModel">
-<code class="descclassname">promod3.modelling.</code><code class="descname">CheckFinalModel</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CheckFinalModel" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CheckFinalModel</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CheckFinalModel" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs samity checks on final models and reports problems.</p>
-<p>Issues are logged and tracked in <a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal"><span class="pre">modelling_issues</span></code></a>
+<p>Issues are logged and tracked in <a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a>
of <em>mhandle</em>. Major issues:</p>
<ul class="simple">
-<li>Chains with less than 3 residues (usually due to bad templates).</li>
-<li>Incomplete models (i.e. some gaps couldn’t be closed). One issue is
-created per unclosed gap and the stems of the gap are added to the issue.</li>
-<li>Complete models with sequence mismatches (should never happen).</li>
-<li>Residues with rings which have been punched by another bond.</li>
+<li><p>Chains with less than 3 residues (usually due to bad templates).</p></li>
+<li><p>Incomplete models (i.e. some gaps couldn’t be closed). One issue is
+created per unclosed gap and the stems of the gap are added to the issue.</p></li>
+<li><p>Complete models with sequence mismatches (should never happen).</p></li>
+<li><p>Residues with rings which have been punched by another bond.</p></li>
</ul>
<p>Minor issues:</p>
<ul class="simple">
-<li>Remaining stereo-chemical problems after energy minimization. The affected
-residues will have the boolean property “stereo_chemical_problem_backbone”
-set to True, if the problem affects backbone atoms.</li>
+<li><p>Remaining stereo-chemical problems after energy minimization. The affected
+residues will have the boolean property “stereo_chemical_problem_backbone”
+set to True, if the problem affects backbone atoms.</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle for which to perform checks.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle for which to perform checks.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ModellingIssue">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ModellingIssue</code><span class="sig-paren">(</span><em>text</em>, <em>severity</em>, <em>residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal"><span class="pre">text</span></code></a>.</li>
-<li><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal"><span class="pre">severity</span></code></a>.</li>
-<li><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal"><span class="pre">residue_list</span></code></a>.</li>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ModellingIssue</code><span class="sig-paren">(</span><em class="sig-param">text</em>, <em class="sig-param">severity</em>, <em class="sig-param">residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal notranslate"><span class="pre">text</span></code></a>.</p></li>
+<li><p><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal notranslate"><span class="pre">severity</span></code></a>.</p></li>
+<li><p><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal notranslate"><span class="pre">residue_list</span></code></a>.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.text">
-<code class="descname">text</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.text" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">text</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.text" title="Permalink to this definition">¶</a></dt>
<dd><p>Description of issue.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.severity">
-<code class="descname">severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.severity" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.severity" title="Permalink to this definition">¶</a></dt>
<dd><p>Severity of issue.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ModellingIssue.Severity" title="promod3.modelling.ModellingIssue.Severity"><code class="xref py py-class docutils literal"><span class="pre">Severity</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.ModellingIssue.Severity" title="promod3.modelling.ModellingIssue.Severity"><code class="xref py py-class docutils literal notranslate"><span class="pre">Severity</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.residue_list">
-<code class="descname">residue_list</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.residue_list" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">residue_list</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.residue_list" title="Permalink to this definition">¶</a></dt>
<dd><p>List of residues affected by issue (or empty list if global issue).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueView</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ModellingIssue.Severity">
-<em class="property">class </em><code class="descname">Severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-name descname">Severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates severities.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.Severity.MAJOR">
-<code class="descname">MAJOR</code><em class="property"> = 10</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MAJOR" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">MAJOR</code><em class="property"> = 10</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MAJOR" title="Permalink to this definition">¶</a></dt>
<dd><p>Major issues like MM-failures, incomplete models and ring punches.</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.Severity.MINOR">
-<code class="descname">MINOR</code><em class="property"> = 0</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MINOR" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">MINOR</code><em class="property"> = 0</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MINOR" title="Permalink to this definition">¶</a></dt>
<dd><p>Minor issues like remaining stereo-chemistry problems after MM.</p>
</dd></dl>
@@ -1369,42 +1240,111 @@ set to True, if the problem affects backbone atoms.</li>
<dl class="method">
<dt id="promod3.modelling.ModellingIssue.is_major">
-<code class="descclassname">ModellingIssue.</code><code class="descname">is_major</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue.is_major" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True if this is a major issue.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">is_major</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue.is_major" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True if this is a major issue.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.AddModellingIssue">
-<code class="descclassname">promod3.modelling.</code><code class="descname">AddModellingIssue</code><span class="sig-paren">(</span><em>mhandle</em>, <em>text</em>, <em>severity</em>, <em>residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AddModellingIssue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Adds a new <a class="reference internal" href="#promod3.modelling.ModellingIssue" title="promod3.modelling.ModellingIssue"><code class="xref py py-class docutils literal"><span class="pre">ModellingIssue</span></code></a> to
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal"><span class="pre">modelling_issues</span></code></a> in <em>mhandle</em>.</p>
-<p>If <em>mhandle</em> doesn’t contain the <a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal"><span class="pre">modelling_issues</span></code></a>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">AddModellingIssue</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">text</em>, <em class="sig-param">severity</em>, <em class="sig-param">residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AddModellingIssue" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adds a new <a class="reference internal" href="#promod3.modelling.ModellingIssue" title="promod3.modelling.ModellingIssue"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingIssue</span></code></a> to
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a> in <em>mhandle</em>.</p>
+<p>If <em>mhandle</em> doesn’t contain the <a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a>
attribute yet, it is added.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Will have the issue added to.</li>
-<li><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal"><span class="pre">ModellingIssue.text</span></code></a>.</li>
-<li><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal"><span class="pre">ModellingIssue.severity</span></code></a>.</li>
-<li><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal"><span class="pre">ModellingIssue.residue_list</span></code></a>.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the issue added to.</p></li>
+<li><p><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.text</span></code></a>.</p></li>
+<li><p><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.severity</span></code></a>.</p></li>
+<li><p><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.residue_list</span></code></a>.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
+</dd></dl>
+
+</div>
+<div class="section" id="alignment-fiddling">
+<h2>Alignment Fiddling<a class="headerlink" href="#alignment-fiddling" title="Permalink to this headline">¶</a></h2>
+<dl class="function">
+<dt id="promod3.modelling.DeleteGapCols">
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">DeleteGapCols</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeleteGapCols" title="Permalink to this definition">¶</a></dt>
+<dd><p>Deletes alignment columns that only contain gaps.</p>
+<p>Columns that only contain gaps (‘-‘) are removed. If no such column can be
+identified, the input alignment gets returned. A new alignment gets
+constructed otherwise. The sequences of the new alignment retain name, offset
+and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
+sequences.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The processed alignment</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="promod3.modelling.PullTerminalDeletions">
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">PullTerminalDeletions</code><span class="sig-paren">(</span><em class="sig-param">aln</em>, <em class="sig-param">min_terminal_anchor_size=4</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PullTerminalDeletions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Fixes deletions close to termini.</p>
+<p>Some alignment tools may produce alignments with deletions close to the
+termini. For example:</p>
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>SEQRES: A-----BCDE...
+ATOMSEQ: ABCDEFGHIJ...
+</pre></div>
+</div>
+<p>where A is the anchor residue. The default loop modelling pipeline would
+keep the position of A fixed and start to omit structural information from
+B, C, … until it is able to resolve the deletion. If the anchor is very
+short, a shift typically results in a better model:</p>
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>SEQRES: -----ABCDE...
+ATOMSEQ: ABCDEFGHIJ...
+</pre></div>
+</div>
+<p>This function checks whether the gap closest to any termini is a deletion
+(one or several ‘-‘ in the first sequence) and estimates the anchor size
+(number of aligned residues towards the respective termini from that gap).
+If the anchor size is smaller than <em>min_terminal_anchor_size</em>, a shift is
+applied and the deletion removed.</p>
+<p>This is done iteratively, until no deletion can be removed anymore.</p>
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>SEQRES: A-B--CDEF...
+ATOMSEQ: ABCDEFGHI...
+</pre></div>
+</div>
+<p>becomes</p>
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>SEQRES: ---ABCDEF...
+ATOMSEQ: ABCDEFGHI...
+</pre></div>
+</div>
+<p>given a <em>min_terminal_anchor_size</em>>2. If no shift can be performed, the
+input alignment gets returned. A new alignment gets constructed otherwise.
+The sequences of the new alignment retain name, offset and the potentially
+attached <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The processed alignment</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -1417,45 +1357,70 @@ attribute yet, it is added.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Modelling Pipeline</a><ul>
-<li><a class="reference internal" href="#build-raw-modelling-handle">Build Raw Modelling Handle</a></li>
-<li><a class="reference internal" href="#the-default-pipeline">The Default Pipeline</a></li>
-<li><a class="reference internal" href="#modelling-steps">Modelling Steps</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
<li>Next: <a href="model_checking.html" title="next chapter">Model Checking</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/pipeline.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1464,11 +1429,11 @@ attribute yet, it is added.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/pipeline.txt"
+ <a href="../_sources/modelling/pipeline.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 30408defd75febb96c9bec57b6ab4becf1d86336..819560fe1d078cf746d0514356c01d2229018e0d 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Sidechain Reconstruction — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Sidechain Reconstruction — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Modelling Algorithms" href="algorithms.html" />
<link rel="prev" title="Generating Loops De Novo" href="monte_carlo.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -51,14 +37,14 @@
<h1>Sidechain Reconstruction<a class="headerlink" href="#sidechain-reconstruction" title="Permalink to this headline">¶</a></h1>
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
-<li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
-<li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
-and used to reconstruct sidechains of single loops</li>
+<li><p>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
+<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p></li>
+<li><p>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
+and used to reconstruct sidechains of single loops</p></li>
</ul>
<p>Example usage:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">mol</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
<span class="c1"># load a protein </span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
@@ -70,8 +56,8 @@ and used to reconstruct sidechains of single loops</li>
<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s1">'sidechain_test_rec.pdb'</span><span class="p">)</span>
</pre></div>
</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">modelling</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">modelling</span>
<span class="c1"># load example (has res. numbering starting at 1)</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
@@ -100,44 +86,40 @@ and used to reconstruct sidechains of single loops</li>
<h2>Reconstruct Function<a class="headerlink" href="#reconstruct-function" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.ReconstructSidechains">
-<code class="descclassname">promod3.modelling.</code><code class="descname">ReconstructSidechains</code><span class="sig-paren">(</span><em>ent</em>, <em>keep_sidechains=False</em>, <em>build_disulfids=True</em>, <em>rotamer_model='frm'</em>, <em>consider_ligands=True</em>, <em>rotamer_library=None</em>, <em>optimize_subrotamers=True</em>, <em>graph_max_complexity=100000000</em>, <em>graph_initial_epsilon=0.02</em>, <em>energy_function='SCWRL4'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReconstructSidechains" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ReconstructSidechains</code><span class="sig-paren">(</span><em class="sig-param">ent</em>, <em class="sig-param">keep_sidechains=False</em>, <em class="sig-param">build_disulfids=True</em>, <em class="sig-param">rotamer_model='frm'</em>, <em class="sig-param">consider_ligands=True</em>, <em class="sig-param">rotamer_library=None</em>, <em class="sig-param">optimize_subrotamers=True</em>, <em class="sig-param">graph_max_complexity=100000000</em>, <em class="sig-param">graph_initial_epsilon=0.02</em>, <em class="sig-param">energy_function='SCWRL4'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReconstructSidechains" title="Permalink to this definition">¶</a></dt>
<dd><p>Reconstruct sidechains for the given structure.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
-reconstruction gets directly applied on the structure itself.</li>
-<li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+reconstruction gets directly applied on the structure itself.</p></li>
+<li><p><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
containing all required atoms) should be kept rigid
-and directly be added to the frame.</li>
-<li><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
+and directly be added to the frame.</p></li>
+<li><p><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
searched. If a disulfid bond is found, the two
participating cysteins are fixed and added to
-the frame.</li>
-<li><strong>rotamer_model</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Rotamer model to be used, can either be “frm” or “rrm”</li>
-<li><strong>consider_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether to add ligands (anything in chain
-‘_’) as static objects.</li>
-<li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code>) – A rotamer library to extract the rotamers from. The
-default is to call <code class="xref py py-meth docutils literal"><span class="pre"><LoadBBDepLib>()</span></code>.</li>
-<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Only considered when <em>rotamer_model</em>
-is “frm”.
+the frame.</p></li>
+<li><p><strong>rotamer_model</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Rotamer model to be used, can either be “frm” or “rrm”</p></li>
+<li><p><strong>consider_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether to add ligands (anything in chain
+‘_’) as static objects.</p></li>
+<li><p><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code>) – A rotamer library to extract the rotamers from. The
+default is to call <code class="xref py py-meth docutils literal notranslate"><span class="pre"><LoadBBDepLib>()</span></code>.</p></li>
+<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Only considered when <em>rotamer_model</em>
+is “frm”.
If set to True, the FRM solution undergoes
some postprocessing by calling
-<code class="xref py py-func docutils literal"><span class="pre">SubrotamerOptimizer()</span></code> with default
-parametrization.</li>
-<li><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. complexity for
-<code class="xref py py-meth docutils literal"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</li>
-<li><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Initial epsilon for
-<code class="xref py py-meth docutils literal"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</li>
-<li><strong>energy_function</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – What energy function to use can be any in
-[“SCWRL4”, “SCWRL3”]</li>
+<code class="xref py py-func docutils literal notranslate"><span class="pre">SubrotamerOptimizer()</span></code> with default
+parametrization.</p></li>
+<li><p><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. complexity for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</p></li>
+<li><p><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Initial epsilon for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</p></li>
+<li><p><strong>energy_function</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – What energy function to use can be any in
+[“SCWRL4”, “SCWRL3”]</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -145,9 +127,9 @@ parametrization.</li>
<h2>SidechainReconstructor Class<a class="headerlink" href="#sidechainreconstructor-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.SidechainReconstructor">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SidechainReconstructor</code><span class="sig-paren">(</span><em>keep_sidechains=True</em>, <em>build_disulfids=True</em>, <em>optimize_subrotamers=False</em>, <em>remodel_cutoff=20</em>, <em>rigid_frame_cutoff=0</em>, <em>graph_max_complexity=100000000</em>, <em>graph_intial_epsilon=0.02</em>, <em>disulfid_score_thresh=45</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SidechainReconstructor</code><span class="sig-paren">(</span><em class="sig-param">keep_sidechains=True</em>, <em class="sig-param">build_disulfids=True</em>, <em class="sig-param">optimize_subrotamers=False</em>, <em class="sig-param">remodel_cutoff=20</em>, <em class="sig-param">rigid_frame_cutoff=0</em>, <em class="sig-param">graph_max_complexity=100000000</em>, <em class="sig-param">graph_intial_epsilon=0.02</em>, <em class="sig-param">disulfid_score_thresh=45</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>Reconstruct sidechains for single loops or residues. Must be linked to an
-all atom env. (<a class="reference internal" href="#promod3.modelling.SidechainReconstructor.AttachEnvironment" title="promod3.modelling.SidechainReconstructor.AttachEnvironment"><code class="xref py py-meth docutils literal"><span class="pre">AttachEnvironment()</span></code></a>) containing the structural data.
+all atom env. (<a class="reference internal" href="#promod3.modelling.SidechainReconstructor.AttachEnvironment" title="promod3.modelling.SidechainReconstructor.AttachEnvironment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AttachEnvironment()</span></code></a>) containing the structural data.
Residues are identified as N- or C-terminal according to the seqres in the
environment. This means that residues preceeded / followed by gaps are not
treated as terminal! In the reconstruction procedure you can specify
@@ -160,25 +142,23 @@ will be considered for remodelling. Everything further away than 20A but
within 20A + 10A = 30A will also be considered as rigid frame (all
backbone atoms and the sidechain if present). The distance criteria is the
CB atom distance between residues (CA in case of glycine).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in env. (i.e.
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in env. (i.e.
containing all required atoms) should be kept rigid
-and directly be added to the result.</li>
-<li><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
+and directly be added to the result.</p></li>
+<li><p><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
searched. If a disulfid bond is found, the two
participating cysteins are fixed and added to
-the result.</li>
-<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether the
-<a class="reference internal" href="../sidechain/subrotamer_optimizer.html#promod3.sidechain.SubrotamerOptimizer" title="promod3.sidechain.SubrotamerOptimizer"><code class="xref py py-func docutils literal"><span class="pre">SubrotamerOptimizer()</span></code></a>
+the result.</p></li>
+<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether the
+<a class="reference internal" href="../sidechain/subrotamer_optimizer.html#promod3.sidechain.SubrotamerOptimizer" title="promod3.sidechain.SubrotamerOptimizer"><code class="xref py py-func docutils literal notranslate"><span class="pre">SubrotamerOptimizer()</span></code></a>
with default parametrization should be called
-if we’re dealing with FRM rotamers.</li>
-<li><strong>remodel_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Cutoff to identify all residues that need to be
-remodelled.</li>
-<li><strong>rigid_frame_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Cutoff to control the visibility of the rigid
+if we’re dealing with FRM rotamers.</p></li>
+<li><p><strong>remodel_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to identify all residues that need to be
+remodelled.</p></li>
+<li><p><strong>rigid_frame_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to control the visibility of the rigid
frame to the reconstruction procedure.
Everything within
[<em>remodel_cutoff</em>,
@@ -186,25 +166,23 @@ Everything within
will be considered as ridig frame. Small sidenote:
if the <em>keep_sidechains</em> flag is true and all
residues within <em>remodel_cutoff</em> already have a
-sidechain, the <em>rigid_frame_cutoff</em> won’t have any
-effect.</li>
-<li><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. complexity for
-<code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</li>
-<li><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Initial epsilon for
-<code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</li>
-<li><strong>disulfid_score_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If <code class="xref py py-meth docutils literal"><span class="pre">DisulfidScore()</span></code> between two CYS is
+sidechain, the <em>rigid_frame_cutoff</em> won’t have any
+effect.</p></li>
+<li><p><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. complexity for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</p></li>
+<li><p><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Initial epsilon for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</p></li>
+<li><p><strong>disulfid_score_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If <code class="xref py py-meth docutils literal notranslate"><span class="pre">DisulfidScore()</span></code> between two CYS is
below this threshold, we consider them to be
-disulfid-bonded.</li>
+disulfid-bonded.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.modelling.SidechainReconstructor.Reconstruct">
-<code class="descname">Reconstruct</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.Reconstruct" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Reconstruct</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.Reconstruct" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">Reconstruct</code><span class="sig-paren">(</span><em>start_resnum_list</em>, <em>num_residues_list</em>, <em>chain_idx_list</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">Reconstruct</code><span class="sig-paren">(</span><em class="sig-param">start_resnum_list</em>, <em class="sig-param">num_residues_list</em>, <em class="sig-param">chain_idx_list</em><span class="sig-paren">)</span></dt>
<dd><p>Reconstruct sidechains for one or several loops extracted from environment.
Overlapping loops are merged and 0-length loops are removed. All residues in
the loop(s) are expected to contain valid CB positions (or CA for GLY),
@@ -214,70 +192,62 @@ loop(s) and in the surrounding with all backbone and sidechain heavy atom
positions set.</p>
<p>Note that the structural data of the loop(s) is expected to be in the linked
environment before calling this!</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</li>
-<li><strong>start_resnum_list</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Starts of loops.</li>
-<li><strong>num_residues_list</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Lengths of loops.</li>
-<li><strong>chain_idx_list</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chains the loops belong to.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</p></li>
+<li><p><strong>start_resnum_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Starts of loops.</p></li>
+<li><p><strong>num_residues_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Lengths of loops.</p></li>
+<li><p><strong>chain_idx_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chains the loops belong to.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A helper object with all the reconstruction results.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructionData</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if reconstructor was never attached
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A helper object with all the reconstruction results.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if reconstructor was never attached
to an environment or if parameters lead to invalid / unset
positions in environment.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.SidechainReconstructor.AttachEnvironment">
-<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em>, <em>use_frm=True</em>, <em>use_bbdep_lib=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em>, <em class="sig-param">use_frm=True</em>, <em class="sig-param">use_bbdep_lib=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em>, <em>use_frm</em>, <em>rotamer_library</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em>, <em class="sig-param">use_frm</em>, <em class="sig-param">rotamer_library</em><span class="sig-paren">)</span></dt>
<dd><p>Link reconstructor to given <em>env</em>. A helper class is used in the background
to provide sidechain-objects for the environment. As this class is reused by
every reconstructor linked to <em>env</em>, the used parameters must be consistent
if multiple reconstructors are used (or you must use a distinct <em>env</em>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) – Link to this environment.</li>
-<li><strong>use_frm</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, use flexible rotamer model, else rigid.</li>
-<li><strong>use_bbdep_lib</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, use default backbone dependent rot. library
-(<code class="xref py py-meth docutils literal"><span class="pre">LoadBBDepLib()</span></code>), else use
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link to this environment.</p></li>
+<li><p><strong>use_frm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, use flexible rotamer model, else rigid.</p></li>
+<li><p><strong>use_bbdep_lib</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, use default backbone dependent rot. library
+(<code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadBBDepLib()</span></code>), else use
backbone independent one
-(<code class="xref py py-meth docutils literal"><span class="pre">LoadLib()</span></code>).</li>
-<li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code>) – Custom rotamer library to be used.</li>
+(<code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadLib()</span></code>).</p></li>
+<li><p><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code>) – Custom rotamer library to be used.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>env</em> was already linked to
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> was already linked to
another reconstructor with inconsistent parameters. Acceptable
changes:</p>
-<ul class="last simple">
-<li><em>keep_sidechains</em> = True, if previously False</li>
-<li><em>build_disulfids</em> = False, if previously True</li>
+<ul class="simple">
+<li><p><em>keep_sidechains</em> = True, if previously False</p></li>
+<li><p><em>build_disulfids</em> = False, if previously True</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -287,32 +257,29 @@ changes:</p>
<h2>The SidechainReconstructionData class<a class="headerlink" href="#the-sidechainreconstructiondata-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.SidechainReconstructionData">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SidechainReconstructionData</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SidechainReconstructionData</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData" title="Permalink to this definition">¶</a></dt>
<dd><p>Contains the results of a sidechain reconstruction
-(<a class="reference internal" href="#promod3.modelling.SidechainReconstructor.Reconstruct" title="promod3.modelling.SidechainReconstructor.Reconstruct"><code class="xref py py-meth docutils literal"><span class="pre">SidechainReconstructor.Reconstruct()</span></code></a>). All attributes are read only!</p>
+(<a class="reference internal" href="#promod3.modelling.SidechainReconstructor.Reconstruct" title="promod3.modelling.SidechainReconstructor.Reconstruct"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SidechainReconstructor.Reconstruct()</span></code></a>). All attributes are read only!</p>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.env_pos">
-<code class="descname">env_pos</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.env_pos" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">env_pos</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.env_pos" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for structural data and mapping to the internal residue indices
-of the used <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>. Useful for scoring and env.
+of the used <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>. Useful for scoring and env.
updates.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnvPositions</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.loop_start_indices">
-<code class="descname">loop_start_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_start_indices" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">loop_start_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_start_indices" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.SidechainReconstructionData.loop_lengths">
-<code class="descname">loop_lengths</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_lengths" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">loop_lengths</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_lengths" title="Permalink to this definition">¶</a></dt>
<dd><p>The first <em>sum(loop_lengths)</em> residues in
-<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnvPositions.res_indices" title="promod3.loop.AllAtomEnvPositions.res_indices"><code class="xref py py-attr docutils literal"><span class="pre">res_indices</span></code></a> of <em>env_pos</em> are
+<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnvPositions.res_indices" title="promod3.loop.AllAtomEnvPositions.res_indices"><code class="xref py py-attr docutils literal notranslate"><span class="pre">res_indices</span></code></a> of <em>env_pos</em> are
guaranteed to belong to the actual input, all the rest comes from the close
environment.</p>
<p>Each input loop (apart from overlapping and 0-length loops) is defined by an
@@ -321,74 +288,59 @@ entry in <em>loop_start_indices</em> and <em>loop_lengths</em>. For loop <em>i_l
<em>res_indices[loop_start_indices[i_loop] + loop_lengths[i_loop] - 1]</em> is the
C-stem of the loop. The loop indices are contiguous in <em>res_indices</em> between
the stems.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.rotamer_res_indices">
-<code class="descname">rotamer_res_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.rotamer_res_indices" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">rotamer_res_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.rotamer_res_indices" title="Permalink to this definition">¶</a></dt>
<dd><p>Indices of residues within <em>env_pos</em> for which we generated a new sidechain
(in [<em>0, len(env_pos.res_indices)-1</em>]).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.disulfid_bridges">
-<code class="descname">disulfid_bridges</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.disulfid_bridges" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">disulfid_bridges</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.disulfid_bridges" title="Permalink to this definition">¶</a></dt>
<dd><p>Pairs of residue indices within <em>env_pos</em> for which we generated a disulfid
bridge (indices in [<em>0, len(env_pos.res_indices)-1</em>]).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.is_n_ter">
-<code class="descname">is_n_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_n_ter" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">is_n_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_n_ter" title="Permalink to this definition">¶</a></dt>
<dd><p>True/False depending on whether a given residue in <em>env_pos</em> is N-terminal
in the environment (same length as <em>env_pos.res_indices</em>)</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.is_c_ter">
-<code class="descname">is_c_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_c_ter" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">is_c_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_c_ter" title="Permalink to this definition">¶</a></dt>
<dd><p>True/False depending on whether a given residue in <em>env_pos</em> is C-terminal
in the environment (same length as <em>env_pos.res_indices</em>)</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -403,21 +355,45 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Sidechain Reconstruction</a><ul>
-<li><a class="reference internal" href="#reconstruct-function">Reconstruct Function</a></li>
-<li><a class="reference internal" href="#sidechainreconstructor-class">SidechainReconstructor Class</a></li>
-<li><a class="reference internal" href="#the-sidechainreconstructiondata-class">The SidechainReconstructionData class</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="monte_carlo.html" title="previous chapter">Generating Loops De Novo</a></li>
<li>Next: <a href="algorithms.html" title="next chapter">Modelling Algorithms</a></li>
</ul></li>
@@ -425,23 +401,24 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/modelling/sidechain_reconstruction.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -450,11 +427,11 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/modelling/sidechain_reconstruction.txt"
+ <a href="../_sources/modelling/sidechain_reconstruction.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 602290626e1f18ec433a41b4583f12e17c2fe4d1..2edbb8c2019816293136aa6a0b53aa7aaa558d89 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index a618910159389fb793673c05bc569d7dd15905f5..dcdb306338c2e39a7d64ae4c39f6f40f35d802d9 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -1,43 +1,29 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Using Binary Files In ProMod3 — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Using Binary Files In ProMod3 — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="License" href="license.html" />
- <link rel="prev" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
+ <link rel="prev" title="ProMod3’s Share Of CMake" href="cmake/index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -54,17 +40,17 @@ files to be loaded and stored. Here, we provide guidelines and describe helper
tools to perform tasks related to loading and storing binary files.</p>
<p>Generally, each binary file consists of a short header and binary data.
The header ensures consistency between the storing and the loading of data,
-while the “binary data” is some binary representation of the data of interest.</p>
+while the “binary data” is some binary representation of the data of interest.</p>
<p>The main issue, we try to address is that in C++, the binary representation
of objects can be machine- and compiler-dependent. The standard guarantees
-though that <code class="docutils literal"><span class="pre">sizeof(char)</span> <span class="pre">=</span> <span class="pre">1</span></code> and that <code class="docutils literal"><span class="pre">std::vector</span></code> is contiguous in
-memory. Everything else (e.g. <code class="docutils literal"><span class="pre">sizeof(int)</span></code>, endianness, padding of structs)
+though that <code class="docutils literal notranslate"><span class="pre">sizeof(char)</span> <span class="pre">=</span> <span class="pre">1</span></code> and that <code class="docutils literal notranslate"><span class="pre">std::vector</span></code> is contiguous in
+memory. Everything else (e.g. <code class="docutils literal notranslate"><span class="pre">sizeof(int)</span></code>, endianness, padding of structs)
can vary. Two approaches can be used:</p>
<ol class="arabic simple">
-<li>Raw binary data files which are very fast to load, but assume a certain
-memory-layout for the internal representation of data</li>
-<li>Portable binary data files which are slow to load, but do not assume a given
-memory-layout for the internal representation of data</li>
+<li><p>Raw binary data files which are very fast to load, but assume a certain
+memory-layout for the internal representation of data</p></li>
+<li><p>Portable binary data files which are slow to load, but do not assume a given
+memory-layout for the internal representation of data</p></li>
</ol>
<p>Portable I/O should always be provided for binary files. If this is too slow
for your needs, you can provide functionality for raw binary files. In that
@@ -72,86 +58,86 @@ case you should still distribute only the portable file and provide a
converter which loads the portable file and stores a raw binary file for
further use. Storing and loading of raw binary files on the same machine with
the same compiler should never be an issue.</p>
-<p>For instance, the classes <a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>,
-<a class="reference internal" href="loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>, <a class="reference internal" href="loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>,
-<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a> and
-<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a> use this approach and the conversion is
-automatically done in the <code class="docutils literal"><span class="pre">make</span></code> process. Code examples are given in the unit
-tests in <code class="file docutils literal"><span class="pre">test_check_io.cc</span></code> and <code class="file docutils literal"><span class="pre">test_portable_binary.cc</span></code> and in the
+<p>For instance, the classes <a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>,
+<a class="reference internal" href="loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>, <a class="reference internal" href="loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>,
+<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a> and
+<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a> use this approach and the conversion is
+automatically done in the <code class="docutils literal notranslate"><span class="pre">make</span></code> process. Code examples are given in the unit
+tests in <code class="file docutils literal notranslate"><span class="pre">test_check_io.cc</span></code> and <code class="file docutils literal notranslate"><span class="pre">test_portable_binary.cc</span></code> and in the
C++ code of the classes listed above (see methods Load, Save, LoadPortable and
SavePortable).</p>
<div class="section" id="file-header">
<h2>File Header<a class="headerlink" href="#file-header" title="Permalink to this headline">¶</a></h2>
<p>The header is written/read with functions provided in the header file
-<code class="file docutils literal"><span class="pre">promod3/core/check_io.hh</span></code>. The header is written/read before the data
+<code class="file docutils literal notranslate"><span class="pre">promod3/core/check_io.hh</span></code>. The header is written/read before the data
itself and is structured as follows:</p>
<ul class="simple">
-<li>a “magic number” (ensures that we can read <code class="docutils literal"><span class="pre">uint32_t</span></code> which is needed for
-the following fields)</li>
-<li>a version number (allows for backwards-compatibility)</li>
-<li>sizes for all types which are treated as raw memory (i.e. casted to a byte
-(<code class="docutils literal"><span class="pre">char</span></code>) array and written either to memory or to a stream)</li>
-<li>example values for the used base-types (ensures we can e.g. read an <code class="docutils literal"><span class="pre">int</span></code>)</li>
+<li><p>a “magic number” (ensures that we can read <code class="docutils literal notranslate"><span class="pre">uint32_t</span></code> which is needed for
+the following fields)</p></li>
+<li><p>a version number (allows for backwards-compatibility)</p></li>
+<li><p>sizes for all types which are treated as raw memory (i.e. casted to a byte
+(<code class="docutils literal notranslate"><span class="pre">char</span></code>) array and written either to memory or to a stream)</p></li>
+<li><p>example values for the used base-types (ensures we can e.g. read an <code class="docutils literal notranslate"><span class="pre">int</span></code>)</p></li>
</ul>
<p>For portable I/O (see below), we only write/read fixed-width fundamental
-data-types (e.g. <code class="docutils literal"><span class="pre">int32_t</span></code>, <code class="docutils literal"><span class="pre">float</span></code>). Hence, we only check if we can
+data-types (e.g. <code class="docutils literal notranslate"><span class="pre">int32_t</span></code>, <code class="docutils literal notranslate"><span class="pre">float</span></code>). Hence, we only check if we can
read/write those types.
-When data is converted from a non-fixed fundamental type <code class="docutils literal"><span class="pre">T</span></code> (e.g. <code class="docutils literal"><span class="pre">uint</span></code>,
-<code class="docutils literal"><span class="pre">short</span></code>, <code class="docutils literal"><span class="pre">Real</span></code>), we furthermore ensure that the used fixed-width type
-(size written to file) is <code class="docutils literal"><span class="pre"><=</span> <span class="pre">sizeof(T)</span></code>.</p>
+When data is converted from a non-fixed fundamental type <code class="docutils literal notranslate"><span class="pre">T</span></code> (e.g. <code class="docutils literal notranslate"><span class="pre">uint</span></code>,
+<code class="docutils literal notranslate"><span class="pre">short</span></code>, <code class="docutils literal notranslate"><span class="pre">Real</span></code>), we furthermore ensure that the used fixed-width type
+(size written to file) is <code class="docutils literal notranslate"><span class="pre"><=</span> <span class="pre">sizeof(T)</span></code>.</p>
<p>All write functions (when saving a binary) should be mirrored by the
corresponding check (or get) function in the exact same order when loading.</p>
<p>All functions are templatized to work with any OST-like data sink or source
-and overloaded to work with <code class="docutils literal"><span class="pre">std::ofstream</span></code> and <code class="docutils literal"><span class="pre">std::ifstream</span></code>.</p>
+and overloaded to work with <code class="docutils literal notranslate"><span class="pre">std::ofstream</span></code> and <code class="docutils literal notranslate"><span class="pre">std::ifstream</span></code>.</p>
</div>
<div class="section" id="portable-binary-data">
<h2>Portable Binary Data<a class="headerlink" href="#portable-binary-data" title="Permalink to this headline">¶</a></h2>
<p>Portable files are written/read with functions and classes provided in the
-header file <code class="file docutils literal"><span class="pre">promod3/core/portable_binary_serializer.hh</span></code>.
+header file <code class="file docutils literal notranslate"><span class="pre">promod3/core/portable_binary_serializer.hh</span></code>.
Generally, we store any data-structure value-by-value as fixed-width types!</p>
<p>Writing and reading is performed by the following classes:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">PortableBinaryDataSink</span></code> to write files (opened as <code class="docutils literal"><span class="pre">std::ofstream</span></code>)</li>
-<li><code class="docutils literal"><span class="pre">PortableBinaryDataSource</span></code> to read files (opened as <code class="docutils literal"><span class="pre">std::ifstream</span></code>)</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">PortableBinaryDataSink</span></code> to write files (opened as <code class="docutils literal notranslate"><span class="pre">std::ofstream</span></code>)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">PortableBinaryDataSource</span></code> to read files (opened as <code class="docutils literal notranslate"><span class="pre">std::ifstream</span></code>)</p></li>
</ul>
-<p>Each serializable class must define a <code class="docutils literal"><span class="pre">Serialize</span></code> function that accepts sinks
+<p>Each serializable class must define a <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> function that accepts sinks
and sources, such as:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="k">template</span> <span class="o"><</span><span class="k">typename</span> <span class="n">DS</span><span class="o">></span>
+<div class="highlight-cpp notranslate"><div class="highlight"><pre><span></span><span class="k">template</span> <span class="o"><</span><span class="k">typename</span> <span class="n">DS</span><span class="o">></span>
<span class="kt">void</span> <span class="n">Serialize</span><span class="p">(</span><span class="n">DS</span><span class="o">&</span> <span class="n">ds</span><span class="p">)</span> <span class="p">{</span>
<span class="c1">// serialize element-by-element</span>
<span class="p">}</span>
</pre></div>
</div>
-<p>Or if this is not possible for an object of type <code class="docutils literal"><span class="pre">T</span></code>, we need to define
+<p>Or if this is not possible for an object of type <code class="docutils literal notranslate"><span class="pre">T</span></code>, we need to define
global functions such as:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSource</span><span class="o">&</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span><span class="o">&</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
+<div class="highlight-cpp notranslate"><div class="highlight"><pre><span></span><span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSource</span><span class="o">&</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span><span class="o">&</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
<span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSink</span><span class="o">&</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
</pre></div>
</div>
-<p>Given a sink or source object <code class="docutils literal"><span class="pre">ds</span></code>, we read/write an object <code class="docutils literal"><span class="pre">v</span></code> as:</p>
+<p>Given a sink or source object <code class="docutils literal notranslate"><span class="pre">ds</span></code>, we read/write an object <code class="docutils literal notranslate"><span class="pre">v</span></code> as:</p>
<ul class="simple">
-<li><code class="docutils literal"><span class="pre">ds</span> <span class="pre">&</span> <span class="pre">v</span></code>, if <code class="docutils literal"><span class="pre">v</span></code> is an instance of a class, a <code class="docutils literal"><span class="pre">bool</span></code> or any
-fixed-width type (e.g. <code class="docutils literal"><span class="pre">char</span></code>, <code class="docutils literal"><span class="pre">int_32_t</span></code>, <code class="docutils literal"><span class="pre">float</span></code>)</li>
-<li><code class="docutils literal"><span class="pre">core::ConvertBaseType<T>(ds,</span> <span class="pre">v)</span></code>, where <code class="docutils literal"><span class="pre">T</span></code> is a fixed-width type.
-<code class="docutils literal"><span class="pre">v</span></code> will then be converted to/from <code class="docutils literal"><span class="pre">T</span></code>. This is needed for any non-fixed
-fundamental type (e.g. <code class="docutils literal"><span class="pre">uint</span></code>, <code class="docutils literal"><span class="pre">short</span></code>, <code class="docutils literal"><span class="pre">Real</span></code>).</li>
+<li><p><code class="docutils literal notranslate"><span class="pre">ds</span> <span class="pre">&</span> <span class="pre">v</span></code>, if <code class="docutils literal notranslate"><span class="pre">v</span></code> is an instance of a class, a <code class="docutils literal notranslate"><span class="pre">bool</span></code> or any
+fixed-width type (e.g. <code class="docutils literal notranslate"><span class="pre">char</span></code>, <code class="docutils literal notranslate"><span class="pre">int_32_t</span></code>, <code class="docutils literal notranslate"><span class="pre">float</span></code>)</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">core::ConvertBaseType<T>(ds,</span> <span class="pre">v)</span></code>, where <code class="docutils literal notranslate"><span class="pre">T</span></code> is a fixed-width type.
+<code class="docutils literal notranslate"><span class="pre">v</span></code> will then be converted to/from <code class="docutils literal notranslate"><span class="pre">T</span></code>. This is needed for any non-fixed
+fundamental type (e.g. <code class="docutils literal notranslate"><span class="pre">uint</span></code>, <code class="docutils literal notranslate"><span class="pre">short</span></code>, <code class="docutils literal notranslate"><span class="pre">Real</span></code>).</p></li>
</ul>
<p>Implementation notes:</p>
<ul class="simple">
-<li>the <code class="docutils literal"><span class="pre">Serialize</span></code> function for fundamental types takes care of endianness
-(all written as little endian and converted from/to native endianness)</li>
-<li>custom <code class="docutils literal"><span class="pre">Serialize</span></code> functions exist for <code class="docutils literal"><span class="pre">String</span></code> (= <code class="docutils literal"><span class="pre">std::string</span></code>),
-<code class="docutils literal"><span class="pre">std::vector<T></span></code> and <code class="docutils literal"><span class="pre">std::pair<T,T2></span></code>. It will throw an error if the
-used type <code class="docutils literal"><span class="pre">T</span></code> or <code class="docutils literal"><span class="pre">T2</span></code> is a fundamental type. In that case, you have to
-serialize the values manually and convert each element appropriately.</li>
-<li>you can use <code class="docutils literal"><span class="pre">ds.IsSource()</span></code> to distinguish sources and sinks.</li>
+<li><p>the <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> function for fundamental types takes care of endianness
+(all written as little endian and converted from/to native endianness)</p></li>
+<li><p>custom <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> functions exist for <code class="docutils literal notranslate"><span class="pre">String</span></code> (= <code class="docutils literal notranslate"><span class="pre">std::string</span></code>),
+<code class="docutils literal notranslate"><span class="pre">std::vector<T></span></code> and <code class="docutils literal notranslate"><span class="pre">std::pair<T,T2></span></code>. It will throw an error if the
+used type <code class="docutils literal notranslate"><span class="pre">T</span></code> or <code class="docutils literal notranslate"><span class="pre">T2</span></code> is a fundamental type. In that case, you have to
+serialize the values manually and convert each element appropriately.</p></li>
+<li><p>you can use <code class="docutils literal notranslate"><span class="pre">ds.IsSource()</span></code> to distinguish sources and sinks.</p></li>
</ul>
</div>
<div class="section" id="code-example">
<h2>Code Example<a class="headerlink" href="#code-example" title="Permalink to this headline">¶</a></h2>
<p>Here is an example of a class which provides functionality for portable
and non-portable I/O:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="c1">// includes for this class</span>
+<div class="highlight-cpp notranslate"><div class="highlight"><pre><span></span><span class="c1">// includes for this class</span>
<span class="cp">#include</span> <span class="cpf"><boost/shared_ptr.hpp></span><span class="cp"></span>
<span class="cp">#include</span> <span class="cpf"><iostream></span><span class="cp"></span>
<span class="cp">#include</span> <span class="cpf"><fstream></span><span class="cp"></span>
@@ -377,60 +363,63 @@ and non-portable I/O:</p>
<h2>Exisiting Binary Files<a class="headerlink" href="#exisiting-binary-files" title="Permalink to this headline">¶</a></h2>
<p>The following binary files are currently in ProMod3:</p>
<ul class="simple">
-<li>module <code class="docutils literal"><span class="pre">loop</span></code>:<ul>
-<li><code class="file docutils literal"><span class="pre">frag_db.dat</span></code>
-(<a class="reference internal" href="loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">structure_db.dat</span></code>
-(<a class="reference internal" href="loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">torsion_sampler_coil.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">torsion_sampler.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">torsion_sampler_extended.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">torsion_sampler_helical.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">ff_lookup_charmm.dat</span></code>
-(<a class="reference internal" href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>)</li>
+<li><p>module <code class="docutils literal notranslate"><span class="pre">loop</span></code>:</p>
+<ul>
+<li><p><code class="file docutils literal notranslate"><span class="pre">frag_db.dat</span></code>
+(<a class="reference internal" href="loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">structure_db.dat</span></code>
+(<a class="reference internal" href="loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_coil.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_extended.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_helical.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">ff_lookup_charmm.dat</span></code>
+(<a class="reference internal" href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>)</p></li>
</ul>
</li>
-<li>module <code class="docutils literal"><span class="pre">scoring</span></code>:<ul>
-<li><code class="file docutils literal"><span class="pre">cbeta_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal"><span class="pre">CBetaScorer</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">cb_packing_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">CBPackingScorer</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">hbond_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal"><span class="pre">HBondScorer</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">reduced_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal"><span class="pre">ReducedScorer</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">ss_agreement_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal"><span class="pre">SSAgreementScorer</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">torsion_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal"><span class="pre">TorsionScorer</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">aa_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomInteractionScorer</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">aa_packing_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPackingScorer</span></code></a>)</li>
+<li><p>module <code class="docutils literal notranslate"><span class="pre">scoring</span></code>:</p>
+<ul>
+<li><p><code class="file docutils literal notranslate"><span class="pre">cbeta_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">cb_packing_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">hbond_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">reduced_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">ss_agreement_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">aa_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">aa_packing_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a>)</p></li>
</ul>
</li>
-<li>module <code class="docutils literal"><span class="pre">sidechain</span></code>:<ul>
-<li><code class="file docutils literal"><span class="pre">bb_dep_lib.dat</span></code>
-(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">lib.dat</span></code>
-(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>)</li>
+<li><p>module <code class="docutils literal notranslate"><span class="pre">sidechain</span></code>:</p>
+<ul>
+<li><p><code class="file docutils literal notranslate"><span class="pre">bb_dep_lib.dat</span></code>
+(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>)</p></li>
+<li><p><code class="file docutils literal notranslate"><span class="pre">lib.dat</span></code>
+(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a>)</p></li>
</ul>
</li>
</ul>
-<p>During the <code class="docutils literal"><span class="pre">make</span></code> process, portable versions of the files (stored in the
-<code class="file docutils literal"><span class="pre"><MODULE>/data</span></code> folder) are converted and corresponding raw binary files
-are stored in the <code class="file docutils literal"><span class="pre">stage/share/promod3/<MODULE>_data</span></code> folder.</p>
-<p>If the stage folder is moved after compilation (e.g. <code class="docutils literal"><span class="pre">make</span> <span class="pre">install</span></code>), the
-location of the <code class="file docutils literal"><span class="pre">share/promod3</span></code> folder is to be stored in an environment
-variable called <code class="docutils literal"><span class="pre">PROMOD3_SHARED_DATA_PATH</span></code>. This variable is automatically set
-if you load any Python module from <code class="docutils literal"><span class="pre">promod3</span></code> or if you use the <code class="docutils literal"><span class="pre">pm</span></code>
+<p>During the <code class="docutils literal notranslate"><span class="pre">make</span></code> process, portable versions of the files (stored in the
+<code class="file docutils literal notranslate"><span class="pre"><MODULE>/data</span></code> folder) are converted and corresponding raw binary files
+are stored in the <code class="file docutils literal notranslate"><span class="pre">stage/share/promod3/<MODULE>_data</span></code> folder.</p>
+<p>If the stage folder is moved after compilation (e.g. <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">install</span></code>), the
+location of the <code class="file docutils literal notranslate"><span class="pre">share/promod3</span></code> folder is to be stored in an environment
+variable called <code class="docutils literal notranslate"><span class="pre">PROMOD3_SHARED_DATA_PATH</span></code>. This variable is automatically set
+if you load any Python module from <code class="docutils literal notranslate"><span class="pre">promod3</span></code> or if you use the <code class="docutils literal notranslate"><span class="pre">pm</span></code>
script or if you use a well-setup module on a cluster.</p>
<p>Code for the generation of the binary files and their portable versions are
-in the <code class="file docutils literal"><span class="pre">extras/data_generation</span></code> folder (provided as-is).</p>
+in the <code class="file docutils literal notranslate"><span class="pre">extras/data_generation</span></code> folder (provided as-is).</p>
</div>
</div>
@@ -441,44 +430,55 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Using Binary Files In ProMod3</a><ul>
-<li><a class="reference internal" href="#file-header">File Header</a></li>
-<li><a class="reference internal" href="#portable-binary-data">Portable Binary Data</a></li>
-<li><a class="reference internal" href="#code-example">Code Example</a></li>
-<li><a class="reference internal" href="#exisiting-binary-files">Exisiting Binary Files</a></li>
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
</ul>
-</li>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="developers.html">Documentation For Developers</a><ul>
- <li>Previous: <a href="cmake/index.html" title="previous chapter">ProMod3‘s Share Of CMake</a></li>
+ <li>Previous: <a href="cmake/index.html" title="previous chapter">ProMod3’s Share Of CMake</a></li>
<li>Next: <a href="license.html" title="next chapter">License</a></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/portableIO.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -487,11 +487,11 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/portableIO.txt"
+ <a href="_sources/portableIO.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index b6a170f8c3173bfb8087efef3a8cf1cd9df076fd..3e99095b3f8111ae5d8dcb0e5eaddbcbdd7ba74a 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -1,32 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Python Module Index — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Python Module Index — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -36,8 +24,7 @@
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -55,7 +42,7 @@
<a href="#cap-t"><strong>t</strong></a>
</div>
- <table class="indextable modindextable" cellspacing="0" cellpadding="2">
+ <table class="indextable modindextable">
<tr class="pcap"><td></td><td> </td><td></td></tr>
<tr class="cap" id="cap-p"><td></td><td>
<strong>p</strong></td><td></td></tr>
@@ -116,7 +103,28 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
@@ -124,15 +132,23 @@
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -141,7 +157,7 @@
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
</div>
diff --git a/doc/html/references.html b/doc/html/references.html
index cf86ad5bd3208deff8cc687d69cad6d85eb97237..2eed9037df971bd421ad3653f05f66c7d6858777 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -1,32 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>References — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>References — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
<link rel="next" title="Changelog" href="changelog.html" />
<link rel="prev" title="License" href="license.html" />
@@ -35,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,145 +35,96 @@
<div class="section" id="references">
<h1>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h1>
-<table class="docutils citation" frame="void" id="biasini2013" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[biasini2013]</td><td>Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
+<dl class="citation">
+<dt class="label" id="biasini2013"><span class="brackets">biasini2013</span></dt>
+<dd><p>Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
Johner N, Schenk AD, Philippsen A and Schwede T (2013).
OpenStructure: an integrated software framework for
-computational structural biology. Acta Cryst.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="canutescu2003" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[canutescu2003]</td><td>Canutescu AA and Dunbrack RL Jr. (2003).
+computational structural biology. Acta Cryst.</p>
+</dd>
+<dt class="label" id="canutescu2003"><span class="brackets">canutescu2003</span></dt>
+<dd><p>Canutescu AA and Dunbrack RL Jr. (2003).
Cyclic coordinate descent: A robotics algorithm for protein
-loop closure. Protein Sci.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[canutescu2003b]</td><td>Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
+loop closure. Protein Sci.</p>
+</dd>
+<dt class="label" id="canutescu2003b"><span class="brackets">canutescu2003b</span></dt>
+<dd><p>Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
A graph-theory algorithm for rapid protein side-chain
-prediction. Protein Sci.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="coutsias2005" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[coutsias2005]</td><td>Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+prediction. Protein Sci.</p>
+</dd>
+<dt class="label" id="coutsias2005"><span class="brackets">coutsias2005</span></dt>
+<dd><p>Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
Resultants and loop closure. International Journal of Quantum
-Chemistry.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="chakravarty1999" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[chakravarty1999]</td><td>Chakravarty S, Varadarajan R (1999).
+Chemistry.</p>
+</dd>
+<dt class="label" id="chakravarty1999"><span class="brackets">chakravarty1999</span></dt>
+<dd><p>Chakravarty S, Varadarajan R (1999).
Residue depth: a novel parameter for the analysis of
-protein structure and stability. Structure.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="davis2006" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[davis2006]</td><td>Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+protein structure and stability. Structure.</p>
+</dd>
+<dt class="label" id="davis2006"><span class="brackets">davis2006</span></dt>
+<dd><p>Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
The backrub motion: how protein backbone shrugs when a sidechain
-dances. Structure.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="goldstein1994" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[goldstein1994]</td><td>Goldstein RF (1994).
+dances. Structure.</p>
+</dd>
+<dt class="label" id="goldstein1994"><span class="brackets">goldstein1994</span></dt>
+<dd><p>Goldstein RF (1994).
Efficient rotamer elimination applied to protein side-chains
-and related spin glasses. Biophys J.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="jones1999" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[Jones1999]</td><td>Jones DT (1999).
+and related spin glasses. Biophys J.</p>
+</dd>
+<dt class="label" id="jones1999"><span class="brackets">Jones1999</span></dt>
+<dd><p>Jones DT (1999).
Protein secondary structure prediction based on position-specific
-scoring matrices. J. Mol. Biol.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="kabsch1983" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[kabsch1983]</td><td>Kabsch W, Sander C (1983).
+scoring matrices. J. Mol. Biol.</p>
+</dd>
+<dt class="label" id="kabsch1983"><span class="brackets">kabsch1983</span></dt>
+<dd><p>Kabsch W, Sander C (1983).
Dictionary of protein secondary structure: pattern recognition of
-hydrogen-bonded and geometrical features. Biopolymers.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="krivov2009" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[krivov2009]</td><td>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
+hydrogen-bonded and geometrical features. Biopolymers.</p>
+</dd>
+<dt class="label" id="krivov2009"><span class="brackets">krivov2009</span></dt>
+<dd><p>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
Improved prediction of protein side-chain conformations with
-SCWRL4. Proteins.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="leach1998" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[leach1998]</td><td>Leach AR, Lemon AP (1998).
+SCWRL4. Proteins.</p>
+</dd>
+<dt class="label" id="leach1998"><span class="brackets">leach1998</span></dt>
+<dd><p>Leach AR, Lemon AP (1998).
Exploring the conformational space of protein side chains using
-dead-end elimination and the A* algorithm. Proteins.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="nussinov1991" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[nussinov1991]</td><td>Nussinov R and Wolfson HJ (1991).
+dead-end elimination and the A* algorithm. Proteins.</p>
+</dd>
+<dt class="label" id="nussinov1991"><span class="brackets">nussinov1991</span></dt>
+<dd><p>Nussinov R and Wolfson HJ (1991).
Efficient detection of three-dimensional structural motifs in
-biological macromolecules by computer vision techniques. PNAS.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[shapovalov2011]</td><td>Shapovalov MV and Dunbrack RL Jr. (2011).
+biological macromolecules by computer vision techniques. PNAS.</p>
+</dd>
+<dt class="label" id="shapovalov2011"><span class="brackets">shapovalov2011</span></dt>
+<dd><p>Shapovalov MV and Dunbrack RL Jr. (2011).
A smoothed backbone-dependent rotamer library for proteins
derived from adaptive kernel density estimates and
-regressions. Structure.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="soding2005" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[soding2005]</td><td>Söding J (2005).
+regressions. Structure.</p>
+</dd>
+<dt class="label" id="soding2005"><span class="brackets">soding2005</span></dt>
+<dd><p>Söding J (2005).
Protein homology detection by HMM-HMM comparison.
-Bioinformatics.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="solis2006" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[solis2006]</td><td>Solis AD, Rackovsky S (2006). Improvement of statistical
+Bioinformatics.</p>
+</dd>
+<dt class="label" id="solis2006"><span class="brackets">solis2006</span></dt>
+<dd><p>Solis AD, Rackovsky S (2006). Improvement of statistical
potentials and threading score functions using information
-maximization. Proteins.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="trott2010" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[trott2010]</td><td>Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
+maximization. Proteins.</p>
+</dd>
+<dt class="label" id="trott2010"><span class="brackets">trott2010</span></dt>
+<dd><p>Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
accuracy of docking with a new scoring function, efficient
-optimization and multithreading. J Comput Chem</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="zhou2005" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[zhou2005]</td><td>Zhou H, Zhou Y (2005).
+optimization and multithreading. J Comput Chem</p>
+</dd>
+<dt class="label" id="zhou2005"><span class="brackets">zhou2005</span></dt>
+<dd><p>Zhou H, Zhou Y (2005).
Fold Recognition by Combining Sequence Profiles Derived From
Evolution and From Depth-Dependent Structural Alignment of
-Fragments. Proteins.</td></tr>
-</tbody>
-</table>
+Fragments. Proteins.</p>
+</dd>
+</dl>
</div>
@@ -195,7 +133,28 @@ Fragments. Proteins.</td></tr>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
+</ul>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
@@ -204,23 +163,24 @@ Fragments. Proteins.</td></tr>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/references.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -229,11 +189,11 @@ Fragments. Proteins.</td></tr>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/references.txt"
+ <a href="_sources/references.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 1326da5fe2f7dac094d818c04ed0bbe1a4f0ec89..7c390c0801c1dd9c0ef412b940b39650fc2a8d7d 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>All Atom Scorers — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>All Atom Scorers — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
<link rel="prev" title="Backbone Scorers" href="backbone_scorers.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -53,132 +39,119 @@
<h2>AllAtomOverallScorer class<a class="headerlink" href="#allatomoverallscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomOverallScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomOverallScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomOverallScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Container that allows for the storage of multiple scorers identified by a key
-(<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) and the computation of combined scores.</p>
+(<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) and the computation of combined scores.</p>
<p>Scorers need to be individually set or loaded by
-<a class="reference internal" href="#promod3.scoring.LoadDefaultAllAtomOverallScorer" title="promod3.scoring.LoadDefaultAllAtomOverallScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadDefaultAllAtomOverallScorer()</span></code></a></p>
+<a class="reference internal" href="#promod3.scoring.LoadDefaultAllAtomOverallScorer" title="promod3.scoring.LoadDefaultAllAtomOverallScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadDefaultAllAtomOverallScorer()</span></code></a></p>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.Contains">
-<code class="descname">Contains</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if a scorer object for this key was already added.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if a scorer object for this key was already added.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.Get">
-<code class="descname">Get</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Scorer with the given <em>key</em> (read-only access).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if there is no scorer with that
-<em>key</em>.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Scorer with the given <em>key</em> (read-only access).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
+<em>key</em>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.AttachEnvironment">
-<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) – Link all scorers to this score environment.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link all scorers to this score environment.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination">
-<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em class="sig-param">linear_weights</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate linear combination of scores for the desired loop(s) (extracted
from environment) against the set environment (see
-<a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">AllAtomScorer.CalculateScore()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>,
-values: <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
+<a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AllAtomScorer.CalculateScore()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
constant value to each score by defining a weight
-with key “intercept”.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
+with key “intercept”.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given set of atoms.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Score for the given set of atoms.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
which no scorer exists or anything raised in
-<a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">AllAtomScorer.CalculateScore()</span></code></a> for any of the used scorers.</p>
-</td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AllAtomScorer.CalculateScore()</span></code></a> for any of the used scorers.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomOverallScorer.__setitem__">
-<code class="descname">__setitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__setitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Allow read/write access (with [<em>key</em>]) to scorer object with given key.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadDefaultAllAtomOverallScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadDefaultAllAtomOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultAllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Loads or creates the default scorers accessible through
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadDefaultAllAtomOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultAllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Loads or creates the default scorers accessible through
following keys:
-“aa_interaction”, “aa_packing”, “aa_clash”</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomOverallScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+“aa_interaction”, “aa_packing”, “aa_clash”</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomOverallScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -186,86 +159,75 @@ following keys:
<h2>AllAtomScorer base class<a class="headerlink" href="#allatomscorer-base-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Base class for all the all atom scorers listed below.</p>
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.AttachEnvironment">
-<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) – Link scorer to this score environment.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link scorer to this score environment.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.CalculateScore">
-<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateScore</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates score for the desired loop(s) (extracted from environment) against
-the set environment. Unless otherwise noted in the scorer, a lower “score”
+the set environment. Unless otherwise noted in the scorer, a lower “score”
is better!</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given set of atoms.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">(for most scorers) <code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if scorer was
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Score for the given set of atoms.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>(for most scorers) <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if scorer was
never attached to a score environment, if scorer has never been
properly initialized or if <em>chain_index</em> / <em>start_resnum</em> lead to
invalid positions.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.CalculateScoreProfile">
-<code class="descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates per residue scores for the desired loop(s) (extracted from
environment) against the set environment.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given loop(s), one for each residue.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>
-of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">same <code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">CalculateScore()</span></code></a>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Scores for the given loop(s), one for each residue.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>same <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateScore()</span></code></a>.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -275,8 +237,8 @@ of <a class="reference external" href="https://docs.python.org/3.6/library/funct
<h2>AllAtomInteractionScorer class<a class="headerlink" href="#allatominteractionscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomInteractionScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomInteractionScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>bins</em>, <em>seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a>. Evaluates a pairwise
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomInteractionScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">bins</em>, <em class="sig-param">seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between all atoms which are located within a
<em>cutoff</em> and which are at least <em>seq_sep</em> residues apart. An energy is
assigned to each distance using equally sized bins and distinguishing all
@@ -287,155 +249,134 @@ including everything, the stuff set in the environment and the coordinates
in the input loops. You can change this behaviour with the according
functions.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="promod3.scoring.LoadAllAtomInteractionScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadAllAtomInteractionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="promod3.scoring.AllAtomInteractionScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</li>
-<li><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
-of [0,*cutoff*]).</li>
-<li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
-be considered.</li>
+<a class="reference internal" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="promod3.scoring.LoadAllAtomInteractionScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadAllAtomInteractionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="promod3.scoring.AllAtomInteractionScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</p></li>
+<li><p><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
+of [0,*cutoff*]).</p></li>
+<li><p><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
+be considered.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
<em>seq_sep</em> < 1.</p>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomInteractionScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.Save" title="promod3.scoring.AllAtomInteractionScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="promod3.scoring.AllAtomInteractionScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.Save" title="promod3.scoring.AllAtomInteractionScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="promod3.scoring.AllAtomInteractionScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomInteractionScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomInteractionScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.SetEnergy">
-<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aaa1</em>, <em>aaa2</em>, <em>bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aaa1</em>, <em class="sig-param">aaa2</em>, <em class="sig-param">bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of heavy atom types and for every <em>bin</em> < <em>bins</em>.
Internal symmetry is enforced => Calling SetEnergy(aaa1, aaa2, bin, energy) is
equivalent to calling SetEnergy(aaa1, aaa2, bin, energy) AND
SetEnergy(aaa2, aaa1, bin, energy).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aaa1</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for first interaction partner.</li>
-<li><strong>aaa2</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for second interaction partner.</li>
-<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aaa1</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for first interaction partner.</p></li>
+<li><p><strong>aaa2</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for second interaction partner.</p></li>
+<li><p><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.DoInternalScores">
-<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
-loop. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
+loop. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.DoExternalScores">
-<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
-environment. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
+environment. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues in the input loop. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadAllAtomInteractionScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadAllAtomInteractionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined AllAtomInteractionScorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomInteractionScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadAllAtomInteractionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined AllAtomInteractionScorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -443,126 +384,111 @@ of residues in the input loop. True by default.</td>
<h2>AllAtomPackingScorer class<a class="headerlink" href="#allatompackingscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomPackingScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomPackingScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a>. Evaluates pseudo
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomPackingScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a>. Evaluates pseudo
energies by counting surrounding atoms within a certain <em>cutoff</em> radius around
all heavy atoms not belonging to the assessed residue itself.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadAllAtomPackingScorer" title="promod3.scoring.LoadAllAtomPackingScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadAllAtomPackingScorer()</span></code></a>) or by setting all energies (see
-<a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="promod3.scoring.AllAtomPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</li>
-<li><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If number of other atoms exceeds <em>max_count</em>, it will
-be set to this number.</li>
+<a class="reference internal" href="#promod3.scoring.LoadAllAtomPackingScorer" title="promod3.scoring.LoadAllAtomPackingScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadAllAtomPackingScorer()</span></code></a>) or by setting all energies (see
+<a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="promod3.scoring.AllAtomPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</p></li>
+<li><p><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If number of other atoms exceeds <em>max_count</em>, it will
+be set to this number.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>max_count</em> < 1.</p>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>max_count</em> < 1.</p>
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.scoring.AllAtomPackingScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomPackingScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.Save" title="promod3.scoring.AllAtomPackingScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="promod3.scoring.AllAtomPackingScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.Save" title="promod3.scoring.AllAtomPackingScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="promod3.scoring.AllAtomPackingScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPackingScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomPackingScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomPackingScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomPackingScorer.SetEnergy">
-<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aaa</em>, <em>count</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aaa</em>, <em class="sig-param">count</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every heavy atom type and for every <em>count</em> <= <em>max_count</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aaa</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for which to set energy.</li>
-<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of surrounding atoms for which to set energy.</li>
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aaa</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for which to set energy.</p></li>
+<li><p><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding atoms for which to set energy.</p></li>
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomPackingScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues in the input loop. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadAllAtomPackingScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadAllAtomPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined AllAtomPackingScorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPackingScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadAllAtomPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined AllAtomPackingScorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -570,54 +496,45 @@ of residues in the input loop. True by default.</td>
<h2>AllAtomClashScorer class<a class="headerlink" href="#allatomclashscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomClashScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomClashScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a>. Calculates a simple
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomClashScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a>. Calculates a simple
clash score of all atoms against the environment. There is no need to define
any parameters here as all interaction energies are fixed (see Eq. (11) in
-<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>). By default, the scorer calculates the scores by
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>). By default, the scorer calculates the scores by
including everything, the stuff set in the environment and the coordinates
in the input loops. You can change this behaviour with the according
functions.</p>
<dl class="method">
<dt id="promod3.scoring.AllAtomClashScorer.DoInternalScores">
-<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
-loop. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
+loop. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomClashScorer.DoExternalScores">
-<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
-environment. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
+environment. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomClashScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues in the input loop. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -632,23 +549,45 @@ of residues in the input loop. True by default.</td>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">All Atom Scorers</a><ul>
-<li><a class="reference internal" href="#allatomoverallscorer-class">AllAtomOverallScorer class</a></li>
-<li><a class="reference internal" href="#allatomscorer-base-class">AllAtomScorer base class</a></li>
-<li><a class="reference internal" href="#allatominteractionscorer-class">AllAtomInteractionScorer class</a></li>
-<li><a class="reference internal" href="#allatompackingscorer-class">AllAtomPackingScorer class</a></li>
-<li><a class="reference internal" href="#allatomclashscorer-class">AllAtomClashScorer class</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li>Previous: <a href="backbone_scorers.html" title="previous chapter">Backbone Scorers</a></li>
<li>Next: <a href="other_scoring_functions.html" title="next chapter">Other Scoring Functions</a></li>
</ul></li>
@@ -656,23 +595,24 @@ of residues in the input loop. True by default.</td>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/scoring/all_atom_scorers.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -681,11 +621,11 @@ of residues in the input loop. True by default.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/scoring/all_atom_scorers.txt"
+ <a href="../_sources/scoring/all_atom_scorers.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index c8701b6f85d9ecc1eb097769ee69595fd66b57fa..32a0e128bc841d2bdaba2551d06a9a962ec1f7fe 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Backbone Score Environment — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Backbone Score Environment — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
<link rel="prev" title="scoring - Loop Scoring" href="index.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -53,7 +39,7 @@
<h2>BackboneScoreEnv class<a class="headerlink" href="#backbonescoreenv-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.BackboneScoreEnv">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">BackboneScoreEnv</code><span class="sig-paren">(</span><em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">BackboneScoreEnv</code><span class="sig-paren">(</span><em class="sig-param">seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv" title="Permalink to this definition">¶</a></dt>
<dd><p>The backbone score environment contains and handles all model-specific data
used by the scorers. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
@@ -62,233 +48,202 @@ prediction, etc). All scorers attached to that environment will see that data
and can calculate scores accordingly.
Scoring with this setup is a two step process:</p>
<ul class="simple">
-<li>Set the positions you want to score in the environment to make it available
-to all attached scorers</li>
-<li>Call the scorers to get the desired scores</li>
+<li><p>Set the positions you want to score in the environment to make it available
+to all attached scorers</p></li>
+<li><p>Call the scorers to get the desired scores</p></li>
</ul>
<p>One problem that might occur is that you mess around with the environment and
at some point you want to restore the original state. The
-<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> provides a Stash / Pop mechanism to perform this
+<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> provides a Stash / Pop mechanism to perform this
task.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
-chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
+</dd>
+</dl>
<p>To access parts of the environment there are two key arguments to consider:</p>
<ul class="simple">
-<li><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</li>
-<li><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
+<li><p><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</p></li>
+<li><p><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
with index <em>chain_idx</em>. <strong>The numbering starts for every chain with the
-value 1</strong>.</li>
+value 1</strong>.</p></li>
</ul>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.Copy">
-<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A copy of the current <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> without any scorers
-attached</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>A copy of the current <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> without any scorers
+attached</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.SetInitialEnvironment">
-<code class="descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em>env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets structural environment with which loops to be scored interact. If
structural data was already set, all the existing data gets cleared first.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
-order as the SEQRES items provided in constructor.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
+order as the SEQRES items provided in constructor.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
SEQRES set in constructor. This can be because of corrupt residue
-numbers or sequence mismatches.</td>
-</tr>
-</tbody>
-</table>
+numbers or sequence mismatches.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.SetEnvironment">
-<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Add/update structural information in environment. If structural data for
specific residues is already set, the data gets resetted for these
positions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is
inconsistent with previously SEQRES set in constructor or when
either <em>start_resnum</em> or <em>chain_idx</em> point to invalid positions in
the SEQRES.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.ClearEnvironment">
-<code class="descname">ClearEnvironment</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ClearEnvironment</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Clears a stretch of length <em>num_residues</em> in the environment in chain
with idx <em>chain_idx</em> starting from residue number <em>start_resnum</em></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start of stretch to clear</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of stretch to clear</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to clear</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to clear</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
<em>chain_idx</em> point to invalid positions in the SEQRES.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.SetPsipredPrediction">
-<code class="descname">SetPsipredPrediction</code><span class="sig-paren">(</span><em>pred</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetPsipredPrediction</code><span class="sig-paren">(</span><em class="sig-param">pred</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the psipred prediction, which is necessary to calculate some scores.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>pred</strong> (<code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
-<code class="xref py py-class docutils literal"><span class="pre">PsipredPrediction</span></code>) – Psipred prediction to set (one per chain).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if the number of predictions is
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>pred</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code>) – Psipred prediction to set (one per chain).</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the number of predictions is
inconsistent with the number of internal chains or when one of the
-predictions’ sizes is inconsistent with the internal SEQRES size.</td>
-</tr>
-</tbody>
-</table>
+predictions’ sizes is inconsistent with the internal SEQRES size.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.AddPairwiseFunction">
-<code class="descname">AddPairwiseFunction</code><span class="sig-paren">(</span><em>function</em>, <em>function_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>Adds a pairwise function that can be used in <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal"><span class="pre">ApplyPairwiseFunction()</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>function</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>) – Pairwise function to be added.</li>
-<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunctionType</span></code></a>) – What distances should be looked at for this function.</li>
+<code class="sig-name descname">AddPairwiseFunction</code><span class="sig-paren">(</span><em class="sig-param">function</em>, <em class="sig-param">function_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adds a pairwise function that can be used in <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyPairwiseFunction()</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>function</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>) – Pairwise function to be added.</p></li>
+<li><p><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – What distances should be looked at for this function.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Function index to be used in <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal"><span class="pre">ApplyPairwiseFunction()</span></code></a>.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Function index to be used in <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyPairwiseFunction()</span></code></a>.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction">
-<code class="descname">ApplyPairwiseFunction</code><span class="sig-paren">(</span><em>chain_idx_one</em>, <em>resnum_one</em>, <em>chain_idx_two</em>, <em>resnum_two</em>, <em>f_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyPairwiseFunction</code><span class="sig-paren">(</span><em class="sig-param">chain_idx_one</em>, <em class="sig-param">resnum_one</em>, <em class="sig-param">chain_idx_two</em>, <em class="sig-param">resnum_two</em>, <em class="sig-param">f_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Define two residues to be evaluated with a given pairwise function. This
data can then be used by scorers. Note that the pairs are symmetric and so
there is no need to add them twice with switched residues.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>chain_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain index of first residue</li>
-<li><strong>resnum_one</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number of first residue</li>
-<li><strong>chain_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain index of second residue</li>
-<li><strong>resnum_two</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number of second residue</li>
-<li><strong>f_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of pairwise function (as returned by
-<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.AddPairwiseFunction"><code class="xref py py-meth docutils literal"><span class="pre">AddPairwiseFunction()</span></code></a>)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>chain_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain index of first residue</p></li>
+<li><p><strong>resnum_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number of first residue</p></li>
+<li><p><strong>chain_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain index of second residue</p></li>
+<li><p><strong>resnum_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number of second residue</p></li>
+<li><p><strong>f_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of pairwise function (as returned by
+<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.AddPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddPairwiseFunction()</span></code></a>)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if any of the chain indices or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any of the chain indices or
res. numbers is invalid, the interaction partners are the same
residue or when <em>f_idx</em> is an invalid index.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.Stash">
-<code class="descname">Stash</code><span class="sig-paren">(</span><em>start_rnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Stash" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Stash</code><span class="sig-paren">(</span><em class="sig-param">start_rnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Stash" title="Permalink to this definition">¶</a></dt>
<dd><p>FILO style stashing. You can perform up to 100 stash operations to save
the current state of certain stretches in the environment. This state can
-be restored by calling <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.Pop" title="promod3.scoring.BackboneScoreEnv.Pop"><code class="xref py py-func docutils literal"><span class="pre">Pop()</span></code></a>. In one stash operation you can either
+be restored by calling <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.Pop" title="promod3.scoring.BackboneScoreEnv.Pop"><code class="xref py py-func docutils literal notranslate"><span class="pre">Pop()</span></code></a>. In one stash operation you can either
stash one stretch by providing integers as input or several stretches by
providing lists of integers.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>start_rnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – start rnum of stretch to stash</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – length of stretch to stash</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – chain idx of stretch to stash</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_rnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – start rnum of stretch to stash</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – length of stretch to stash</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – chain idx of stretch to stash</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.Pop">
-<code class="descname">Pop</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Pop" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Pop</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Pop" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove and apply the the last stash operation.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.GetSeqres">
-<code class="descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -298,84 +253,75 @@ providing lists of integers.</p>
<h2>Pairwise function classes<a class="headerlink" href="#pairwise-function-classes" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.PairwiseFunctionType">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">PairwiseFunctionType</code><a class="headerlink" href="#promod3.scoring.PairwiseFunctionType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">PairwiseFunctionType</code><a class="headerlink" href="#promod3.scoring.PairwiseFunctionType" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the pairwise function types. Possible values:</p>
<ul class="simple">
-<li><em>CA_PAIRWISE_FUNCTION</em> - Evaluate CA atoms distances.</li>
-<li><em>CB_PAIRWISE_FUNCTION</em> - Evaluate CB atoms distances.</li>
+<li><p><em>CA_PAIRWISE_FUNCTION</em> - Evaluate CA atoms distances.</p></li>
+<li><p><em>CB_PAIRWISE_FUNCTION</em> - Evaluate CB atoms distances.</p></li>
</ul>
</dd></dl>
<dl class="class">
<dt id="promod3.scoring.PairwiseFunction">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">PairwiseFunction</code><a class="headerlink" href="#promod3.scoring.PairwiseFunction" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">PairwiseFunction</code><a class="headerlink" href="#promod3.scoring.PairwiseFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Base class for any pairwise function.</p>
<dl class="method">
<dt id="promod3.scoring.PairwiseFunction.Score">
-<code class="descname">Score</code><span class="sig-paren">(</span><em>distance</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseFunction.Score" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Score for a given pairwise distance</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Pairwise distance</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Score</code><span class="sig-paren">(</span><em class="sig-param">distance</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseFunction.Score" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Score for a given pairwise distance</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Pairwise distance</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.scoring.ConstraintFunction">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ConstraintFunction</code><span class="sig-paren">(</span><em>min_dist</em>, <em>max_dist</em>, <em>values</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ConstraintFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>.
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ConstraintFunction</code><span class="sig-paren">(</span><em class="sig-param">min_dist</em>, <em class="sig-param">max_dist</em>, <em class="sig-param">values</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ConstraintFunction" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>.
Defines a constraint function. The score for a distance between <em>min_dist</em> and
<em>max_dist</em> is determined by linear interpolation assuming the first and last
value exactly lying on <em>min_dist</em> and <em>max_dist</em>. For distances outside the
range defined by <em>min_dist</em> and <em>max_dist</em>, the returned score is 0.0.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>min_dist</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Minimal distance to be considered</li>
-<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal distance to be considered</li>
-<li><strong>values</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The possible values that get returned when the distance is
-between <em>min_dist</em> and <em>max_dist</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>min_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal distance to be considered</p></li>
+<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance to be considered</p></li>
+<li><p><strong>values</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The possible values that get returned when the distance is
+between <em>min_dist</em> and <em>max_dist</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>min_dist</em> >= <em>max_dist</em> or when
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>min_dist</em> >= <em>max_dist</em> or when
<em>min_dist</em> or <em>max_dist</em> are negative or when <em>values</em> contains no
elements</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="class">
<dt id="promod3.scoring.ContactFunction">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ContactFunction</code><span class="sig-paren">(</span><em>max_dist</em>, <em>score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ContactFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>.
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ContactFunction</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ContactFunction" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>.
Defines a simple contact function. The score value is <em>score</em> if
distance < <em>max_dist</em> and 0.0 otherwise.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal distance to be in contact</li>
-<li><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Value that gets returned if in contact</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance to be in contact</p></li>
+<li><p><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Value that gets returned if in contact</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -383,48 +329,42 @@ distance < <em>max_dist</em> and 0.0 otherwise.</p>
<h2>Convenient construction of pairwise functions<a class="headerlink" href="#convenient-construction-of-pairwise-functions" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.DiscoContainer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">DiscoContainer</code><span class="sig-paren">(</span><em>seqres</em><span class="optional">[</span>, <em>function_type = CA_PAIRWISE_FUNCTION</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">DiscoContainer</code><span class="sig-paren">(</span><em class="sig-param">seqres</em><span class="optional">[</span>, <em class="sig-param">function_type = CA_PAIRWISE_FUNCTION</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer" title="Permalink to this definition">¶</a></dt>
<dd><p>A container collecting structural information until it can be added in form
-of <a class="reference internal" href="#promod3.scoring.ConstraintFunction" title="promod3.scoring.ConstraintFunction"><code class="xref py py-class docutils literal"><span class="pre">ConstraintFunction</span></code></a> to a <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> .
+of <a class="reference internal" href="#promod3.scoring.ConstraintFunction" title="promod3.scoring.ConstraintFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">ConstraintFunction</span></code></a> to a <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> .
The constraint functions are built after the principle of QMEANDisCo.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
-<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
-or CB atoms</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</p></li>
+<li><p><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
+or CB atoms</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="function">
<dt id="promod3.scoring.DiscoContainer.AddStructuralInfo">
-<code class="descname">AddStructuralInfo</code><span class="sig-paren">(</span><em>aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AddStructuralInfo" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<code class="sig-name descname">AddStructuralInfo</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AddStructuralInfo" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
-info. The second sequence must have a view attached.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if number of sequences in <em>aln</em> is
+info. The second sequence must have a view attached.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if number of sequences in <em>aln</em> is
not two, the SEQRES does not match or when the second sequence in
-<em>aln</em> has no view attached.</td>
-</tr>
-</tbody>
-</table>
+<em>aln</em> has no view attached.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.DiscoContainer.AttachConstraints">
-<code class="descname">AttachConstraints</code><span class="sig-paren">(</span><em>env</em>, <em>chain_indices</em><span class="optional">[</span>, <em>cluster_thresh = 0.5</em>, <em>gamma = 70.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AttachConstraints" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AttachConstraints</code><span class="sig-paren">(</span><em class="sig-param">env</em>, <em class="sig-param">chain_indices</em><span class="optional">[</span>, <em class="sig-param">cluster_thresh = 0.5</em>, <em class="sig-param">gamma = 70.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AttachConstraints" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates distance constraints and adds it to <em>env</em>.
It first clusters the added sequences with a pairwise normalised sequence
-similarity based on BLOSUM62. It’s a hierarchical clustering with with an
+similarity based on BLOSUM62. It’s a hierarchical clustering with with an
average distance metric and <em>cluster_thresh</em> as threshold to merge two
clusters. Constraint functions are built for every cluster and finally
merged. The influence of the per cluster constraint functions to the overall
@@ -433,29 +373,25 @@ target SEQRES. How fast this influence vanishes gets controlled by gamma.
The higher it is, the faster vanishes the influence of structural info
from distant clusters. The final pairwise cluster functions get then
directly added to the scoring <em>env</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>env</strong> (<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring env to which the constraint
-should be added</li>
-<li><strong>chain_indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Indices of chains for which the constraints should
-be added</li>
-<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Controls the clustering behaviour at the initial
-stage of constraint construction</li>
-<li><strong>gamma</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Controls how fast the influence of constraint
-functions of distant clusters vanishes</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>env</strong> (<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring env to which the constraint
+should be added</p></li>
+<li><p><strong>chain_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Indices of chains for which the constraints should
+be added</p></li>
+<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Controls the clustering behaviour at the initial
+stage of constraint construction</p></li>
+<li><p><strong>gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Controls how fast the influence of constraint
+functions of distant clusters vanishes</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if one of the <em>chain_indices</em> is
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the <em>chain_indices</em> is
invalid or the SEQRES set in <em>env</em> for specified chain is
inconsistent with SEQRES you initialized the DiscoContainer with</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -470,45 +406,70 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Backbone Score Environment</a><ul>
-<li><a class="reference internal" href="#backbonescoreenv-class">BackboneScoreEnv class</a></li>
-<li><a class="reference internal" href="#pairwise-function-classes">Pairwise function classes</a></li>
-<li><a class="reference internal" href="#convenient-construction-of-pairwise-functions">Convenient construction of pairwise functions</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
<li>Next: <a href="backbone_scorers.html" title="next chapter">Backbone Scorers</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/scoring/backbone_score_env.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -517,11 +478,11 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/scoring/backbone_score_env.txt"
+ <a href="../_sources/scoring/backbone_score_env.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 4dd2f344d31cd7a05b49c7f2e9e1c27abad907c8..c04f69dbbc0b50c22759b1fa7265bc8777d4d366 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Backbone Scorers — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Backbone Scorers — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
<link rel="prev" title="Backbone Score Environment" href="backbone_score_env.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -53,165 +39,148 @@
<h2>BackboneOverallScorer class<a class="headerlink" href="#backboneoverallscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.BackboneOverallScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">BackboneOverallScorer</code><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">BackboneOverallScorer</code><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Container that allows for the storage of multiple scorers identified by a key
-(<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) and the computation of combined scores.</p>
+(<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) and the computation of combined scores.</p>
<p>Scorers need to be individually set or loaded by
-<a class="reference internal" href="#promod3.scoring.LoadDefaultBackboneOverallScorer" title="promod3.scoring.LoadDefaultBackboneOverallScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadDefaultBackboneOverallScorer()</span></code></a></p>
+<a class="reference internal" href="#promod3.scoring.LoadDefaultBackboneOverallScorer" title="promod3.scoring.LoadDefaultBackboneOverallScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadDefaultBackboneOverallScorer()</span></code></a></p>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.Contains">
-<code class="descname">Contains</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if a scorer object for this key was already added.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>True, if a scorer object for this key was already added.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.Get">
-<code class="descname">Get</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Scorer with the given <em>key</em> (read-only access).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if there is no scorer with that
-<em>key</em>.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Scorer with the given <em>key</em> (read-only access).</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a></p>
+</dd>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
+<em>key</em>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.AttachEnvironment">
-<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>) – Link all scorers to this score environment.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – Link all scorers to this score environment.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.Calculate">
-<code class="descname">Calculate</code><span class="sig-paren">(</span><em>key</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Calculate" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Calculate</code><span class="sig-paren">(</span><em class="sig-param">key</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Calculate" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate score for one or several stretches of amino acids given the
current scoring environment.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score calculated with the desired scorer for the given stretch(es).</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if there is no scorer with that
-<em>key</em> or anything raised in <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScorer.CalculateScore()</span></code></a>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Score calculated with the desired scorer for the given stretch(es).</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
+<em>key</em> or anything raised in <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BackboneScorer.CalculateScore()</span></code></a>.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination">
-<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em class="sig-param">linear_weights</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate linear combination of scores for one or several stretches of
amino acids given the current scoring environment.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#dict" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>,
-values: <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
constant value to each score by defining a weight
-with key “intercept”.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+with key “intercept”.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Linear combination of the scores calculated with the desired
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Linear combination of the scores calculated with the desired
scorers for the given stretch(es)</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
which no scorer exists or anything raised in
-<a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScorer.CalculateScore()</span></code></a> for any of the used scorers.</p>
-</td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BackboneScorer.CalculateScore()</span></code></a> for any of the used scorers.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.BackboneOverallScorer.__setitem__">
-<code class="descname">__setitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__setitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Allow read/write access (with [<em>key</em>]) to scorer object with given key.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadDefaultBackboneOverallScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadDefaultBackboneOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultBackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Loads or creates the default scorers accessible through
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadDefaultBackboneOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultBackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Loads or creates the default scorers accessible through
following keys:
-“cb_packing”, “cbeta”, “reduced”, “clash”, “hbond”, “ss_agreement”,”torsion”, “pairwise”</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+“cb_packing”, “cbeta”, “reduced”, “clash”, “hbond”, “ss_agreement”,”torsion”, “pairwise”</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -219,86 +188,75 @@ following keys:
<h2>BackboneScorer base class<a class="headerlink" href="#backbonescorer-base-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.BackboneScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">BackboneScorer</code><a class="headerlink" href="#promod3.scoring.BackboneScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">BackboneScorer</code><a class="headerlink" href="#promod3.scoring.BackboneScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Base class for all the backbone scorers listed below.</p>
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.AttachEnvironment">
-<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>) – Link scorer to this score environment.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – Link scorer to this score environment.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.CalculateScore">
-<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateScore</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates score for one or several stretches given the structural
information in the attached environment. Unless otherwise noted in the
-scorer, a lower “score” is better!</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+scorer, a lower “score” is better!</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given stretch(es).</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">(for most scorers) <code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if scorer was
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Score for the given stretch(es).</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>(for most scorers) <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if scorer was
never attached to a score environment, if scorer has never been
properly initialized or if <em>start_resnum</em> / <em>num_residues</em> /
<em>chain_idx</em> lead to invalid positions.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.CalculateScoreProfile">
-<code class="descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates per residue scores for one or several stretches given the
structural information in the attached environment.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
+<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given stretch(es), one for each residue.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> or <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>
-of <a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">same <code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">CalculateScore()</span></code></a>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Scores for the given stretch(es), one for each residue.</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> or <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p>same <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateScore()</span></code></a>.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -308,126 +266,111 @@ of <a class="reference external" href="https://docs.python.org/3.6/library/funct
<h2>CBPackingScorer class<a class="headerlink" href="#cbpackingscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.CBPackingScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">CBPackingScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">CBPackingScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
energies by counting the number of other CB positions within a certain
<em>cutoff</em> radius of the CB position of the residue to be evaluated.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadCBPackingScorer" title="promod3.scoring.LoadCBPackingScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadCBPackingScorer()</span></code></a>) or by setting all energies (see
-<a class="reference internal" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="promod3.scoring.CBPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are counted.</li>
-<li><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If number of other cbeta atoms exceeds <em>max_count</em>, it will
-be set to this number.</li>
+<a class="reference internal" href="#promod3.scoring.LoadCBPackingScorer" title="promod3.scoring.LoadCBPackingScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadCBPackingScorer()</span></code></a>) or by setting all energies (see
+<a class="reference internal" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="promod3.scoring.CBPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are counted.</p></li>
+<li><p><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If number of other cbeta atoms exceeds <em>max_count</em>, it will
+be set to this number.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0 or <em>max_count</em> < 1.</p>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0 or <em>max_count</em> < 1.</p>
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.scoring.CBPackingScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBPackingScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.CBPackingScorer.Save" title="promod3.scoring.CBPackingScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.CBPackingScorer.SavePortable" title="promod3.scoring.CBPackingScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.CBPackingScorer.Save" title="promod3.scoring.CBPackingScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.CBPackingScorer.SavePortable" title="promod3.scoring.CBPackingScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">CBPackingScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBPackingScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBPackingScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBPackingScorer.SetEnergy">
-<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aa</em>, <em>count</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">count</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every type of amino acids and for every <em>count</em> <= <em>max_count</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
-<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</li>
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</p></li>
+<li><p><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</p></li>
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBPackingScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadCBPackingScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadCBPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBPackingScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined CBPackingScorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">CBPackingScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadCBPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBPackingScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined CBPackingScorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -435,163 +378,142 @@ of residues to be scored. True by default.</td>
<h2>CBetaScorer class<a class="headerlink" href="#cbetascorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.CBetaScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">CBetaScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>bins</em>, <em>seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">CBetaScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">bins</em>, <em class="sig-param">seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between CB atoms which are located within a <em>cutoff</em>
and which are at least <em>seq_sep</em> residues apart. An energy is assigned to each
distance using equally sized bins and distinguishing all possible pairs
of amino acids.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadCBetaScorer" title="promod3.scoring.LoadCBetaScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadCBetaScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.CBetaScorer.SetEnergy" title="promod3.scoring.CBetaScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are considered.</li>
-<li><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
-of [0, <em>cutoff</em>]).</li>
-<li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Minimal separation in sequence two cbeta atoms must have to
-be considered.</li>
+<a class="reference internal" href="#promod3.scoring.LoadCBetaScorer" title="promod3.scoring.LoadCBetaScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadCBetaScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.CBetaScorer.SetEnergy" title="promod3.scoring.CBetaScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are considered.</p></li>
+<li><p><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
+of [0, <em>cutoff</em>]).</p></li>
+<li><p><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two cbeta atoms must have to
+be considered.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
<em>seq_sep</em> < 1.</p>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.scoring.CBetaScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBetaScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.CBetaScorer.Save" title="promod3.scoring.CBetaScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.CBetaScorer.SavePortable" title="promod3.scoring.CBetaScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.CBetaScorer.Save" title="promod3.scoring.CBetaScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.CBetaScorer.SavePortable" title="promod3.scoring.CBetaScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal"><span class="pre">CBetaScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBetaScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.SetEnergy">
-<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aa1</em>, <em>aa2</em>, <em>bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aa1</em>, <em class="sig-param">aa2</em>, <em class="sig-param">bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of amino acids and for every <em>bin</em> < <em>bins</em>.
Internal symmetry is enforced => Calling SetEnergy(aa1, aa2, bin, energy) is
equivalent to calling SetEnergy(aa1, aa2, bin, energy) AND
SetEnergy(aa2, aa1, bin, energy).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
-<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
+<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
+<li><p><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.DoInternalScores">
-<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.DoExternalScores">
-<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</td>
-</tr>
-</tbody>
-</table>
+True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadCBetaScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadCBetaScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBetaScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined CBetaScorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal"><span class="pre">CBetaScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadCBetaScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBetaScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined CBetaScorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -599,93 +521,87 @@ of residues to be scored. True by default.</td>
<h2>ReducedScorer class<a class="headerlink" href="#reducedscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.ReducedScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ReducedScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>dist_bins</em>, <em>angle_bins</em>, <em>dihedral_bins</em>, <em>seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ReducedScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">dist_bins</em>, <em class="sig-param">angle_bins</em>, <em class="sig-param">dihedral_bins</em>, <em class="sig-param">seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between the reduced representation of residues.
Every residue gets represented by its CA position p and a directional
-component <code class="docutils literal"><span class="pre">v</span> <span class="pre">=</span> <span class="pre">norm(p-n_pos)</span> <span class="pre">+</span> <span class="pre">norm(p-c_pos)</span></code>. Residues with CA
+component <code class="docutils literal notranslate"><span class="pre">v</span> <span class="pre">=</span> <span class="pre">norm(p-n_pos)</span> <span class="pre">+</span> <span class="pre">norm(p-c_pos)</span></code>. Residues with CA
distance < <em>cutoff</em> and which are at least <em>seq_sep</em> residues apart are
considered to be interacting. For interacting residues r1 and r2, we can
define a line l between p1 and p2. The potential then considers:</p>
<ul class="simple">
-<li>dist => distance between p1 and p2</li>
-<li>alpha => angle between v1 and l</li>
-<li>beta => angle between v2 and l</li>
-<li>gamma => dihedral between (p1+v1,p1,p2,p2+v2)</li>
+<li><p>dist => distance between p1 and p2</p></li>
+<li><p>alpha => angle between v1 and l</p></li>
+<li><p>beta => angle between v2 and l</p></li>
+<li><p>gamma => dihedral between (p1+v1,p1,p2,p2+v2)</p></li>
</ul>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadReducedScorer" title="promod3.scoring.LoadReducedScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadReducedScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.ReducedScorer.SetEnergy" title="promod3.scoring.ReducedScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Radius in which other CA atoms are searched.</li>
-<li><strong>dist_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
-of [0, <em>cutoff</em>]).</li>
-<li><strong>angle_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize angles (range
-of [0, pi]).</li>
-<li><strong>dihedral_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize dihedrals
-(range of [-pi, pi]).</li>
-<li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
-be considered.</li>
+<a class="reference internal" href="#promod3.scoring.LoadReducedScorer" title="promod3.scoring.LoadReducedScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadReducedScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.ReducedScorer.SetEnergy" title="promod3.scoring.ReducedScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other CA atoms are searched.</p></li>
+<li><p><strong>dist_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
+of [0, <em>cutoff</em>]).</p></li>
+<li><p><strong>angle_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize angles (range
+of [0, pi]).</p></li>
+<li><p><strong>dihedral_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize dihedrals
+(range of [-pi, pi]).</p></li>
+<li><p><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
+be considered.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>dist_bins</em> < 1,
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>dist_bins</em> < 1,
<em>angle_bins</em> < 1, <em>dihedral_bins</em> < 1 or <em>seq_sep</em> < 1.</p>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.scoring.ReducedScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.ReducedScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.ReducedScorer.Save" title="promod3.scoring.ReducedScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.ReducedScorer.SavePortable" title="promod3.scoring.ReducedScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.ReducedScorer.Save" title="promod3.scoring.ReducedScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.ReducedScorer.SavePortable" title="promod3.scoring.ReducedScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal"><span class="pre">ReducedScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.ReducedScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.SetEnergy">
-<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aa1</em>, <em>aa2</em>, <em>dist_bin</em>, <em>alpha_bin</em>, <em>beta_bin</em>, <em>gamma_bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aa1</em>, <em class="sig-param">aa2</em>, <em class="sig-param">dist_bin</em>, <em class="sig-param">alpha_bin</em>, <em class="sig-param">beta_bin</em>, <em class="sig-param">gamma_bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of amino acids, every <em>dist_bin</em> < <em>dist_bins</em>, every
<em>alpha_bin</em> < <em>angle_bins</em>, every <em>beta_bin</em> < <em>angle_bins</em> and every
@@ -695,86 +611,71 @@ SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) is
equivalent to calling
SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) AND
SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
-<li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
-<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</li>
-<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</li>
-<li><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the gamma dihedral.</li>
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
+<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
+<li><p><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
+<li><p><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</p></li>
+<li><p><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</p></li>
+<li><p><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the gamma dihedral.</p></li>
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.DoInternalScores">
-<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.DoExternalScores">
-<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</td>
-</tr>
-</tbody>
-</table>
+True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadReducedScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadReducedScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadReducedScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined ReducedScorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal"><span class="pre">ReducedScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadReducedScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadReducedScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined ReducedScorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -782,52 +683,43 @@ of residues to be scored. True by default.</td>
<h2>ClashScorer class<a class="headerlink" href="#clashscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.ClashScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ClashScorer</code><a class="headerlink" href="#promod3.scoring.ClashScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Calculates a simple
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ClashScorer</code><a class="headerlink" href="#promod3.scoring.ClashScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Calculates a simple
clash score of a loop itself and with the set environment. There is no need to
define any parameters here as all interaction energies are fixed (see Eq. (11)
-in <a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>).</p>
+in <a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>).</p>
<dl class="method">
<dt id="promod3.scoring.ClashScorer.DoInternalScores">
-<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ClashScorer.DoExternalScores">
-<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</td>
-</tr>
-</tbody>
-</table>
+True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ClashScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -837,17 +729,17 @@ of residues to be scored. True by default.</td>
<h2>HBondScorer class<a class="headerlink" href="#hbondscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.HBondScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">HBondScorer</code><span class="sig-paren">(</span><em>min_d</em>, <em>max_d</em>, <em>min_alpha</em>, <em>max_alpha</em>, <em>min_beta</em>, <em>max_beta</em>, <em>min_gamma</em>, <em>max_gamma</em>, <em>d_bins</em>, <em>alpha_bins</em>, <em>beta_bins</em>, <em>gamma_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates pairwise
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">HBondScorer</code><span class="sig-paren">(</span><em class="sig-param">min_d</em>, <em class="sig-param">max_d</em>, <em class="sig-param">min_alpha</em>, <em class="sig-param">max_alpha</em>, <em class="sig-param">min_beta</em>, <em class="sig-param">max_beta</em>, <em class="sig-param">min_gamma</em>, <em class="sig-param">max_gamma</em>, <em class="sig-param">d_bins</em>, <em class="sig-param">alpha_bins</em>, <em class="sig-param">beta_bins</em>, <em class="sig-param">gamma_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates pairwise
HBond pseudo energies similar to the one defined in the Rosetta energy
function. It considers the CA, C and O positions from backbone hbond acceptors
in interaction with the N and H positions from the backbone hbond donors. 4
Parameters describe their relative orientation.</p>
<ul class="simple">
-<li>dist => H-O distance</li>
-<li>alpha => O-H-N angle</li>
-<li>beta => C-N-H angle</li>
-<li>gamma => CA-C-O-H dihedral angle</li>
+<li><p>dist => H-O distance</p></li>
+<li><p>alpha => O-H-N angle</p></li>
+<li><p>beta => C-N-H angle</p></li>
+<li><p>gamma => CA-C-O-H dihedral angle</p></li>
</ul>
<p>A pseudo energy function for these parameters is evaluated for three different
states. State 1 for helical residues, state 2 for extended residues and state
@@ -855,169 +747,148 @@ states. State 1 for helical residues, state 2 for extended residues and state
thats the one from which the energy is extracted. In all other cases, the
energy is extracted from the 0 state.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadHBondScorer" title="promod3.scoring.LoadHBondScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadHBondScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.HBondScorer.SetEnergy" title="promod3.scoring.HBondScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>min_d</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Minimal H-O distance to consider interaction</li>
-<li><strong>max_d</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal H-O distance to consider interaction</li>
-<li><strong>min_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Minimal O-H-N angle to consider interaction</li>
-<li><strong>max_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal O-H-N angle to consider interaction</li>
-<li><strong>min_beta</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Minimal C-N-H angle to consider interaction</li>
-<li><strong>max_beta</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal C-N-H angle to consider interaction</li>
-<li><strong>min_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Minimal CA-C-O-H dihedral to consider interaction</li>
-<li><strong>max_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal CA-C-O-H dihedral to consider interaction</li>
-<li><strong>d_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize H-O distances
-(range of [<em>min_d</em>, <em>max_d</em>]).</li>
-<li><strong>alpha_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize O-H-N angles
-(range of [<em>min_alpha</em>, <em>max_alpha</em>]).</li>
-<li><strong>beta_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize C-N-H angles
-(range of [<em>min_beta</em>, <em>max_beta</em>]).</li>
-<li><strong>gamma_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize CA-C-O-H angles
-(range of [<em>min_gamma</em>, <em>max_gamma</em>]).</li>
+<a class="reference internal" href="#promod3.scoring.LoadHBondScorer" title="promod3.scoring.LoadHBondScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadHBondScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.HBondScorer.SetEnergy" title="promod3.scoring.HBondScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>min_d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal H-O distance to consider interaction</p></li>
+<li><p><strong>max_d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal H-O distance to consider interaction</p></li>
+<li><p><strong>min_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal O-H-N angle to consider interaction</p></li>
+<li><p><strong>max_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal O-H-N angle to consider interaction</p></li>
+<li><p><strong>min_beta</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal C-N-H angle to consider interaction</p></li>
+<li><p><strong>max_beta</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal C-N-H angle to consider interaction</p></li>
+<li><p><strong>min_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal CA-C-O-H dihedral to consider interaction</p></li>
+<li><p><strong>max_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal CA-C-O-H dihedral to consider interaction</p></li>
+<li><p><strong>d_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize H-O distances
+(range of [<em>min_d</em>, <em>max_d</em>]).</p></li>
+<li><p><strong>alpha_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize O-H-N angles
+(range of [<em>min_alpha</em>, <em>max_alpha</em>]).</p></li>
+<li><p><strong>beta_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize C-N-H angles
+(range of [<em>min_beta</em>, <em>max_beta</em>]).</p></li>
+<li><p><strong>gamma_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize CA-C-O-H angles
+(range of [<em>min_gamma</em>, <em>max_gamma</em>]).</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if one of the bin parameters is
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the bin parameters is
< 1 or a max parameter is smaller than its min counterpart.</p>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.scoring.HBondScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.HBondScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.HBondScorer.Save" title="promod3.scoring.HBondScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.HBondScorer.SavePortable" title="promod3.scoring.HBondScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.HBondScorer.Save" title="promod3.scoring.HBondScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.HBondScorer.SavePortable" title="promod3.scoring.HBondScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal"><span class="pre">HBondScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.HBondScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.SetEnergy">
-<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>state</em>, <em>d_bin</em>, <em>alpha_bin</em>, <em>beta_bin</em>, <em>gamma_bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">state</em>, <em class="sig-param">d_bin</em>, <em class="sig-param">alpha_bin</em>, <em class="sig-param">beta_bin</em>, <em class="sig-param">gamma_bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every state ([0, 1, 2]), every <em>d_bin</em> < <em>d_bins</em>, every
<em>alpha_bin</em> < <em>alpha_bins</em>, every <em>beta_bin</em> < <em>beta_bins</em> and every
<em>gamma_bin</em> < <em>gamma_bins</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>state</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – State describing the actual secondary structure
-(1: helical, 2: extended, 0: other)</li>
-<li><strong>d_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the H-O distance.</li>
-<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the O-H-N angle.</li>
-<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the C-N-H angle.</li>
-<li><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the CA-C-O-H dihedral.</li>
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – State describing the actual secondary structure
+(1: helical, 2: extended, 0: other)</p></li>
+<li><p><strong>d_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the H-O distance.</p></li>
+<li><p><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the O-H-N angle.</p></li>
+<li><p><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the C-N-H angle.</p></li>
+<li><p><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the CA-C-O-H dihedral.</p></li>
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.DoInternalScores">
-<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.DoExternalScores">
-<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</td>
-</tr>
-</tbody>
-</table>
+True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadHBondScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadHBondScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadHBondScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined HBondScorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal"><span class="pre">HBondScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadHBondScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadHBondScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined HBondScorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -1025,8 +896,8 @@ of residues to be scored. True by default.</td>
<h2>SSAgreementScorer class<a class="headerlink" href="#ssagreementscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.SSAgreementScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">SSAgreementScorer</code><a class="headerlink" href="#promod3.scoring.SSAgreementScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates a secondary
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">SSAgreementScorer</code><a class="headerlink" href="#promod3.scoring.SSAgreementScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a secondary
structure agreement score. The scorer has a score for each combination of
psipred prediction, its confidence and the actually occurring secondary
structure in the model. In every score evaluation, the secondary structure of
@@ -1034,111 +905,100 @@ the loop is estimated by searching for hydrogen bonds leading to a secondary
structure as defined by dssp. The hbonds are searched internally in the loop
as well as in the environment.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadSSAgreementScorer" title="promod3.scoring.LoadSSAgreementScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadSSAgreementScorer()</span></code></a>) or by setting scores for all possible states
-(see <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.SetScore" title="promod3.scoring.SSAgreementScorer.SetScore"><code class="xref py py-meth docutils literal"><span class="pre">SetScore()</span></code></a>).</p>
+<a class="reference internal" href="#promod3.scoring.LoadSSAgreementScorer" title="promod3.scoring.LoadSSAgreementScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadSSAgreementScorer()</span></code></a>) or by setting scores for all possible states
+(see <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.SetScore" title="promod3.scoring.SSAgreementScorer.SetScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetScore()</span></code></a>).</p>
<p>This scorer assumes that the attached environment has a psipred prediction
-defined (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction" title="promod3.scoring.BackboneScoreEnv.SetPsipredPrediction"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScoreEnv.SetPsipredPrediction()</span></code></a>) as soon as a score
+defined (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction" title="promod3.scoring.BackboneScoreEnv.SetPsipredPrediction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BackboneScoreEnv.SetPsipredPrediction()</span></code></a>) as soon as a score
is to be calculated.</p>
-<p>Note that for this scorer a higher “score” is better! So take care when
+<p>Note that for this scorer a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.scoring.SSAgreementScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.SSAgreementScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.Save" title="promod3.scoring.SSAgreementScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="promod3.scoring.SSAgreementScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.Save" title="promod3.scoring.SSAgreementScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="promod3.scoring.SSAgreementScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal"><span class="pre">SSAgreementScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SSAgreementScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.SSAgreementScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SSAgreementScorer.SetScore">
-<code class="descname">SetScore</code><span class="sig-paren">(</span><em>psipred_state</em>, <em>psipred_confidence</em>, <em>dssp_state</em>, <em>score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SetScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetScore</code><span class="sig-paren">(</span><em class="sig-param">psipred_state</em>, <em class="sig-param">psipred_confidence</em>, <em class="sig-param">dssp_state</em>, <em class="sig-param">score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SetScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup a single score for a combination of states. Unless a predefined scorer
is loaded, this must be called for every combination of states.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>psipred_state</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’]</li>
-<li><strong>psipred_confidence</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – must be in range [0, 9]</li>
-<li><strong>dssp_state</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’, ‘G’, ‘B’, ‘S’, ‘T’, ‘I’]</li>
-<li><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – score to be set</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>psipred_state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’]</p></li>
+<li><p><strong>psipred_confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – must be in range [0, 9]</p></li>
+<li><p><strong>dssp_state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’, ‘G’, ‘B’, ‘S’, ‘T’, ‘I’]</p></li>
+<li><p><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – score to be set</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SSAgreementScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadSSAgreementScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadSSAgreementScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadSSAgreementScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined structure agreement scorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal"><span class="pre">SSAgreementScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadSSAgreementScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadSSAgreementScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined structure agreement scorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -1146,134 +1006,119 @@ of residues to be scored. True by default.</td>
<h2>TorsionScorer class<a class="headerlink" href="#torsionscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.TorsionScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">TorsionScorer</code><span class="sig-paren">(</span><em>group_definitions</em>, <em>torsion_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">TorsionScorer</code><span class="sig-paren">(</span><em class="sig-param">group_definitions</em>, <em class="sig-param">torsion_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
energies based on the identity of three consecutive residues and the phi/psi
dihedral angles of the central residue. The first phi and last psi angle get
determined with the help of the environment if set.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
-<a class="reference internal" href="#promod3.scoring.LoadTorsionScorer" title="promod3.scoring.LoadTorsionScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadTorsionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.TorsionScorer.SetEnergy" title="promod3.scoring.TorsionScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>)
+<a class="reference internal" href="#promod3.scoring.LoadTorsionScorer" title="promod3.scoring.LoadTorsionScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadTorsionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.TorsionScorer.SetEnergy" title="promod3.scoring.TorsionScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>)
for each group definition.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid
triplets (same style as used in the
-<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> class).</li>
-<li><strong>torsion_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize the torsion
-angles (range of [0, 2*pi]).</li>
+<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> class).</p></li>
+<li><p><strong>torsion_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize the torsion
+angles (range of [0, 2*pi]).</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>torsion_bins</em> < 1 or if there is
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>torsion_bins</em> < 1 or if there is
a possible combination of the 20 standard amino acids not matching
any entry of <em>group_definitions</em></p>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.scoring.TorsionScorer.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.TorsionScorer.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.TorsionScorer.Save" title="promod3.scoring.TorsionScorer.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.TorsionScorer.SavePortable" title="promod3.scoring.TorsionScorer.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.TorsionScorer.Save" title="promod3.scoring.TorsionScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.TorsionScorer.SavePortable" title="promod3.scoring.TorsionScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal"><span class="pre">TorsionScorer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The loaded scorer</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.TorsionScorer.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.TorsionScorer.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.TorsionScorer.SetEnergy">
-<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>group_idx</em>, <em>phi_bin</em>, <em>psi_bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">group_idx</em>, <em class="sig-param">phi_bin</em>, <em class="sig-param">psi_bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every <em>group_idx</em> < len(<em>group_definitions</em>), every <em>phi_bin</em> <
<em>torsion_bins</em> and every <em>psi_bin</em> < <em>torsion_bins</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>group_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of group definition as set in constructor with
-numbering starting at 0.</li>
-<li><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the phi angle.</li>
-<li><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the psi angle.</li>
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>group_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of group definition as set in constructor with
+numbering starting at 0.</p></li>
+<li><p><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the phi angle.</p></li>
+<li><p><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the psi angle.</p></li>
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.TorsionScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadTorsionScorer">
-<code class="descclassname">promod3.scoring.</code><code class="descname">LoadTorsionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadTorsionScorer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined TorsionScorer (loaded from disk)</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal"><span class="pre">TorsionScorer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadTorsionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadTorsionScorer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The default predefined TorsionScorer (loaded from disk)</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -1281,54 +1126,45 @@ of residues to be scored. True by default.</td>
<h2>PairwiseScorer class<a class="headerlink" href="#pairwisescorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.PairwiseScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">PairwiseScorer</code><a class="headerlink" href="#promod3.scoring.PairwiseScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates a list of
-generic pairwise functions (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>).
+<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">PairwiseScorer</code><a class="headerlink" href="#promod3.scoring.PairwiseScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a list of
+generic pairwise functions (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>).
That are set in the attached scoring environment
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScoreEnv.ApplyPairwiseFunction()</span></code></a>).</p>
-<p>Note that for this scorer a higher “score” is better! So take care when
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BackboneScoreEnv.ApplyPairwiseFunction()</span></code></a>).</p>
+<p>Note that for this scorer a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
<dl class="method">
<dt id="promod3.scoring.PairwiseScorer.DoInternalScores">
-<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.PairwiseScorer.DoExternalScores">
-<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>, true by default.) – Whether to include pairwise interactions of the scored
+<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>, true by default.) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</td>
-</tr>
-</tbody>
-</table>
+True by default.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.PairwiseScorer.DoNormalize">
-<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -1343,28 +1179,45 @@ of residues to be scored. True by default.</td>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Backbone Scorers</a><ul>
-<li><a class="reference internal" href="#backboneoverallscorer-class">BackboneOverallScorer class</a></li>
-<li><a class="reference internal" href="#backbonescorer-base-class">BackboneScorer base class</a></li>
-<li><a class="reference internal" href="#cbpackingscorer-class">CBPackingScorer class</a></li>
-<li><a class="reference internal" href="#cbetascorer-class">CBetaScorer class</a></li>
-<li><a class="reference internal" href="#reducedscorer-class">ReducedScorer class</a></li>
-<li><a class="reference internal" href="#clashscorer-class">ClashScorer class</a></li>
-<li><a class="reference internal" href="#hbondscorer-class">HBondScorer class</a></li>
-<li><a class="reference internal" href="#ssagreementscorer-class">SSAgreementScorer class</a></li>
-<li><a class="reference internal" href="#torsionscorer-class">TorsionScorer class</a></li>
-<li><a class="reference internal" href="#pairwisescorer-class">PairwiseScorer class</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li>Previous: <a href="backbone_score_env.html" title="previous chapter">Backbone Score Environment</a></li>
<li>Next: <a href="all_atom_scorers.html" title="next chapter">All Atom Scorers</a></li>
</ul></li>
@@ -1372,23 +1225,24 @@ of residues to be scored. True by default.</td>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/scoring/backbone_scorers.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1397,11 +1251,11 @@ of residues to be scored. True by default.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/scoring/backbone_scorers.txt"
+ <a href="../_sources/scoring/backbone_scorers.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index 54a2836841bc5c07da3ca4897e400396a4395720..0c77470050da4a5292176740595012f205b660c4 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>scoring - Loop Scoring — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>scoring - Loop Scoring — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
<link rel="prev" title="Subrotamer Optimization" href="../sidechain/subrotamer_optimizer.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,7 +34,7 @@
<div class="body" role="main">
<div class="section" id="module-promod3.scoring">
-<span id="scoring-loop-scoring"></span><h1><a class="reference internal" href="#module-promod3.scoring" title="promod3.scoring: Loop Scoring"><code class="xref py py-mod docutils literal"><span class="pre">scoring</span></code></a> - Loop Scoring<a class="headerlink" href="#module-promod3.scoring" title="Permalink to this headline">¶</a></h1>
+<span id="scoring-loop-scoring"></span><h1><a class="reference internal" href="#module-promod3.scoring" title="promod3.scoring: Loop Scoring"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code></a> - Loop Scoring<a class="headerlink" href="#module-promod3.scoring" title="Permalink to this headline">¶</a></h1>
<p>Tools and algorithms to score loops. The scoring system is split between an
environment and scorers.
Several scorers can be attached to the same environment containing the
@@ -57,8 +43,8 @@ The environment is updated as the modelling proceeds and manages efficient
spatial lookups to be used by the attached scorers.</p>
<p>In this example, we load a structure, setup a score environment, link a few
scorers to it and finally score some loops:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span>
<span class="c1"># load data</span>
<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">"data/1CRN.pdb"</span><span class="p">)</span>
@@ -125,7 +111,41 @@ scorers to it and finally score some loops:</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
@@ -136,23 +156,24 @@ scorers to it and finally score some loops:</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/scoring/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -161,11 +182,11 @@ scorers to it and finally score some loops:</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/scoring/index.txt"
+ <a href="../_sources/scoring/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 0370e146230fb469e69c7d0bca26510749e89f65..ddf537dcee086399955e71e2001852608a04287c 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Other Scoring Functions — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Other Scoring Functions — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
<link rel="prev" title="All Atom Scorers" href="all_atom_scorers.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -53,64 +39,56 @@
<h2>Scoring Functions from SCWRL3<a class="headerlink" href="#scoring-functions-from-scwrl3" title="Permalink to this headline">¶</a></h2>
<dl class="method">
<dt id="promod3.scoring.SCWRL3PairwiseScore">
-<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3PairwiseScore</code><span class="sig-paren">(</span><em>d</em>, <em>Rij</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3PairwiseScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">SCWRL3PairwiseScore</code><span class="sig-paren">(</span><em class="sig-param">d</em>, <em class="sig-param">Rij</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3PairwiseScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Pairwise score from the SCWRL3 sidechain construction algorithm
-<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>d</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Distance between the two interacting particles</li>
-<li><strong>Rij</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <p>Summed hard-sphere radii of the interacting particles.
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Distance between the two interacting particles</p></li>
+<li><p><strong>Rij</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <p>Summed hard-sphere radii of the interacting particles.
Suggestions from the paper:</p>
<ul>
-<li>carbon: 1.6</li>
-<li>oxygen: 1.3</li>
-<li>nitrogen: 1.3</li>
-<li>sulfur: 1.7</li>
+<li><p>carbon: 1.6</p></li>
+<li><p>oxygen: 1.3</p></li>
+<li><p>nitrogen: 1.3</p></li>
+<li><p>sulfur: 1.7</p></li>
</ul>
-</li>
+</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The score</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The score</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SCWRL3DisulfidScore">
-<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3DisulfidScore</code><span class="sig-paren">(</span><em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>sg_pos_one ca_pos_two</em>, <em>cb_pos_two</em>, <em>sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3DisulfidScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">SCWRL3DisulfidScore</code><span class="sig-paren">(</span><em class="sig-param">ca_pos_one</em>, <em class="sig-param">cb_pos_one</em>, <em class="sig-param">sg_pos_one ca_pos_two</em>, <em class="sig-param">cb_pos_two</em>, <em class="sig-param">sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3DisulfidScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Implements the empirically derived disulfid score from the SCWRL3 sidechain
-construction algorithm <a class="reference internal" href="../references.html#canutescu2003b" id="id2">[canutescu2003b]</a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>ca_pos_one</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of first amino acid</li>
-<li><strong>cb_pos_one</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of first amino acid</li>
-<li><strong>sg_pos_one</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of first amino acid</li>
-<li><strong>ca_pos_two</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of second amino acid</li>
-<li><strong>cb_pos_two</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of second amino acid</li>
-<li><strong>sg_pos_two</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of second amino acid</li>
+construction algorithm <a class="reference internal" href="../references.html#canutescu2003b" id="id2"><span>[canutescu2003b]</span></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ca_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of first amino acid</p></li>
+<li><p><strong>cb_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of first amino acid</p></li>
+<li><p><strong>sg_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of first amino acid</p></li>
+<li><p><strong>ca_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of second amino acid</p></li>
+<li><p><strong>cb_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of second amino acid</p></li>
+<li><p><strong>sg_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of second amino acid</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The score</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The score</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -123,43 +101,70 @@ construction algorithm <a class="reference internal" href="../references.html#ca
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Other Scoring Functions</a><ul>
-<li><a class="reference internal" href="#scoring-functions-from-scwrl3">Scoring Functions from SCWRL3</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li>Previous: <a href="all_atom_scorers.html" title="previous chapter">All Atom Scorers</a></li>
- <li>Next: <a href="../loop/index.html" title="next chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a></li>
+ <li>Next: <a href="../loop/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/scoring/other_scoring_functions.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -168,11 +173,11 @@ construction algorithm <a class="reference internal" href="../references.html#ca
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/scoring/other_scoring_functions.txt"
+ <a href="../_sources/scoring/other_scoring_functions.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/search.html b/doc/html/search.html
index 8af83fdc1f802d41c7adf0e556ff370cd7899faf..ab70ca2d779af8b23aa3a431e35f32b4f9cfe350 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -1,38 +1,23 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Search — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Search — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<script type="text/javascript" src="_static/searchtools.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="#" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
- <script type="text/javascript">
- jQuery(function() { Search.loadIndex("searchindex.js"); });
- </script>
-
- <script type="text/javascript" id="searchindexloader"></script>
+ <script type="text/javascript" src="searchindex.js" defer></script>
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -41,8 +26,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -81,13 +65,42 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
</ul></li>
</ul>
</div>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -96,7 +109,7 @@
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
</div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 16e4229f705f4a34c033614ac204054082876d32..4448039b7fd9119e7893a37b8082624151d7344d 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:50,filenames:["actions/index","actions/index_dev","buildsystem","changelog","cmake/index","container/docker","container/index","container/singularity","contributing","core/geometry","core/graph_minimizer","core/helper","core/index","core/pm3argparse","core/runtime_profiling","core/setcompoundschemlib","dev_setup","developers","gettingstarted","index","license","loop/all_atom","loop/backbone","loop/index","loop/load_loop_objects","loop/mm_system_creation","loop/structure_db","loop/torsion_sampler","modelling/algorithms","modelling/gap_handling","modelling/index","modelling/loop_candidates","modelling/loop_closing","modelling/model_checking","modelling/monte_carlo","modelling/pipeline","modelling/sidechain_reconstruction","portableIO","references","scoring/all_atom_scorers","scoring/backbone_score_env","scoring/backbone_scorers","scoring/index","scoring/other_scoring_functions","sidechain/disulfid","sidechain/frame","sidechain/graph","sidechain/index","sidechain/loading","sidechain/rotamer","sidechain/rotamer_constructor","sidechain/rotamer_lib","sidechain/subrotamer_optimizer","user_contributions","users"],objects:{"":{"--backbone-independent":[0,7,1,"cmdoption--backbone-independent"],"--energy_function":[0,7,1,"cmdoption--energy_function"],"--keep-sidechains":[0,7,1,"cmdoption--keep-sidechains"],"--no-disulfids":[0,7,1,"cmdoption--no-disulfids"],"--no-subrotamer-optimization":[0,7,1,"cmdoption--no-subrotamer-optimization"],"--rigid-rotamers":[0,7,1,"cmdoption--rigid-rotamers"],"-f":[0,7,1,"cmdoption-f"],"-i":[0,7,1,"cmdoption-i"],"-k":[0,7,1,"cmdoption-k"],"-n":[0,7,1,"cmdoption-n"],"-r":[0,7,1,"cmdoption-r"],"-s":[0,7,1,"cmdoption-s"],"command:add_doc_dependency":[4,0,1,""],"command:add_doc_source":[4,0,1,""],"command:convert_module_data":[4,0,1,""],"command:module":[4,0,1,""],"command:pm_action":[4,0,1,""],"command:promod3_unittest":[4,0,1,""],"command:pymod":[4,0,1,""],test_actions:[1,2,0,"-"]},"promod3.core":{ConstructAtomPos:[9,1,1,""],ConstructCBetaPos:[9,1,1,""],ConstructCTerminalOxygens:[9,1,1,""],EvaluateGromacsPosRule:[9,1,1,""],GraphMinimizer:[10,3,1,""],RotationAroundLine:[9,1,1,""],StaticRuntimeProfiler:[14,3,1,""],StemCoords:[9,3,1,""],StemPairOrientation:[9,3,1,""],helper:[11,2,0,"-"],pm3argparse:[13,2,0,"-"]},"promod3.core.GraphMinimizer":{AStarSolve:[10,4,1,""],AddEdge:[10,4,1,""],AddNode:[10,4,1,""],ApplyDEE:[10,4,1,""],ApplyEdgeDecomposition:[10,4,1,""],MCSolve:[10,4,1,""],NaiveSolve:[10,4,1,""],Prune:[10,4,1,""],Reset:[10,4,1,""],TreeSolve:[10,4,1,""]},"promod3.core.StaticRuntimeProfiler":{Clear:[14,5,1,""],IsEnabled:[14,5,1,""],PrintSummary:[14,5,1,""],Start:[14,5,1,""],StartScoped:[14,5,1,""],Stop:[14,5,1,""]},"promod3.core.StemCoords":{c_coord:[9,6,1,""],ca_coord:[9,6,1,""],n_coord:[9,6,1,""]},"promod3.core.StemPairOrientation":{angle_four:[9,6,1,""],angle_one:[9,6,1,""],angle_three:[9,6,1,""],angle_two:[9,6,1,""],distance:[9,6,1,""]},"promod3.core.helper":{FileExists:[11,1,1,""],FileExtension:[11,1,1,""],FileGzip:[11,1,1,""],MsgErrorAndExit:[11,1,1,""]},"promod3.core.pm3argparse":{PM3ArgumentParser:[13,3,1,""]},"promod3.core.pm3argparse.PM3ArgumentParser":{AddAlignment:[13,4,1,""],AddFragments:[13,4,1,""],AddProfile:[13,4,1,""],AddStructure:[13,4,1,""],AssembleParser:[13,4,1,""],Parse:[13,4,1,""],__init__:[13,4,1,""],action:[13,6,1,""]},"promod3.loop":{AllAtomEnv:[21,3,1,""],AllAtomEnvPositions:[21,3,1,""],AllAtomPositions:[21,3,1,""],AminoAcidAtom:[21,3,1,""],AminoAcidHydrogen:[21,3,1,""],AminoAcidLookup:[21,3,1,""],BackboneList:[22,3,1,""],CoordInfo:[26,3,1,""],ForcefieldAminoAcid:[25,3,1,""],ForcefieldBondInfo:[25,3,1,""],ForcefieldConnectivity:[25,3,1,""],ForcefieldHarmonicAngleInfo:[25,3,1,""],ForcefieldHarmonicImproperInfo:[25,3,1,""],ForcefieldLJPairInfo:[25,3,1,""],ForcefieldLookup:[25,3,1,""],ForcefieldPeriodicDihedralInfo:[25,3,1,""],ForcefieldUreyBradleyAngleInfo:[25,3,1,""],FragDB:[26,3,1,""],Fragger:[26,3,1,""],FraggerMap:[26,3,1,""],FragmentInfo:[26,3,1,""],LoadFragDB:[24,4,1,""],LoadStructureDB:[24,4,1,""],LoadTorsionSampler:[24,4,1,""],LoadTorsionSamplerCoil:[24,4,1,""],LoadTorsionSamplerExtended:[24,4,1,""],LoadTorsionSamplerHelical:[24,4,1,""],MmSystemCreator:[25,3,1,""],PsipredPrediction:[26,3,1,""],StructureDB:[26,3,1,""],StructureDBDataType:[26,3,1,""],TorsionSampler:[27,3,1,""]},"promod3.loop.AllAtomEnv":{ClearEnvironment:[21,4,1,""],GetAllAtomPositions:[21,4,1,""],GetEnvironment:[21,4,1,""],GetSeqres:[21,4,1,""],SetEnvironment:[21,4,1,""],SetInitialEnvironment:[21,4,1,""]},"promod3.loop.AllAtomEnvPositions":{all_pos:[21,6,1,""],res_indices:[21,6,1,""]},"promod3.loop.AllAtomPositions":{AllAtomPositions:[21,4,1,""],ClearPos:[21,4,1,""],ClearResidue:[21,4,1,""],Copy:[21,4,1,""],Extract:[21,4,1,""],ExtractBackbone:[21,4,1,""],GetAA:[21,4,1,""],GetFirstIndex:[21,4,1,""],GetIndex:[21,4,1,""],GetLastIndex:[21,4,1,""],GetNumAtoms:[21,4,1,""],GetNumResidues:[21,4,1,""],GetOmegaTorsion:[21,4,1,""],GetPhiTorsion:[21,4,1,""],GetPos:[21,4,1,""],GetPsiTorsion:[21,4,1,""],GetSequence:[21,4,1,""],InsertInto:[21,4,1,""],IsAllSet:[21,4,1,""],IsAnySet:[21,4,1,""],IsSet:[21,4,1,""],SetPos:[21,4,1,""],SetResidue:[21,4,1,""],ToEntity:[21,4,1,""]},"promod3.loop.AminoAcidLookup":{GetAA:[21,5,1,""],GetAAA:[21,5,1,""],GetAAH:[21,5,1,""],GetAnchorAtomIndex:[21,5,1,""],GetAtomName:[21,5,1,""],GetAtomNameAmber:[21,5,1,""],GetAtomNameCharmm:[21,5,1,""],GetElement:[21,5,1,""],GetH1Index:[21,5,1,""],GetH2Index:[21,5,1,""],GetH3Index:[21,5,1,""],GetHNIndex:[21,5,1,""],GetHydrogenIndex:[21,5,1,""],GetIndex:[21,5,1,""],GetMaxNumAtoms:[21,5,1,""],GetMaxNumHydrogens:[21,5,1,""],GetNumAtoms:[21,5,1,""],GetNumHydrogens:[21,5,1,""],GetOLC:[21,5,1,""]},"promod3.loop.BackboneList":{ApplyTransform:[22,4,1,""],BackboneList:[22,4,1,""],CARMSD:[22,4,1,""],Copy:[22,4,1,""],Extract:[22,4,1,""],GetAA:[22,4,1,""],GetBounds:[22,4,1,""],GetC:[22,4,1,""],GetCA:[22,4,1,""],GetCB:[22,4,1,""],GetN:[22,4,1,""],GetO:[22,4,1,""],GetOLC:[22,4,1,""],GetOmegaTorsion:[22,4,1,""],GetPhiTorsion:[22,4,1,""],GetPsiTorsion:[22,4,1,""],GetSequence:[22,4,1,""],GetTransform:[22,4,1,""],InsertInto:[22,4,1,""],MinCADistance:[22,4,1,""],RMSD:[22,4,1,""],ReconstructCBetaPositions:[22,4,1,""],ReconstructCStemOxygen:[22,4,1,""],ReconstructOxygenPositions:[22,4,1,""],ReplaceFragment:[22,4,1,""],RotateAroundOmegaTorsion:[22,4,1,""],RotateAroundPhiPsiTorsion:[22,4,1,""],RotateAroundPhiTorsion:[22,4,1,""],RotateAroundPsiTorsion:[22,4,1,""],Set:[22,4,1,""],SetAA:[22,4,1,""],SetAroundOmegaTorsion:[22,4,1,""],SetAroundPhiPsiTorsion:[22,4,1,""],SetAroundPhiTorsion:[22,4,1,""],SetAroundPsiTorsion:[22,4,1,""],SetBackrub:[22,4,1,""],SetC:[22,4,1,""],SetCA:[22,4,1,""],SetCB:[22,4,1,""],SetN:[22,4,1,""],SetO:[22,4,1,""],SetOLC:[22,4,1,""],SetSequence:[22,4,1,""],SuperposeOnto:[22,4,1,""],ToDensity:[22,4,1,""],ToEntity:[22,4,1,""],TransOmegaTorsions:[22,4,1,""],__len__:[22,4,1,""],append:[22,4,1,""],clear:[22,4,1,""],empty:[22,4,1,""],resize:[22,4,1,""]},"promod3.loop.CoordInfo":{chain_name:[26,6,1,""],id:[26,6,1,""],offset:[26,6,1,""],shift:[26,6,1,""],size:[26,6,1,""],start_resnum:[26,6,1,""]},"promod3.loop.ForcefieldBondInfo":{bond_length:[25,6,1,""],force_constant:[25,6,1,""],index_one:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldConnectivity":{harmonic_angles:[25,6,1,""],harmonic_bonds:[25,6,1,""],harmonic_impropers:[25,6,1,""],lj_pairs:[25,6,1,""],periodic_dihedrals:[25,6,1,""],periodic_impropers:[25,6,1,""],urey_bradley_angles:[25,6,1,""]},"promod3.loop.ForcefieldHarmonicAngleInfo":{angle:[25,6,1,""],force_constant:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldHarmonicImproperInfo":{angle:[25,6,1,""],force_constant:[25,6,1,""],index_four:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldLJPairInfo":{epsilon:[25,6,1,""],index_one:[25,6,1,""],index_two:[25,6,1,""],sigma:[25,6,1,""]},"promod3.loop.ForcefieldLookup":{GetAA:[25,4,1,""],GetCharges:[25,4,1,""],GetDefault:[25,5,1,""],GetDisulfidConnectivity:[25,4,1,""],GetEpsilons:[25,4,1,""],GetFudgeLJ:[25,4,1,""],GetFudgeQQ:[25,4,1,""],GetHeavyIndex:[25,4,1,""],GetHydrogenIndex:[25,4,1,""],GetInternalConnectivity:[25,4,1,""],GetMasses:[25,4,1,""],GetNumAtoms:[25,4,1,""],GetOXTIndex:[25,4,1,""],GetPeptideBoundConnectivity:[25,4,1,""],GetSigmas:[25,4,1,""],Load:[25,5,1,""],LoadCHARMM:[25,5,1,""],LoadPortable:[25,5,1,""],Save:[25,4,1,""],SavePortable:[25,4,1,""],SetCharges:[25,4,1,""],SetDefault:[25,5,1,""],SetDisulfidConnectivity:[25,4,1,""],SetEpsilons:[25,4,1,""],SetFudgeLJ:[25,4,1,""],SetFudgeQQ:[25,4,1,""],SetInternalConnectivity:[25,4,1,""],SetMasses:[25,4,1,""],SetPeptideBoundConnectivity:[25,4,1,""],SetSigmas:[25,4,1,""]},"promod3.loop.ForcefieldPeriodicDihedralInfo":{force_constant:[25,6,1,""],index_four:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""],multiplicity:[25,6,1,""],phase:[25,6,1,""]},"promod3.loop.ForcefieldUreyBradleyAngleInfo":{angle:[25,6,1,""],angle_force_constant:[25,6,1,""],bond_force_constant:[25,6,1,""],bond_length:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.FragDB":{AddFragments:[26,4,1,""],GetAngularBinSize:[26,4,1,""],GetDistBinSize:[26,4,1,""],GetNumFragments:[26,4,1,""],GetNumStemPairs:[26,4,1,""],HasFragLength:[26,4,1,""],Load:[26,5,1,""],LoadPortable:[26,5,1,""],MaxFragLength:[26,4,1,""],PrintStatistics:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SearchDB:[26,4,1,""]},"promod3.loop.Fragger":{AddSSAgreeParameters:[26,4,1,""],AddSeqIDParameters:[26,4,1,""],AddSeqSimParameters:[26,4,1,""],AddSequenceProfileParameters:[26,4,1,""],AddStructureProfileParameters:[26,4,1,""],AddTorsionProbabilityParameters:[26,4,1,""],Fill:[26,4,1,""],GetFragmentInfo:[26,4,1,""],GetScore:[26,4,1,""],__getitem__:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.FraggerMap":{Contains:[26,4,1,""],Load:[26,4,1,""],LoadBB:[26,4,1,""],Save:[26,4,1,""],SaveBB:[26,4,1,""],__getitem__:[26,4,1,""],__setitem__:[26,4,1,""]},"promod3.loop.FragmentInfo":{chain_index:[26,6,1,""],length:[26,6,1,""],offset:[26,6,1,""]},"promod3.loop.MmSystemCreator":{ExtractLoopPositions:[25,4,1,""],GetCpuPlatformSupport:[25,4,1,""],GetDisulfidBridges:[25,4,1,""],GetForcefieldAminoAcids:[25,4,1,""],GetIndexing:[25,4,1,""],GetLoopLengths:[25,4,1,""],GetLoopStartIndices:[25,4,1,""],GetNumLoopResidues:[25,4,1,""],GetNumResidues:[25,4,1,""],GetSimulation:[25,4,1,""],SetCpuPlatformSupport:[25,4,1,""],SetupSystem:[25,4,1,""],UpdatePositions:[25,4,1,""]},"promod3.loop.PsipredPrediction":{Add:[26,4,1,""],Extract:[26,4,1,""],FromHHM:[26,4,1,""],FromHoriz:[26,4,1,""],GetConfidence:[26,4,1,""],GetConfidences:[26,4,1,""],GetPrediction:[26,4,1,""],GetPredictions:[26,4,1,""],PsipredPrediction:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.StructureDB":{AddCoordinates:[26,4,1,""],GenerateStructureProfile:[26,4,1,""],GetBackboneList:[26,4,1,""],GetCoordIdx:[26,4,1,""],GetCoordInfo:[26,4,1,""],GetDSSPStates:[26,4,1,""],GetDihedralAngles:[26,4,1,""],GetNumCoords:[26,4,1,""],GetResidueDepths:[26,4,1,""],GetSequence:[26,4,1,""],GetSequenceProfile:[26,4,1,""],GetSolventAccessibilitites:[26,4,1,""],GetStructureProfile:[26,4,1,""],GetSubDB:[26,4,1,""],HasData:[26,4,1,""],Load:[26,5,1,""],LoadPortable:[26,5,1,""],PrintStatistics:[26,4,1,""],RemoveCoordinates:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SetStructureProfile:[26,4,1,""]},"promod3.loop.TorsionSampler":{Draw:[27,4,1,""],DrawPhiGivenPsi:[27,4,1,""],DrawPsiGivenPhi:[27,4,1,""],ExtractStatistics:[27,4,1,""],GetBinSize:[27,4,1,""],GetBinsPerDimension:[27,4,1,""],GetHistogramIndex:[27,4,1,""],GetHistogramIndices:[27,4,1,""],GetPhiProbabilityGivenPsi:[27,4,1,""],GetProbability:[27,4,1,""],GetPsiProbabilityGivenPhi:[27,4,1,""],Load:[27,5,1,""],LoadPortable:[27,5,1,""],Save:[27,4,1,""],SavePortable:[27,4,1,""],UpdateDistributions:[27,4,1,""]},"promod3.modelling":{AddModellingIssue:[35,1,1,""],AllAtomRelaxer:[32,3,1,""],BackboneRelaxer:[32,3,1,""],BuildFromRawModel:[35,1,1,""],BuildRawModel:[35,1,1,""],BuildSidechains:[35,1,1,""],CCD:[32,3,1,""],CCDCloser:[34,3,1,""],CTerminalCloser:[34,3,1,""],CheckFinalModel:[35,1,1,""],ClearGaps:[29,1,1,""],CloseGaps:[35,1,1,""],CloseLargeDeletions:[35,1,1,""],CloseSmallDeletions:[35,1,1,""],CloserBase:[34,3,1,""],CoolerBase:[34,3,1,""],CountEnclosedGaps:[29,1,1,""],CountEnclosedInsertions:[29,1,1,""],DeNovoCloser:[34,3,1,""],DirtyCCDCloser:[34,3,1,""],ExponentialCooler:[34,3,1,""],FillLoopsByDatabase:[35,1,1,""],FillLoopsByMonteCarlo:[35,1,1,""],FilterCandidates:[33,1,1,""],FilterCandidatesWithSC:[33,1,1,""],FindMotifs:[28,4,1,""],FraggerHandle:[28,3,1,""],FragmentSampler:[34,3,1,""],FullGapExtender:[29,3,1,""],GapExtender:[29,3,1,""],GenerateDeNovoTrajectories:[28,1,1,""],GetRingPunches:[33,1,1,""],GetRings:[33,1,1,""],HasRingPunches:[33,1,1,""],InsertLoop:[35,1,1,""],InsertLoopClearGaps:[29,1,1,""],IsAllAtomScoringSetUp:[35,1,1,""],IsBackboneScoringSetUp:[35,1,1,""],KIC:[32,3,1,""],KICCloser:[34,3,1,""],LinearScorer:[34,3,1,""],LoopCandidates:[31,3,1,""],MergeGaps:[29,1,1,""],MergeGapsByDistance:[35,1,1,""],MergeMHandle:[35,1,1,""],MinimizeModelEnergy:[35,1,1,""],ModelTermini:[35,1,1,""],ModellingHandle:[35,3,1,""],ModellingIssue:[35,3,1,""],MotifMatch:[28,3,1,""],MotifQuery:[28,3,1,""],NTerminalCloser:[34,3,1,""],PhiPsiSampler:[34,3,1,""],ReconstructSidechains:[36,1,1,""],RemoveTerminalGaps:[35,1,1,""],ReorderGaps:[35,1,1,""],ReportMolProbityScores:[33,1,1,""],RigidBlocks:[28,4,1,""],RunMolProbity:[33,1,1,""],RunMolProbityEntity:[33,1,1,""],SampleMonteCarlo:[34,1,1,""],SamplerBase:[34,3,1,""],ScoreContainer:[31,3,1,""],ScorerBase:[34,3,1,""],ScoringGapExtender:[29,3,1,""],ScoringWeights:[31,3,1,""],SetFraggerHandles:[35,1,1,""],SetPsipredPredictions:[35,1,1,""],SetSequenceProfiles:[35,1,1,""],SetupDefaultAllAtomScoring:[35,1,1,""],SetupDefaultBackboneScoring:[35,1,1,""],ShiftExtension:[29,3,1,""],SidechainReconstructionData:[36,3,1,""],SidechainReconstructor:[36,3,1,""],SoftSampler:[34,3,1,""],StructuralGap:[29,3,1,""],StructuralGapList:[29,3,1,""]},"promod3.modelling.AllAtomRelaxer":{GetSystemCreator:[32,4,1,""],Run:[32,4,1,""],UpdatePositions:[32,4,1,""]},"promod3.modelling.BackboneRelaxer":{AddCARestraint:[32,4,1,""],AddCBRestraint:[32,4,1,""],AddCRestraint:[32,4,1,""],AddNRestraint:[32,4,1,""],AddORestraint:[32,4,1,""],GetNonBondedCutoff:[32,4,1,""],Run:[32,4,1,""],SetNonBondedCutoff:[32,4,1,""]},"promod3.modelling.CCD":{CCD:[32,4,1,""],Close:[32,4,1,""]},"promod3.modelling.CCDCloser":{Close:[34,4,1,""]},"promod3.modelling.CTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.CloserBase":{Close:[34,4,1,""]},"promod3.modelling.CoolerBase":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.DeNovoCloser":{Close:[34,4,1,""]},"promod3.modelling.DirtyCCDCloser":{Close:[34,4,1,""]},"promod3.modelling.ExponentialCooler":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.FraggerHandle":{Get:[28,4,1,""],GetList:[28,4,1,""],LoadCached:[28,4,1,""],SaveCached:[28,4,1,""]},"promod3.modelling.FragmentSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.FullGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.GapExtender":{Extend:[29,4,1,""]},"promod3.modelling.KIC":{Close:[32,4,1,""],KIC:[32,4,1,""]},"promod3.modelling.KICCloser":{Close:[34,4,1,""]},"promod3.modelling.LinearScorer":{GetScore:[34,4,1,""]},"promod3.modelling.LoopCandidates":{Add:[31,4,1,""],AddFragmentInfo:[31,4,1,""],ApplyCCD:[31,4,1,""],ApplyKIC:[31,4,1,""],CalculateAllAtomScores:[31,4,1,""],CalculateBackboneScores:[31,4,1,""],CalculateSequenceProfileScores:[31,4,1,""],CalculateStemRMSDs:[31,4,1,""],CalculateStructureProfileScores:[31,4,1,""],Extract:[31,4,1,""],FillFromDatabase:[31,5,1,""],FillFromMonteCarloSampler:[31,5,1,""],GetClusteredCandidates:[31,4,1,""],GetClusters:[31,4,1,""],GetFragmentInfo:[31,4,1,""],GetLargestCluster:[31,4,1,""],GetSequence:[31,4,1,""],HasFragmentInfos:[31,4,1,""],Remove:[31,4,1,""]},"promod3.modelling.ModellingHandle":{Copy:[35,4,1,""],all_atom_scorer:[35,6,1,""],all_atom_scorer_env:[35,6,1,""],all_atom_sidechain_env:[35,6,1,""],backbone_scorer:[35,6,1,""],backbone_scorer_env:[35,6,1,""],fragger_handles:[35,6,1,""],gaps:[35,6,1,""],model:[35,6,1,""],modelling_issues:[35,6,1,""],profiles:[35,6,1,""],psipred_predictions:[35,6,1,""],seqres:[35,6,1,""],sidechain_reconstructor:[35,6,1,""]},"promod3.modelling.ModellingIssue":{Severity:[35,3,1,""],is_major:[35,4,1,""],residue_list:[35,6,1,""],severity:[35,6,1,""],text:[35,6,1,""]},"promod3.modelling.ModellingIssue.Severity":{MAJOR:[35,6,1,""],MINOR:[35,6,1,""]},"promod3.modelling.MotifMatch":{alignment:[28,6,1,""],mat:[28,6,1,""],query_idx:[28,6,1,""]},"promod3.modelling.MotifQuery":{GetIdentifiers:[28,4,1,""],GetN:[28,4,1,""],GetPositions:[28,4,1,""],Load:[28,5,1,""],Save:[28,4,1,""]},"promod3.modelling.NTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.PhiPsiSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.SamplerBase":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.ScoreContainer":{Contains:[31,4,1,""],Copy:[31,4,1,""],Extend:[31,4,1,""],Extract:[31,4,1,""],Get:[31,4,1,""],GetNumCandidates:[31,4,1,""],IsEmpty:[31,4,1,""],LinearCombine:[31,4,1,""],Set:[31,4,1,""]},"promod3.modelling.ScorerBase":{GetScore:[34,4,1,""]},"promod3.modelling.ScoringGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.ScoringWeights":{GetAllAtomScoringKeys:[31,5,1,""],GetAllAtomWeights:[31,5,1,""],GetBackboneScoringKeys:[31,5,1,""],GetBackboneWeights:[31,5,1,""],GetSequenceProfileScoresKey:[31,5,1,""],GetStemRMSDsKey:[31,5,1,""],GetStructureProfileScoresKey:[31,5,1,""],GetWeights:[31,5,1,""],SetAllAtomScoringKeys:[31,5,1,""],SetBackboneScoringKeys:[31,5,1,""],SetSequenceProfileScoresKey:[31,5,1,""],SetStemRMSDsKey:[31,5,1,""],SetStructureProfileScoresKey:[31,5,1,""],SetWeights:[31,5,1,""]},"promod3.modelling.ShiftExtension":{Extend:[29,4,1,""]},"promod3.modelling.SidechainReconstructionData":{disulfid_bridges:[36,6,1,""],env_pos:[36,6,1,""],is_c_ter:[36,6,1,""],is_n_ter:[36,6,1,""],loop_lengths:[36,6,1,""],loop_start_indices:[36,6,1,""],rotamer_res_indices:[36,6,1,""]},"promod3.modelling.SidechainReconstructor":{AttachEnvironment:[36,4,1,""],Reconstruct:[36,4,1,""]},"promod3.modelling.SoftSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.StructuralGap":{Copy:[29,4,1,""],ExtendAtCTerm:[29,4,1,""],ExtendAtNTerm:[29,4,1,""],GetChain:[29,4,1,""],GetChainIndex:[29,4,1,""],GetChainName:[29,4,1,""],GetLength:[29,4,1,""],IsCTerminal:[29,4,1,""],IsNTerminal:[29,4,1,""],IsTerminal:[29,4,1,""],ShiftCTerminal:[29,4,1,""],after:[29,6,1,""],before:[29,6,1,""],full_seq:[29,6,1,""],length:[29,6,1,""],seq:[29,6,1,""]},"promod3.scoring":{AllAtomClashScorer:[39,3,1,""],AllAtomInteractionScorer:[39,3,1,""],AllAtomOverallScorer:[39,3,1,""],AllAtomPackingScorer:[39,3,1,""],AllAtomScorer:[39,3,1,""],BackboneOverallScorer:[41,3,1,""],BackboneScoreEnv:[40,3,1,""],BackboneScorer:[41,3,1,""],CBPackingScorer:[41,3,1,""],CBetaScorer:[41,3,1,""],ClashScorer:[41,3,1,""],ConstraintFunction:[40,3,1,""],ContactFunction:[40,3,1,""],DiscoContainer:[40,3,1,""],HBondScorer:[41,3,1,""],LoadAllAtomInteractionScorer:[39,1,1,""],LoadAllAtomPackingScorer:[39,1,1,""],LoadCBPackingScorer:[41,1,1,""],LoadCBetaScorer:[41,1,1,""],LoadDefaultAllAtomOverallScorer:[39,1,1,""],LoadDefaultBackboneOverallScorer:[41,1,1,""],LoadHBondScorer:[41,1,1,""],LoadReducedScorer:[41,1,1,""],LoadSSAgreementScorer:[41,1,1,""],LoadTorsionScorer:[41,1,1,""],PairwiseFunction:[40,3,1,""],PairwiseFunctionType:[40,3,1,""],PairwiseScorer:[41,3,1,""],ReducedScorer:[41,3,1,""],SCWRL3DisulfidScore:[43,4,1,""],SCWRL3PairwiseScore:[43,4,1,""],SSAgreementScorer:[41,3,1,""],TorsionScorer:[41,3,1,""]},"promod3.scoring.AllAtomClashScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""]},"promod3.scoring.AllAtomInteractionScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""],Load:[39,5,1,""],LoadPortable:[39,5,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomOverallScorer":{AttachEnvironment:[39,4,1,""],CalculateLinearCombination:[39,4,1,""],Contains:[39,4,1,""],Get:[39,4,1,""],__getitem__:[39,4,1,""],__setitem__:[39,4,1,""]},"promod3.scoring.AllAtomPackingScorer":{DoNormalize:[39,4,1,""],Load:[39,5,1,""],LoadPortable:[39,5,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomScorer":{AttachEnvironment:[39,4,1,""],CalculateScore:[39,4,1,""],CalculateScoreProfile:[39,4,1,""]},"promod3.scoring.BackboneOverallScorer":{AttachEnvironment:[41,4,1,""],Calculate:[41,4,1,""],CalculateLinearCombination:[41,4,1,""],Contains:[41,4,1,""],Get:[41,4,1,""],__getitem__:[41,4,1,""],__setitem__:[41,4,1,""]},"promod3.scoring.BackboneScoreEnv":{AddPairwiseFunction:[40,4,1,""],ApplyPairwiseFunction:[40,4,1,""],ClearEnvironment:[40,4,1,""],Copy:[40,4,1,""],GetSeqres:[40,4,1,""],Pop:[40,4,1,""],SetEnvironment:[40,4,1,""],SetInitialEnvironment:[40,4,1,""],SetPsipredPrediction:[40,4,1,""],Stash:[40,4,1,""]},"promod3.scoring.BackboneScorer":{AttachEnvironment:[41,4,1,""],CalculateScore:[41,4,1,""],CalculateScoreProfile:[41,4,1,""]},"promod3.scoring.CBPackingScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.CBetaScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.ClashScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.DiscoContainer":{AddStructuralInfo:[40,1,1,""],AttachConstraints:[40,1,1,""]},"promod3.scoring.HBondScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.PairwiseFunction":{Score:[40,4,1,""]},"promod3.scoring.PairwiseScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.ReducedScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.SSAgreementScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetScore:[41,4,1,""]},"promod3.scoring.TorsionScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.sidechain":{AAToRotID:[49,4,1,""],BBDepRotamerLib:[51,3,1,""],CreateSCWRL3Particle:[49,4,1,""],CreateSCWRL4Particle:[49,4,1,""],CreateVINAParticle:[49,4,1,""],DihedralConfiguration:[51,3,1,""],DisulfidScore:[44,4,1,""],FRMRotamer:[49,3,1,""],FRMRotamerGroup:[49,3,1,""],Frame:[45,3,1,""],FrameResidue:[45,3,1,""],GetDihedralConfiguration:[51,4,1,""],GetRotamericConfiguration:[51,4,1,""],LoadBBDepLib:[48,4,1,""],LoadLib:[48,4,1,""],PScoringFunction:[49,3,1,""],Particle:[49,3,1,""],RRMRotamer:[49,3,1,""],RRMRotamerGroup:[49,3,1,""],ReadDunbrackFile:[48,4,1,""],ResolveCysteins:[44,4,1,""],RotamerConstructor:[50,3,1,""],RotamerGraph:[46,3,1,""],RotamerID:[49,3,1,""],RotamerLib:[51,3,1,""],RotamerLibEntry:[51,3,1,""],SCWRL3RotamerConstructor:[50,3,1,""],SCWRL4ParticleType:[49,3,1,""],SCWRL4RotamerConstructor:[50,3,1,""],SubrotamerOptimizer:[52,4,1,""],TLCToRotID:[49,4,1,""],VINAParticleType:[49,3,1,""],VINARotamerConstructor:[50,3,1,""]},"promod3.sidechain.BBDepRotamerLib":{AddRotamer:[51,4,1,""],Load:[51,5,1,""],LoadPortable:[51,5,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""],SetInterpolate:[51,4,1,""]},"promod3.sidechain.FRMRotamer":{AddFrameEnergy:[49,4,1,""],AddSubrotamerDefinition:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetActiveSubrotamer:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetNumSubrotamers:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],GetSubrotamerDefinition:[49,4,1,""],GetTemperature:[49,4,1,""],SetActiveSubrotamer:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],SetTemperature:[49,4,1,""],ToFrameResidue:[49,4,1,""],ToRRMRotamer:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FrameResidue":{__getitem__:[45,4,1,""],__len__:[45,4,1,""]},"promod3.sidechain.Particle":{GetCollisionDistance:[49,4,1,""],GetName:[49,4,1,""],GetPos:[49,4,1,""],GetScoringFunction:[49,4,1,""],PairwiseScore:[49,4,1,""]},"promod3.sidechain.RRMRotamer":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],ToFrameResidue:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructBackboneFrameResidue:[50,4,1,""],ConstructRRMRotamerGroup:[50,4,1,""],ConstructSidechainFrameResidue:[50,4,1,""]},"promod3.sidechain.RotamerGraph":{CreateFromFRMList:[46,5,1,""],CreateFromRRMList:[46,5,1,""]},"promod3.sidechain.RotamerLib":{AddRotamer:[51,4,1,""],Load:[51,5,1,""],LoadPortable:[51,5,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""]},"promod3.sidechain.RotamerLibEntry":{FromResidue:[51,5,1,""],IsSimilar:[51,4,1,""],SimilarDihedral:[51,4,1,""],chi1:[51,6,1,""],chi2:[51,6,1,""],chi3:[51,6,1,""],chi4:[51,6,1,""],probability:[51,6,1,""],sig1:[51,6,1,""],sig2:[51,6,1,""],sig3:[51,6,1,""],sig4:[51,6,1,""]},"promod3.sidechain.SCWRL3RotamerConstructor":{AssignInternalEnergies:[50,4,1,""]},"promod3.sidechain.SCWRL4RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFrameResidue:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""]},"promod3.sidechain.VINARotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFRMRotamerHeuristic:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""],ConstructRRMRotamerHeuristic:[50,4,1,""]},"test_actions.ActionTestCase":{RunAction:[1,4,1,""],RunExitStatusTest:[1,4,1,""],pm_action:[1,6,1,""],pm_bin:[1,6,1,""],testPMExists:[1,4,1,""]},promod3:{SetCompoundsChemlib:[15,1,1,""],core:[12,2,0,"-"],loop:[23,2,0,"-"],modelling:[30,2,0,"-"],scoring:[42,2,0,"-"],sidechain:[47,2,0,"-"]},test_actions:{ActionTestCase:[1,3,1,""]}},objnames:{"0":["cmake","command","CMake command"],"1":["py","function","Python function"],"2":["py","module","Python module"],"3":["py","class","Python class"],"4":["py","method","Python method"],"5":["py","staticmethod","Python static method"],"6":["py","attribute","Python attribute"],"7":["std","option","option"]},objtypes:{"0":"cmake:command","1":"py:function","2":"py:module","3":"py:class","4":"py:method","5":"py:staticmethod","6":"py:attribute","7":"std:option"},terms:{"10a":36,"1ake":28,"1aki":26,"1crn":[21,23,25,26,30,31,32,34,35,36,42,47],"1crn_cut":[30,31,35],"1crna":[26,31],"1e2q":28,"1ey":8,"1eye_rec":8,"1ko5":28,"20a":36,"2iyw":28,"2jlp":0,"30a":36,"3x3":9,"655a":26,"abstract":[34,50],"boolean":[11,13,35],"break":[3,4,8,16],"byte":[10,37],"case":[0,1,5,8,13,16,22,26,27,28,29,32,34,35,36,37,41,44,47,49,50,51],"catch":26,"char":[22,37],"class":[0,1,3,5,8,9,10,12,13,14,17,20],"const":37,"default":[0,1,2,3,4,5,8,10,13,14,15,18,21,22,25,26,27,28,30,31,32,34],"enum":[26,49],"export":[8,21],"final":[8,18,26,28,30,31,35,40,42,44,46,47,49],"float":[9,10,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,49,50,51,52],"function":[0,1,3],"import":[0,1,5,8,11,13,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,42,47,49,50],"int":[1,9,10,11,14,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,45,49,50,51,52],"long":35,"new":[1,3,7,8,13,16,17,21,22,25,26,29,31,32,34,35,36,37,38,47,49],"null":26,"public":[8,37,49],"return":[1,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,45,48,49,50,51],"s\u00f6ding":38,"short":[8,16,37],"static":[8,14,21,25,26,27,28,31,36,37,39,41,46,48,51],"super":47,"switch":[8,16,40],"throw":[1,37,47,48],"true":[1,11,13,14,21,22,23,25,26,28,29,31,32,33,34,35,36,37,39,41,44,47,50],"try":[1,8,18,29,35,37,51],"void":37,"while":[1,4,8,14,20,21,25,35,37,49],__doc__:[11,13],__getitem__:[26,39,41,45,49],__init__:[1,8,13,16],__len__:[22,26,45,49],__main__:[1,8],__name__:[1,8],__setitem__:[26,39,41],_data:37,_name:4,_run:[1,4],_xml:4,a3m:[0,13],a3mtoprofil:[0,13],aa1:41,aa2:41,aa_aft:26,aa_befor:26,aa_clash:[35,39],aa_interact:[35,39],aa_pack:[35,39],aa_packing_scor:37,aa_relax_test:32,aa_res_idx:50,aa_scor:37,aa_with_rotam:47,aaa1:39,aaa2:39,aaa:[21,39],aaaaaaaa:22,aaaaggggggggggggggggggggaaaaaa:35,aafrequenc:26,aafrequenciesstruct:26,aah:21,aatorotid:49,abcdefghijklmnopqrstuvwxyz0123456789abcdefghijklmnopqrstuvwxyz:35,abil:16,abl:[2,8],abort:[8,10,32,35],about:[1,4,8,10,26,28,35],abov:[0,1,5,8,13,16,20,22,29,31,35,37,49,51],absolut:[4,5,34],academ:8,accept:[10,13,20,31,32,34,37],acceptabl:36,acceptanc:35,acceptor:[41,49,50],access:[4,5,8,21,22,26,27,31,35,39,40,41,49],accessibl:26,accessor:26,accord:[0,5,10,16,21,22,25,26,27,28,29,31,34,35,36,39,44,47,49,50,51],accordingli:[26,40],account:[8,53],accumul:28,accur:28,accuraci:[0,28,35,38],achiev:[10,16],acknowledg:8,across:[1,51],act:[20,32],acta:38,action_name:16,action_unit_tests:1,actiontest:1,activ:[13,14,16,35,44,49,52],activat:13,active_internal_energi:52,actual:[3,8,13,16,22,26,28,34,35,36,40,41,42,50,51],actual_posit:34,actual_step:34,adapt:[8,25,26,32,34,35,38],add:[1,2,4,6,8,10,13,18,20,21,26,27,28,31,32,35,36,39,40,41,44,47,49,50,53],add_argu:11,add_custom_target:8,add_doc_depend:4,add_doc_sourc:[4,8],add_flag:28,add_subdirectori:8,addalignment:13,addcarestraint:32,addcbrestraint:32,addcoordin:26,addcrestraint:32,added:3,addedge:10,addendum:20,addfragment:[13,26],addfragmentinfo:31,addframeenergi:49,addharmonicangl:25,addharmonicbond:25,addharmonicimprop:25,adding:[3,4],addit:[3,4,11,13,14,16,20,22,23,25,26,33,37],addition:[1,4,16,20,21,25,26,28,35],addljpair:25,addmodellingissu:35,addnode:10,addnrestraint:32,addorestraint:32,addpairwisefunct:40,addperiodicdihedr:25,addperiodicimprop:25,addprofil:13,addresidu:28,address:37,addrotam:51,addseqidparamet:26,addseqsimparamet:[23,26],addsequenceprofileparamet:26,addssagreeparamet:26,addstructur:13,addstructuralinfo:40,addstructureprofileparamet:26,addsubrotamerdefinit:49,addtorsionprobabilityparamet:26,addureybradleyangl:25,admir:8,advanc:28,advantag:25,advic:[8,16],advis:20,affect:[8,22,35,49,50],after:[1,2,4,5,8,10,13,16,21,22,25,26,27,29,31,32,34,35,37,40,51],after_c_stem:22,afterward:[8,26,35],again:[2,3,8,26,28,50],against:[20,28,39],agg:27,agglom:31,ago:1,agre:20,agreement:[13,20,26,28,41],agress:[2,10],aim:19,ala:[22,27,32,47,49,50,51],ala_cb:21,ala_h1:21,ala_h:21,alanin:[3,49],alg:[23,26,35],algorithm:[3,10,22,23,26],alia:29,align:[0,13,18,26,28,30,35],alignedcuboid:22,alignment:[13,38,40],alignmenthandl:[28,35,40],alignmentlist:[0,13,35],all:[0,1,2,3,4,7,8,10,13,14,16,18,20],all_atom:[21,22,25,49],all_atom_env:21,all_atom_po:[21,50],all_atom_scor:35,all_atom_scorer_env:35,all_atom_sidechain_env:35,all_po:[21,25,32],all_scor:31,allatom:[32,35,36],allatomclashscor:35,allatominteractionscor:[35,37],allatomoverallscor:[31,35],allatompackingscor:[35,37],allatomrelax:[25,32],alleg:20,alloc:26,allow:[0,2,3,5,8,11,16,22,26,27,28,31,34,35,37,39,41,46,51],allow_multitempl:13,allow_prepro_ci:22,almost:[4,32,35],aln:[0,28,30,31,35,40],aln_sourc:13,alon:[11,20],along:[1,8,20],alongsid:20,alot:8,alpha:[9,22,41,47],alpha_bin:41,alreadi:[1,4,8,10,16,22,25,26,28,31,35,36,39,40,41,49,50,51,52],also:[1,2,4,8,11,16,20,26,27,28,31,32,33,34,35,36,44,45,46,50,51],alter:[31,34],altern:[4,5,8,31,34,35,48,50],alwai:[0,1,8,16,29,34,35,37],amber:[21,35],ambig:51,ambigu:[0,13,51],aminoacid:[21,22,25,27,41,49,51],aminoacidatom:[21,39],aminoacidhydrogen:21,aminoacidlookup:[21,25],among:31,amount:[3,18,28,51],analog:28,analysi:[32,33,38],analyt:[31,51],anchor:[9,21],ancient:15,angl:[0,9,21,22,25,26,27,31,32,33,34,35,41,47,50,51],angle:[9,22,23,25],angle_bin:41,angle_bin_s:26,angle_force_const:25,angle_four:9,angle_on:9,angle_thre:9,angle_two:9,angstrom:[26,32],ani:[0,1,4,5,8,10,13,14,15,18,20,21,22,25,26,27,28,29,31,33,34,35,36,37,39,40,41,45,47,49,50],anneal:[10,31,34],annot:20,announc:[1,8],anoth:[4,14,22,29,35,36,44],another:32,any:20,anymor:[3,10,28],anyon:[8,16],anyth:[0,2,5,8,13,14,15,28,31,32,36,39,41],anywai:8,anywher:16,apach:[3,20],apart:[1,31,35,36,39,41],appear:20,append:[0,13,22,26,27,28,35,47],appendix:20,appli:[7,10,11,16,20,22,26,28,29,31,32,34,35,36,38,40,44,47,49,51],applic:[1,20,32,50],apply:[3,15],applyccd:31,applydee:10,applyedgedecomposit:10,applykic:31,applyonresidu:[47,49],applypairwisefunct:[40,41],applysd:25,applyselfenergythresh:[47,49],applytransform:[22,28],approach:[0,2,10,26,28,35,37,44,47,50],appropri:[10,20,27,35,37,50],approx:35,approxim:25,arbitrari:[3,21,26,44],arbitrarili:34,archiv:20,arendal:38,arg:[1,4,13,49],arg_ca:21,arg_hd3:21,arg_sorted_scor:31,arginin:49,argpars:13,args:4,argument:[0,1,2,4,11,12],argumentpars:13,argv:13,aris:20,around:[1,4,8,9,16,22,31,32,35,39,40,41,51],arrai:[0,8,37],arrang:28,artifici:26,ascend:29,ask:8,asn:[49,51],asn_c:21,asn_hb2:21,asp:[21,49,51],asp_ha:21,asp_o:21,asparagin:49,aspart:51,aspartat:49,ass:34,assembl:13,assemblepars:13,assert:20,assertequ:8,assess:[39,40],assign:[3,10,22,26,31,34,39,41,50,52],assigninternalenergi:50,assignsecstruct:35,associ:[20,26,29,45],assum:[1,4,5,8,20,25,26,32,35,37,40,41,44,50],assume:8,assur:44,astar:3,astarsolv:10,atom:[3,8,9],atom_idx:[21,25],atom_nam:[21,25],atomhandl:50,atp:28,atp_at:28,atp_idx:28,atp_list:28,atp_r:28,atp_sel:28,atp_view:28,attach:[0,4,8,13,20,21,25,28,29,31,35,36,39,40,41,42],attach_view:13,attachconstraint:40,attachenviron:[31,32,34,36,39,41,42],attachview:[30,31,35],attent:[1,16],attribut:[8,13,20,26,35,36,51],author:20,authorship:20,autodock:[38,49],autom:[2,4],automat:[1,8,10,11,14,16,26,30,31,37,50,51],automatis:8,avaibl:50,avail:[1,2,5,7,8,15,16,18,20,25,26,31,34,35,40,47,49],availab:20,availabl:3,averag:[31,40,44],avg:26,avg_sampling_per_posit:28,avoid:[0,3,6,11,13,15,26,28,32,34],awai:[16,36],awar:[0,3,8,35,50],awesom:[1,8],axi:[9,22],back:[1,16,25,34],backbon:[0,3,9,18,21,22,26,27,28,29,30,31],backbone_scor:35,backbone_scorer_env:35,backbonelist:[18,21],backboneoverallscor:[28,31,34,35],backbonerelax:[32,35],backbonescor:8,backbonescoreenv:[8,28,31,34,35],backbonescoreenvlisten:8,background:[2,36],backrub:[22,38],backward:[2,37],bad:[25,35],bare:26,base:[0,3,4,5,9,11,13,20,22,23],base_target:4,baseclass:47,basel:[8,53],bashrc:8,basi:[4,8,16,28,32,34,48],basic:[1,2,8,11,16,27,34,35,47,51],basis:20,bb_dep_lib:37,bb_list:[18,21,22,23,26,29,31,32,34,35,40],bb_list_on:28,bb_list_two:28,bb_score:31,bbdeprotamerlib:[35,36,37,48,50,51],becaus:[8,16,21,28,35,40],becom:[10,51],been:[2,3,10,16,20,24,26,31,32,35,39,41,44,51],befor:[0,1,4,7,8,13,16,22,25,26,27,29,31,32,34,35,36,37,50],begin:[1,8,21,22,28,34,40],behalf:20,behav:[1,51],behaviour:[0,13,39,40,49,50,51],behind:8,believ:53,bell:8,belong:[3,4,16,21,22,26,29,31,34,35,36,39,40,41,45,49,50],belov:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,block:3,blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],boost_libraries:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8],branchname:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_function:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48],cand:35,candid:[3,30],cannot:[0,8,13,20,25,26,27,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:37,categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_function:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37],cbpackingscor:[8,35,37],ccd:[3,30,31],ccdcloser:34,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],chanact:35,chanc:[8,10,35],chang:[1,3,4,5,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],chapter:[29,33],charact:[13,20,26],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32],check_duplicates:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:28,closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:0,cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,7,8,11,13,14,15,16,17,18,20,21,22,26,27,33,35],codetest:[4,8],coil:[24,28],collect:[11,14,21,28,40],collis:49,column:[26,28],combin:[20,25,26,27,28,31,34,35,38,39,41,44,49,51],come:[1,3,4,8,11,13,35,36,42,46,51],command:[0,1,7,8,11,12],commandlin:13,comment:[16,20],commerci:[8,20],commit:[8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib:50,compar:[3,8,22,23,26,31,32,51],comparison:[35,38,51],compat:[2,3,16,25,37],compensatori:22,compil:[1,2,3,4,8,14,16,18,20,37,54],complain:1,complaint:16,complet:[14,16,22,25,32,34,35,36,51],complex:[8,16,36,44,49,52],compli:20,complianc:20,complib_dir_container:[5,7],complib_dir_localhost:[5,7],compon:[5,7,10,15,26,33,41,50],compound:3,compoundlib:[5,50],compress:[11,26],comput:[3,8,19,20,31,33,38,39,41],concaten:21,concept:8,concern:8,condit:[8,20,27],conditions:20,conf:[2,8],confid:[26,41],config:[4,8],config_head:4,configur:[2,8,10,16,20,31,47],conflict:16,conform:[26,32,34,38,46,51],connect:[4,5,10,16,21,25,26,31],connectivi:5,conop:[5,21,22,25,27,41,49,50],conquer:8,consecut:[26,27,41],consequenti:20,conserv:[18,29],consid:[0,4,8,10,13,14,16,21,22,26,27,28,31,32,34,35,36,39,40,41,44,47,49,50,51,53],consider_all_nod:10,consider_hydrogen:49,consider_ligand:36,consist:[3,8,20,21,25,28,29,31,32,34,35,36,37,40,44,49,51],conspicu:20,constant:[3,25,32,39,41,52],constitut:20,constraint:[13,26,32,34,40],constraintfunct:40,constru:20,construct:[0,3,9,21,22,26,28,29,34,37],constructatompo:9,constructbackboneframeresidu:[47,50],constructcbetapo:9,constructcterminaloxygen:9,constructetd:10,constructframeresidu:50,constructframeresidueheurist:50,constructfrmrotamergroup:[47,50],constructfrmrotamerheurist:50,constructor:[21,25,28,29,32,34,37,40,41,47,49],constructrrmrotamergroup:50,constructrrmrotamerheurist:50,constructsidechainframeresidu:50,contact:[40,53],contactfunct:40,contain:[0,1,2,3,4,5],content:[8,12,17,20,23,26,42,47,54],contigu:[25,36,37],continu:[1,21,29,32,47],contract:20,contrast:45,contribut:4,contributor:20,contributori:20,control:[0,3,8,10,20,31,34,36,40,49,50,51,52],conveni:[1,8,18,28,31,34,35],convent:[1,49],converg:[28,31,32,34],convers:[20,37],convert:[4,5,22,25,26,27,35,37,39,41,51,52],convert_module_data:4,convertbasetyp:37,cooler:[3,30,31],coolerbas:34,cooling_factor:[10,34],coord:[26,31],coord_idx:26,coordin:[3,9,26,28,31,32,34,35,38,39,47],coordinfo:26,cope:16,copi:[2,3,4,8,16,18,20,21,22,28,29,31,34,35,40],copyright:20,copyright_cmak:20,core:[0,8,9,10,11],correct:[5,25,50],correctli:35,correspond:[0,10,16,21,22,25,26,27,28,31,37,49,50,51],corrupt:[21,40],could:[1,4,5,8,13,16,25,26,35],couldn:35,count:[14,28,29,34,35,39,41],countenclosedgap:29,countenclosedinsert:29,counter:[28,34],counterclaim:20,counterpart:[31,41,50],coupl:[1,8,16,35],cours:8,coutsia:38,coutsias2005:[32,38],coval:49,cover:[0,1,8,12,13,14,21,25,28,30,34,35],coverag:[0,3,35],cparticl:49,cpp:4,cpr:[49,51],cpu:[18,25,35],cpu_platform_support:25,crambin:[26,31,34],crash:47,createalign:[31,35],createemptyview:28,createentityfromview:[28,36,47],createfromfrmlist:[46,47],createfromrrmlist:46,createfullview:[30,31,35],createscwrl3particl:49,createscwrl4particl:49,createsequ:[26,31,35],createvinaparticl:49,creation:[25,32,49],creator:[25,32],criteria:36,criterion:[10,34],criterium:31,croak:16,cross:[20,28],crucial:8,crude:[0,35],cryst:38,cterminalclos:34,cumul:50,current:[2,4,5,8,10,14,16,21,22,25,26,31,34,35,37,40,41,42,49,50,52],custom:[8,26,34,35,36,37,48,49],customari:20,cutoff:[24,25,31,32,36,39,41],cycl:29,cyclic:[31,32,38],cyd:[49,51],cyh:[49,51],cys:[25,36,49,51],cys_hb3:21,cys_sg:21,cystein:[25,36,44,47,49],d_bin:41,dai:11,damag:20,dampen:25,danc:38,dare:4,dat:[26,37],data1:4,data2:4,data:[0,1,3,4,8,16,17,21,23,24,25],data_:37,data_gener:[3,37,48],data_to_stor:26,data_typ:26,databas:[0,9,23,24],databs:26,datatyp:26,date:[5,7,16,20],davi:38,davis2006:[22,38],dbg:8,dcmake_install_prefix:2,deactiv:10,dead:[10,38],deal:[35,36],debug:[8,10,21],decent:15,decid:[3,8,32,50],decis:27,declar:[4,8,16],decod:13,decompos:[3,10],decomposit:[10,28,46],decreas:34,dedic:[4,8,16],dee:10,deep:[22,35],def:[1,8,21,35],def_angl:21,defend:20,defin:[1,4,8,9,13,14,15,20,21,22,23,24,25],defineme:8,degre:[22,26,27],delet:[0,2,8,22,35,49],deliber:20,deliv:[1,26,34,35],delta_scor:34,demand:35,demonstr:26,denovoclos:34,densiti:[22,32,38],dep1:4,dep2:4,dep:4,depend:0,dependency1:4,dependency2:4,dependency:4,depends_on:4,depth:[26,38],deriv:[1,20,26,38,43,44],descend:35,descent:[31,32,38],describ:[0,4,7,8,10,11,17,20,21,22,26,28,29,30,32,33,37,39,41,44,47,48,49,50,51,54],descript:[0,5,13,20,34,35,51],description:16,descriptor:[26,28],descsrib:10,design:[1,3,19,20],desir:[9,18,25,26,31,32,34,35,39,40,41],despit:3,detail:[0,9,13,16,20,25,26,27,31,33,34,35,39,41,48,49,51],detect:[0,11,28,30],determin:[8,11,20,25,26,31,34,40,41],determinist:28,deuterium:[35,50],develop:[1,3,8,16],deviat:[22,33,34,51],devot:12,dict:[4,28,31,33,34,39,41],dictionari:[4,5,13,15,33,38],did:[8,26,31,35],didn:[7,28],didnt:5,differ:[1,2,4,7,8,10,15,16,20,21,26,28,29,31,35,39,41,47,49,51],differenti:49,dihedr:[9,18,22,23,25,26],dihedral_angl:22,dihedral_bin:41,dihedral_idx:51,dihedral_pair:27,dihedralconfigur:51,dill:38,dimens:27,dimension:38,dir:[4,8,18],direct:[8,20,22,24,26,41,49,50],directli:[8,10,18,26,31,35,36,40,44,49,51,53],directori:[1,2,4,5,7,8],dirti:1,dirtyccdclos:34,disabl:[1,16],disable_doctest:2,disable_documentation:2,disable_linkcheck:2,discard:26,disclaim:20,discocontain:40,disconnect:3,discret:[28,39,41],discuss:[20,26],disk:[8,25,28,39,41,51],displai:[11,13,14,20],dissimilar:28,dist:41,dist_bin:41,dist_bin_s:26,distanc:[7,9,22,26,28,31,35,36,39,40,41,43,49],distance_thresh:28,distant:40,distinct:[21,28,36,51],distinguish:3,distribut:[1,8,20,25,26,27,34,37,39,41,48,51],distribution:20,disulfid:[0,25,32,36,43],disulfid_bridg:[25,36],disulfid_score_thresh:36,disulfidscor:[36,44],dive:[16,35],diverg:8,divers:[26,28],dng:18,do_it:[39,41],doc:[2,4,8,16,20],dock:38,docker:3,dockerfil:[5,7],docstr:13,doctest:[2,8,16],document:[1,2],doe:[1,3,4,8,9,10,11,13,15,16,20,22,26,30,31,34,35,37,40,48],doesn:[8,16,29,32,34,35,51],doesnt:51,doexternalscor:[39,41],dointernalscor:[39,41],domain:28,domin:10,don:[2,10,20,31,35,50],done:[1,8,11,13,16,23,25,27,31,34,35,37],donor:[41,49,50],donorm:[39,41],dont:[0,34],dont_write_bytecod:1,dost_root:2,doubl:28,doubt:13,down:[13,22,26,28,34],download:5,dpm3_runtime_profiling_level:14,draw:[22,27,34],drawback:8,drawn:[27,34],drawphigivenpsi:27,drawpsigivenphi:27,drop:[3,8],dssp:[3,26,41],dssp_state:41,due:[0,26,31,32,35,44],dump:[28,51],dunbrack:[3,38,48],duplic:6,dure:[1,3,21,32,35,37,45,51],dynam:51,dynamicspatialorgan:3,e_cut:10,e_thresh:[10,35],e_tresh:10,each:[0,7,8,10,13,14,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,41],earli:3,earlier:2,easi:8,easier:[1,8,20],easili:[4,16,35],echo:8,edg:[10,28],edge:10,edge_idx:10,editor:1,editori:20,editxcs:28,educ:8,effect:[4,8,10,25,36,44],effici:[21,28,34,38,42],efficient:38,egg:26,eigen3_include_dir:2,eigen:[2,3],either:[0,8,13,16,20,21,22,27,29,31,32,34,35,36,37,39,40,41,45,49,51],elabor:[8,20],electron:20,electrostat:[25,32],element:[1,10,21,22,26,28,31,33,37,40,44,50],elimin:[10,38],els:[8,16,36,37],emerg:1,empir:[43,44],emploi:16,empti:[8,11,13,22,26,28,31,35,49],enabl:[1,2,3,11,13,15,25,26],enable_mm:2,enable_sse:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_translate:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,52],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,31,35,37],ensure:18,ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,28,33,35,42,47],entityhandl:[13,21,22,26,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,31,32,33,36,41,50,51],entry:47,entrypoint:5,enumer:[8,10,21,25,26,28,31,35,40,47,49,50,51],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39],epsilon:[10,25,36,52],equal:[28,34,39,41,44,50],equidist:51,equip:5,equival:[28,35,39,41],error:[0,11,13,14,26,32,35,37],especi:28,estim:[10,28,33,34,38,41,44,49,50,51],estimat:51,etc:[1,3,8,16,22,26,31,40],evalu:[4,8,32,35,40,41,44,46,49,51],evaluat:[39,40,41],evaluategromacsposrul:9,even:[2,8,10,20,22,25,29,35],event:[20,28],eventu:13,ever:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,51,52],everyth:[1,2,3,7,8],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,49],exampl:[0,1,2,3,8,11,13,16,17,18,20,21,23,25,26,27,28,30],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35],exclud:[8,20,26],exclus:[1,8,20,25],execut:0,exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,31,32,33,34,35,37,39,40,41,48,49,51],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:34,expect:[1,3,7,21,25,26,35,36,40,44,50,52],expens:26,experiment:35,explain:[1,8],explan:8,explicit:2,explicitli:20,explor:5,explore:38,exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28,29,31,35,41,46],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,29,35],extension:[0,13],extension_penalti:29,extent:26,extern:[3,4,5,8,34],external:3,external_script:[3,8],extra:[2,3,8,16,22,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:[22,28],f_i:26,f_idx:40,f_vinaparticl:49,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,35,51],fall:32,fallback:51,fals:[1,8,10,11,13,22,25,26,29,31,34,35,36,44,47,49,50],fantast:8,far:[31,35],fast:[0,9,18,19,21,25,26,27,37,39,40,41,51],fasta:[0,13,30,35],faster:[10,25,26,32,33,40],fastest:[32,35],favor:33,favourit:1,fed:[4,16],fedora:8,fee:20,feed:[4,21,31],feel:[8,16],fellow:8,fetch:[13,16,18,28],few:[2,8,16,25,37,42],ff_aa:25,ff_aa_on:25,ff_aa_two:25,ff_ala:25,ff_arg:25,ff_asn:25,ff_asp:25,ff_cys2:25,ff_cys:25,ff_gln:25,ff_glu:25,ff_gly:25,ff_hisd:25,ff_hise:25,ff_ile:25,ff_leu:25,ff_lookup:[25,32,35],ff_lookup_charmm:37,ff_lys:25,ff_met:25,ff_phe:25,ff_pro:25,ff_ser:25,ff_thr:25,ff_trp:25,ff_tyr:25,ff_val:25,ff_xxx:25,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,8],filecheck:16,fileexist:11,fileextens:11,filegzip:11,filenam:[0,8,11,13,25,26,27,28,37,39,41,48,51],filename:[0,11],filenotfound:33,fill:[4,8,13,16,23,26,29,30,31,33,35],fillfromdatabas:[31,35],fillfrommontecarlosampl:[31,35],fillloopsbydatabas:35,fillloopsbymontecarlo:35,filo:40,filtercandid:33,filtercandidateswithsc:33,final_model:[30,35],find:[3,4,7,8,10,16,21,23],findatom:28,findchain:42,findeigen3:20,findmotif:28,findwithin:[8,28],fine:8,finish:52,fire:1,first:[0,1,3,8,10,13,16,18,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,22,26,30,31],fitness:20,fix:[3,8,11,16,25,32,36,37,39,41],fix_cterm:32,fix_nterm:32,fix_surrounding_hydrogen:25,flag1:4,flag2:4,flag:[0,2,4,8,10,11,13,22,26,28,35,36,49,50],flanking_rot_angle_on:22,flanking_rot_angle_two:22,fletch:[26,47],fletcher:35,flexibl:[0,19,36,44,47,49,50,52],flip:51,flood:26,fluorin:49,flush:[1,16],fold:38,folder:[2,4,8,16,18,37],follow:[0,1,2,4,5,7,8,10,11,16,18,20,22,23,25,26,28,29,30,31,35,36,37,39,41,47,49,50,51],fontsiz:27,forbidden:8,forc:[25,32,35],force_const:[25,32],forcefield:23,forcefieldaminoacid:25,forcefieldbondinfo:25,forcefieldconnect:25,forcefieldharmonicangleinfo:25,forcefieldharmonicimproperinfo:25,forcefieldljpairinfo:25,forcefieldlookup:[25,32,35,37],forcefieldperiodicdihedralinfo:25,forcefieldureybradleyangleinfo:25,forg:16,forget:[1,8],form:[14,20,24,25,26,30,35,40,51],formal:[31,32,49,51],format:[0,5,13,20,26,48],formula:33,forward:16,found:[1,3,4,8,11,13,16,19,21,23,26,28,31,32,33,34,35,36,44,46,49,51],foundat:1,four:[9,34],fraction:[26,28,32,34],frag_db:[23,26,31,37],frag_length:[23,26,28],frag_map:26,frag_po:[23,26,28],frag_residu:[23,26],frag_seq:[23,26],frag_siz:26,fragdb:[23,24,26,31,35,37],fragger:[13,23,26,28,34,35],fragger_handl:[13,35],fragger_map:26,fraggerhandl:[0,13,26,28,35],fraggermap:[26,28],fragment:[0,3,9,13,22,23,24],fragment_db:35,fragment_handl:28,fragment_info:26,fragment_length:[26,28],fragmentinfo:[26,31],fragments_per_posit:28,fragmentsampl:34,frame:[3,16,35,36],frame_energi:49,frame_residu:[45,47],frameresidu:[45,49,50],framework:[8,19,38],free:[0,8,20,35,49,51],frequenc:[26,34],frm:36,frmrotam:[44,49,50,52],frmrotamergroup:[44,46,49,50],from:[0,1,2,3,4,5,7,8,9,10,11,13,16,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42],fromhhm:26,fromhoriz:26,fromresidu:51,front:[1,11,16],fstream:37,fudg:25,fulfil:[26,51],full:[0,1,3,8,10,21,25,26,28,29,30,31,34,35,36,47,49,50],full_queri:28,full_seq:[29,31],fullgapextend:[29,35],fulli:[8,16,21,22,26,29,30,36],function_typ:40,functions_specific_to_your_act:8,fundament:37,funni:[2,8],further:[10,28,29,35,36,37,50],furthermor:[37,50],futur:[3,25,26],gamma:[40,41,44],gamma_bin:41,gap:[0,3,9,18,24,25],gapextend:[29,35],gapfre:26,gapless:[0,13],gather:[4,12,16,26,28,47,49,51],gauc:51,gauch:51,gauche_minus:51,gauche_plus:51,gaussian1:49,gaussian2:49,gciiipgatcpgdyan:[31,35],gener:[0,1,2,3,5,8,10,13,14,16,18,20,23,24],generatedenovotrajectori:28,generatestructureprofil:26,geom:[21,22,25,26,28,32,35,44,49],geometr:[3,9,23],geoom:43,get:[0,1,2,8,16],getaa:[21,22,25],getaaa:21,getaah:21,getactivesubrotam:49,getallatomposit:[21,32,36],getallatomscoringkei:31,getallatomweight:31,getanchoratomindex:21,getangl:47,getangularbins:26,getatomcount:8,getatomnam:21,getatomnameamb:21,getatomnamecharmm:21,getaveragescor:31,getbackbonelist:[23,26],getbackbonescoringkei:31,getbackboneweight:31,getbins:27,getbinsperdimens:27,getbound:22,getc:22,getca:22,getcb:22,getchain:29,getchainindex:29,getchainnam:29,getchains:8,getcharg:25,getclust:31,getclusteredcandid:31,getcollisiondist:49,getconfid:26,getcoordidx:26,getcoordinfo:26,getcpuplatformsupport:25,getcreationd:5,getdefault:[25,32,35],getdefaultlib:5,getdihedralangl:26,getdihedralconfigur:51,getdistbins:26,getdisulfidbridg:25,getdisulfidconnect:25,getdsspstat:26,getelement:21,getenviron:21,getenvsetdata:8,getepsilon:25,getfirstindex:21,getforcefieldaminoacid:25,getfragmentinfo:[26,31],getframeenergi:49,getfudgelj:25,getfudgeqq:25,geth1index:21,geth2index:21,geth3index:21,getheavyindex:25,gethistogramindex:[22,27],gethistogramindic:27,gethnindex:21,gethydrogenindex:[21,25],getidentifi:28,getindex:[21,25],getinternalconnect:25,getinternalenergi:49,getinternalenergyprefactor:49,getlargestclust:31,getlastindex:21,getlength:29,getlist:28,getlooplength:25,getloopstartindic:25,getmass:25,getmaxnumatom:21,getmaxnumhydrogen:21,getn:[22,28],getnam:[47,49],getnonbondedcutoff:32,getnum:31,getnumatom:[21,25],getnumb:31,getnumcandid:31,getnumchain:8,getnumcoord:26,getnumfrag:26,getnumhydrogen:21,getnumloopresidu:25,getnumresidu:[8,21,25],getnumstempair:26,getnumsubrotam:49,geto:22,getolc:[21,22],getomegators:[21,22],getoxtindex:25,getpeptideboundconnect:25,getphiprobabilitygivenpsi:27,getphitors:[21,22,47],getpo:[21,28,49],getposit:28,getpotentialenergi:25,getpredict:26,getprob:[27,49],getpsiprobabilitygivenphi:27,getpsitors:[21,22,47],getr:33,getresidu:28,getresiduedepth:26,getringpunch:33,getrotamericconfigur:51,getscor:[26,34],getscoringfunct:49,getselfenergi:49,getseqr:[21,40],getsequ:[21,22,26,31],getsequenceprofil:26,getsequenceprofilescoreskei:31,getsigma:25,getsimul:25,getsolventaccessibilitit:26,getstemrmsdskei:31,getstructureprofil:26,getstructureprofilescoreskei:31,getsubdb:26,getsubrotamerdefinit:49,getsystemcr:32,gettemperatur:[34,49],gettransform:22,getversionnumb:37,getweight:[28,31],ggg:35,gggaggg:35,gggggggggggggggggggg:35,git:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15],gitignor:8,gitlab:[5,53],give:[4,8,16,20,23,28,31,34,35,49],given:[0,1,3,4,8,9,10,11,13,14,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51],glass:38,gln:[49,51],gln_ne2:21,global:[15,26,31,35,37],glu:[21,49,51],glu_oe1:21,glutam:49,glutamin:49,gly:[35,36,47,49,50],gly_n:21,glycin:[3,22,26,32,36,49],goal:[1,10,28,30],goe:[2,8,14,16,35,51],goldfarb:35,goldstein1994:[10,38],goldstein:[10,38],good:[4,8,18,25,26,35],goodwil:20,got:2,govern:20,grain:8,grant:20,graph:3,graph_initial_epsilon:36,graph_intial_epsilon:36,graph_max_complex:36,graphminim:[10,46],greatest:5,grep:2,grid:26,gromac:9,grossli:20,group:[4,14,24,26,27,28,41,44,45,46,47],group_definit:[27,41],group_idx:41,guarante:[26,28,31,34,36,37],gui:[8,27],guid:32,guidelin:[8,37],gzip:[0,5,11,13],haa:38,hand:[0,2,4,13],handl:[3,8,9,13],handler:28,happen:[1,8,25,28,29,34,35,49],hard:[43,49],hardwar:18,harmless:20,harmon:[25,32],harmonic_angl:25,harmonic_bond:25,harmonic_improp:25,hasattr:35,hasdata:26,hasfraglength:26,hasfragmentinfo:31,hash:[3,26,28],hash_thresh:28,hash_tresh:28,hasringpunch:33,have:0,hbond:[28,35,41,49,50],hbond_scor:37,hbondscor:[35,37],headach:8,header1:4,header2:4,header3:4,header4:4,header:[0,2,4,16,17],header_output_dir:4,headers:4,headlin:8,heavi:[21,25,36,39,49,50],heavili:[26,47],helic:[22,24,25,28,35,41],helix:[18,22,34,47],hell:28,hello:37,hello_world:8,hellyeah:18,help:[0,1,2,4,7,8,13,16,18,25,41],helpactiontest:1,helper:4,hen:26,henc:[8,14,21,26,37],here:[0,1,2,4,8,11,13,14,16,18,19,21,22,25,26,27,28,30,31,32,34,35,37,39,41,44,48,51],herebi:20,herein:20,het:35,heurist:[3,35,50],heuristicprocessor:21,hg_po:49,hgfhvhefgdntngcmssgphfnpygkehgapvdenrhlg:0,hhblit:[0,13],hhm:[0,13,26,31],hhsearch:26,hide:[8,16],hierarch:[31,40],hierarchi:15,high:[3,8,16,28,30,35],high_resolut:22,higher:[31,40,41],highest:15,highli:[2,8],hint:13,his:[21,25,49,51],histidin:[25,49],histogram:[27,34],histori:16,hit:[1,10,16,27,32],hmm:38,hold:[20,28],home:[4,5],homo:[0,13],homolog:[0,12,18,19,35,38],homologu:26,honor:35,honour:35,hook:8,horiz:26,horribl:50,host:[4,7,8,16],hotfix:16,how:1,howev:[5,20,26],hparticl:49,hpp:37,hsd:[49,51],hse:[49,51],html:[2,8,16],http:[8,18,19,20,53],hybrid:51,hydrogen:[3,21,22,25,35,38,41,49,50],hydrophob:49,hyphen:1,i_loop:[25,36],i_vinaparticl:49,id_:37,idea:[1,8,21,23,25,26,35,40,49,52],ideal:[22,32,52],ident:[3,26,27,28,41,51],identif:20,identifi:[0,3,13,14,20,26,28,31,35,36,39,41,49,50,51],identiti:51,idx:[10,21,22,25,26,28,32,40,49],idx_ca_res_37:21,idxhandler:8,iff:[26,29,33],ifstream:37,ignor:[0,25,28,32,35],iii:20,ile:[27,49],illustr:26,imag:[5,7],image_name:5,imagehandl:22,imagin:8,imaginari:1,img:[7,22],immedi:[1,8,15,16],impact:[0,25,26],implement:[3,16,19,26,28,29,32,34,35,37,43,44,46,47,49,50,53],impli:20,implicit:2,important:[16,35,50],improp:25,improv:[3,20,25,35,38,44],improve:[3,38],improvement:38,in_dir:4,in_fil:8,in_path:4,in_stream:37,in_stream_:37,inabl:20,inaccur:25,inaccurate_pot_energi:25,inact:52,inactive_internal_energi:52,incident:20,incl:[25,26,35],includ:[2,3,7,8,11,16,18,20,21,25,26,28,29,31,33,35,37,39,41,47],include_atoms:28,include_ligand:35,inclus:[20,35],incompat:[31,32],incomplet:[35,48],inconsist:[10,13,21,22,25,26,29,31,32,36,40,49],inconveni:16,incorpor:20,increas:[0,10,28,31,32,35,50],increment:28,incur:20,indemn:20,indemnifi:20,independ:[0,3,25,36,48],index:[8,10,21,22,25,26,27,28,29,31,32,33,34,35,39,40,41,45,49,50,51],index_four:25,index_on:25,index_thre:25,index_two:25,indic:[8,10,11,20,21,22,25,26,27,28,29,31,32,35,36,40,44,47,49],indicat:[11,13],indice:[26,36,40],indirect:20,individu:[7,20,39,41],inf:[10,32,35],infin:32,infinit:32,influenc:[13,28,40,50],info:[26,31,35,40],inform:[0,5,7,8,13,16,20,22,23,26,28,29,31,34,35,38,40,41,42,53],infring:20,infringement:20,inherit:[1,39,40,41,46],init:16,init_bb_list:34,init_frag:34,initi:[3,10,21,22,26,28,31,32,34,35,36,39,40,41,46,49,50,51],initial:[3,31,34,36],initial_bb:31,initial_epsilon:[10,52],initialis:1,inlin:37,inner:14,input:[0,1,3,13,16,18,25,26,27,28,32,34,35,36,39,40,41,44,48,52],insert:[21,22,29,31,34,35,52],insertinto:[21,22,31],insertloop:[29,35],insertloopcleargap:[29,31,35],insid:[1,4],inside:1,insight:16,instal:[2,8,16,37],instanc:[3,8,13,24,25,37,53],instead:[0,1,2,3,4,8,11,26,28,29,31,34,35,50],institut:20,instruct:2,int16_t:37,int32_t:37,int_32_t:37,integ:[8,13,21,40],integr:[4,8,38],intend:[1,8,34,49],intent:26,intention:20,interact:[3,8,25,32,39,40,41,43,44,45,49],intercept:[39,41],interest:[1,10,25,26,34,37,49,51],interfac:[0,3,4,8,20,50],intermedi:8,intern:[0,1,3,4,5,8,16,21,24,25,26,27,28,31,32,34,35,36,37,40,41,46,49,50,52],internal:[21,25,26,39,40,41,49,52],internal_e_prefac:50,internal_e_prefactor:49,internal_energi:49,internat:38,internet:8,interpl:51,interpol:[40,51],interpret:[8,11],intervent:8,intrins:2,introduc:[1,3,4,8,16,32,35],invalid:[8,21,25,26,29,32,35,36,39,40,41,45,49,51],invalid_vinaparticl:49,invok:[2,4,8,15,16],involv:[16,30,44,49],iodin:49,iostream:37,ipython:7,irrevoc:20,is_c_ter:[25,36],is_cter:25,is_hbond_acceptor:50,is_hbond_donor:50,is_major:35,is_n_ter:[25,36],is_nter:25,isallatomscoringsetup:[31,35],isallset:21,isanyset:21,isbackbonescoringsetup:35,isctermin:29,isempty:31,isenabl:14,isntermin:29,isoleucin:49,isset:21,issimilar:51,issourc:37,issu:[3,8,12,16,20,32,35,37],istermin:29,isvalid:47,item:[1,8,16,21,22,25,26,35,40],iter:[10,27,28,31,32,34,35],iterat:[26,28,32,49],itself:[3,4,8,16,26,34,36,37,39,41],januari:20,job:[8,26,34,35],johner:38,join:[8,21,23,26,31,32,34,36],jone:[38,49],jones1999:[26,38],journal:38,json:[0,13],jupyt:7,just:[1,2,8,13,15,16,23,25,26,28,29,31,35,50],kabsch1983:[26,38],kabsch:38,keep:[0,1,2,4,5,8,13,16,28,30],keep_non_converg:31,keep_sidechain:[8,36],kei:[0,13,26,28,31,34,35,39,40,41],kept:[8,16,25,31,32,36,45,49],kernel:38,keyword:27,kic:[30,31],kiccloser:34,kick:13,kill_electrostat:25,kind:[1,8,20],kinemat:32,know:[2,51],knowledg:51,known:[4,11,21,40,50],krivov2009:[10,38,47,49],krivov:38,kwarg:1,l_e:49,lab:48,label:[16,25],lack:35,languag:[4,20],larg:[5,27,32,35],larger:[10,14,22,26,28,35,50],largest:[28,31,44],last:[1,2,3,4,21,22,25,29,31,32,34,35,40,41,48],last_psi:22,later:[1,8,10,21,28,47],latest:[2,5,8],latter:[0,5,16,35],launcher:[4,8],law:20,lawsuit:20,layer:44,layout:[26,37],lbfgs:35,lddt:7,leach1998:[10,38],leach:38,lead:[0,8,9,11,22,25,31,32,36,39,41,48],learn:28,least:[0,2,4,8,10,16,20,22,25,26,35,39,41,44],leav:1,left:[11,32],legal:[8,20],lemon:38,len:[22,23,25,26,28,31,35,36,41,47],length:[0,9,10,21,24,25,26,27,28,29,31,32,34,35,36,37,39,40,44],length_dep_weight:35,length_depend:31,lennard:49,less:[0,10,16,22,25,26,27,31,35,39,41,50,51],let:[1,8,22,26,28,31,47],letter:[3,5,21,22,26,27,34,49],leu:49,leu_h:21,leucin:49,level:[2,3,8,14,15,16,30,35],lexicograph:35,liabil:20,liabl:20,lib64:8,lib:[5,7,37],libexec:[4,8],libpromod3_name:4,librari:[0,3,4],library1:4,library2:4,licenc:48,licens:3,license:20,licensor:20,life:16,ligand:[3,35,36,49,50],like:[0,1,4,8,16,35,37,48],limit:[0,3,20,26,32,35],line:[0,1,7,8,9,12],linear:[26,28,31,34,39,40,41],linear_weight:[31,34,39,41],linearcombin:31,linearscor:34,link:[0,2,4,8,16,20,21,25,26,28,34,36,39,40,41,42],link_cmd:4,linkcheck:[2,8,16],linker:[4,35],linker_length:35,list:[0,1,2,3,4,7,8,9,10,11,13,20,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,45,46,47,49,50,51,52],listen:8,literalinclud:8,litig:20,littl:[4,8,16,37],live:[4,8],lj_pair:25,load:[1,8,13,15,21,23],loadalign:[30,35],loadallatominteractionscor:39,loadallatompackingscor:39,loadamberforcefield:35,loadbb:26,loadbbdeplib:[0,36,47,48],loadcach:28,loadcbetascor:[31,34,41,42],loadcbpackingscor:41,loadcharmm:25,loadcharmmforcefield:35,loaddefaultallatomoverallscor:39,loaddefaultbackboneoverallscor:41,loadentiti:[0,13],loadfragdb:[23,24,31,35],loadhbondscor:41,loadlib:[0,36,48],loadpdb:[8,21,23,25,26,28,30,31,32,34,35,36,42,47],loadport:[25,26,27,37,39,41,51],loadreducedscor:41,loadsequenceprofil:[13,26,31],loadssagreementscor:41,loadstructuredb:[23,24,26,31,35],loadtorsionsampl:[22,24,27,34],loadtorsionsamplercoil:[24,31,35],loadtorsionsamplerextend:24,loadtorsionsamplerhel:24,loadtorsionscor:41,local:[2,5,7,25,26,27,39,41,51],localhost:7,locat:[2,3,4,5,10,22,24,26,28,29,37,39,41,49],log:[11,16,33,35,49,50],logic:0,loginfo:33,lone:49,lone_pair:49,longest:26,look:[5,8,11,16,22,26,36,40,50],lookup:[9,21,23],looooooong:10,loop:[0,3,8,13,18,21],loop_candid:31,loop_length:[25,26,31,36],loop_main:8,loop_po:25,loop_seq:31,loop_start_indic:[25,36],loopcandid:[28,30],loss:[16,20],lossi:26,lost:[1,16],lot:[1,8,13,16],low:[1,8,10,50],lower:[31,34,35,39,41],lowest:[31,34,49],lowest_energy_conform:34,lys:49,lysin:49,m_idx:28,m_vinaparticl:[49,50],machin:[25,26,27,37,39,41,51],macro:[4,8],macromolecul:38,made:[4,5,20,51],magic:[8,37],mai:[0,1,2,4,8,11,13,16,20,21,25,29,32,35],mail:20,main:[8,35,37,51],mainli:[21,34,49],maintain:[8,16],maintin:34,major:[16,35],makefil:[2,8],makestat:51,malfunct:20,malici:16,man:[2,8],manag:[4,8,20,42],mani:[11,13,26,28,32,33,35,50],manipul:22,manner:[8,10,34],manual:[1,2,5,8,9,16,26,31,34,35,37,49],map:[0,13,21,22,26,28,33,36],mariani:38,mark:[4,20,50],mass:25,massiv:28,master:[8,16],mat3:9,mat4:[9,22,28,35],mat:28,match:[0,4,13,22,25,26,27,28,31,32,34,35,40,41],materi:[1,8],math:33,mathemat:[31,32],matplotlib:27,matric:38,matrix:[9,26,28],matter:[4,7,28,53],max:[9,10,21,29,33,35,36,41,51,52],max_alpha:41,max_beta:41,max_complex:[10,52],max_count:[39,41],max_d:41,max_dev:34,max_dist:[31,40],max_extens:35,max_gamma:41,max_iter:[28,31,35],max_iter_lbfg:35,max_iter_sd:35,max_length:29,max_loops_to_search:35,max_n:10,max_num_all_atom:35,max_p:50,max_prob:49,max_res_extens:35,max_step:32,max_to_show:14,max_triangle_edge_length:28,max_visited_nod:10,maxfraglength:26,maxim:[10,26,28,31,32,34,35,38,40,41],maximum:[10,26,31,32,34,49,50],mc_closer:34,mc_cooler:34,mc_num_loop:35,mc_sampler:34,mc_scorer:34,mc_step:[10,35],mcsolv:10,mean:[4,8,13,16,20,21,25,28,32,35,36],meaning:[26,31],meant:[18,21,26,33,35,50],measur:28,mechan:[18,20,31,32,34,35,40],meddl:[7,35],media:20,medium:20,meet:20,member:[8,13,31,35],memori:[10,26,35,37],mention:[1,2],merchantability:20,mere:20,merg:[16,25,28,29,31,35,36,40,49],merge_dist:35,mergegap:29,mergegapsbydist:35,mergemhandl:35,mess:[8,16,40],messi:16,met:49,metal:49,methionin:[35,49],method:[0,1,10,13,21,25,26,27,32,35,36,37,50],metric:40,metropoli:[10,31,34],mhandl:[29,30,31,35],middl:16,might:[10,25,26,28,31,32,34,40,50,52],min:[31,41],min_alpha:41,min_beta:41,min_candid:31,min_d:41,min_dist:40,min_gamma:41,min_loops_requir:35,min_scor:31,min_triangle_edge_length:28,mincadist:22,mind:[1,8],minim:3,minimizemodelenergi:35,minimum:[22,26,28,44],minor:[3,25,35],mirror:37,miser:14,mismatch:[21,35,40],miss:[0,11,13,25,35],mix:[0,4],mkdir:[2,8],mm_sy:[25,32],mm_sys_output:25,mm_system_cr:32,mmcif:[5,11],mmsystemcr:[25,32],mod:8,mode:[1,51],model_termini:35,modelling_issu:35,modellinghandl:[3,29,31,35],modellingissu:35,modeltermini:35,modif:[20,35],modifi:[8,16,20,22,31,35],modified_crambin:31,modul:[1,3],modular:19,module:[1,4,8,37],module_data:4,mol:[8,9,18,21,22,23],molck:7,molecular:[7,18,32,35],molprob:30,molprobity_bin:33,molprobity_executable:33,moment:8,monitor:1,monolith:8,mont:[0,3,10,28,31,34,35,46],montecarlo:3,mood:8,more:[1,2,4,7,8,10,13,14,16,20,28,35,44,49,53],most:[0,3,4,5,8,22,25,26,27,28,31,32,35,39,41,48,50],mostli:[4,16],motif:3,motiffind:28,motifmatch:28,motifqueri:28,motion:[22,38],mount:[5,7],movabl:25,move:[2,3,8,16,25,31,32,34,35,37],movement:28,mpscore:33,msg:11,msgerrorandexit:11,msm:3,msse4:2,much:[10,26,35],multi:18,multipl:[0,2,3,4,8,13,14,18,25,28,31,35,36,39,41],multipli:[10,34],multitempl:13,multithread:38,must:0,mutlipl:13,my_db_on:26,my_db_two:26,my_script:7,myclass:37,myclassptr:37,mytrg:0,n_a_vinaparticl:49,n_ad_vinaparticl:49,n_coord:9,n_d_vinaparticl:49,n_num:29,n_po:[9,22,41],n_stem:[9,23,26,29,31,32,34],n_stem_phi:34,n_ter:[32,50],n_vinaparticl:49,naivesolv:10,name:[0,1,3,4,5,7,8,11,13,14,20,21,25,26,27,29,31,33,35,44,48,49,51],name_pymod:4,namespac:[13,37],nan:[32,35,51],nativ:37,necessari:[8,22,34,40],necessarili:[20,52],need:[1,2,3,4,5,8,11,13,15,16,22,25,26,27,28,31,32,35,36,37,39,40,41,47,50],need_config_header:4,neg:[1,10,25,32,40],negelect:[0,35],neglect:[28,32,45,49,50],neglect_size_on:31,neglig:20,neighbor:[8,21,35],neighbour:[28,35,51],network:[22,44],never:[13,16,26,31,35,36,37,39,41],nevertheless:8,new_default:25,new_env_po:21,new_po:21,new_res_nam:49,new_siz:22,newli:[5,21,34],next:[1,8,16,22,27,28,29,37],next_aa:34,nglview:7,nice:8,nitrogen:[9,22,32,43,49,50],nobodi:1,node:10,node_idx:10,node_idx_on:10,node_idx_two:10,non:[0,4,10,13,16,20,24,25,27,28,29,31,32,35,37,47,48,50],non_rotameric:51,nonbonded_cutoff:[25,32],none:[13,26,28,33,34,35,36,49],nonredund:26,nonzero:51,norm:[28,41],normal:[20,39,41],normalis:40,notabl:26,note:[0,2,8,13,14,21,22,25,26,28,31,32,34,35,36,37,39,40,41,47,49,50],notebook:7,noth:[0,4,8,13,14,20,28,34,49],notic:[1,4,16,20],notice:20,notwithstand:20,novel:[19,38],novo:3,now:[3,8,14,16,18,22,26],nparticl:49,nterminalclos:34,null_model:31,num:[23,28,31,32,36],num_frag:[26,35],num_gap_extens:29,num_loop:31,num_residu:[21,25,34,36,39,40,41],num_residues_list:36,num_trajectori:28,number:[0,1,8,9,10,13,14,18,21,22,24,25,26,27,28,29,31,32,34,35,36,37,39,40,41,42,44,45,49,51],numer:35,numpi:[27,34],nussinov1991:[28,38],nussinov:[28,38],o_a_vinaparticl:[49,50],o_ad_vinaparticl:49,o_d_vinaparticl:49,o_po:22,o_vinaparticl:49,object:[0,3,8,13,14,20,21,22,23],oblig:20,observ:[10,26,28,32,50,52],obtain:[10,18,20,23,28,35],obviou:16,occupi:[45,50],occur:[21,28,35,40,41],ocparticl:49,odd:26,off:[1,8,14,35],offend:33,offer:[6,20,24,30,49,51],offset:[0,3,13,26,31,35],ofstream:37,often:[8,11,13,32],og_po:49,olc:22,old:[33,35],oligom:[0,13,30],oligomer:3,olson:38,omega:[21,22],onc:[1,3,16,25,28,31,34,52],once:[8,16,28,31,32,46,51],one:[16,21,22,26,28,35,40,44,49,52],one_letter_cod:[21,23,26,31,32,34,36],onli:[0,1,2,4,8,10,11,13,14,15,16,20,21,22,25,26,28,29,31,33,34,35,36,37,39,41,44,47,48,49,50],only:[25,26,28,29,35,36,50],only_longest_stretch:26,onto:[1,22,26,28],oparticl:49,open:[13,25,26,27,37,39,41,51,53],openmm:[2,18,25,32],openstructur:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],oper:[3,10,16,18,21,26,40],opt:[11,13,16],optim:[0,2,3,10,13,25,26,27,31,35,38,39,41,44,48,51,52],optimis:8,optimiz:47,optimize:2,optimize_subrotam:[36,44],option:[0,2,3,5,13,26,31,32,35,51],optional:[26,35],order:[0,5,13,21,25,26,29,31,35,37,40],org:20,organ:[8,26,51],orient:[9,32,41],orig_indic:[31,33],origin:[5,7,9,13,16,20,22,26,31,34,35,40,52],orthogon:28,ost:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24],ost_double_precision:2,ost_ent:33,ost_libraries:4,ost_root:[2,8],other:[0,1,2,3,4,8,10,14,16,20,21,22,31,32,35,36,39,41,42],other_index:22,other_particl:49,other_res_index:21,otherwis:[1,4,8,10,14,16,20,21,22,25,26,28,29,31,32,34,39,40,41,49,51],our:[4,5,8,16,26,28,31],out:[0,1,2,4,8,14,16,20,21,25,26,27,28,29,31,34,47,51],out_path:4,out_po:25,out_stream:37,out_stream_:37,outdat:[5,7],outer:[14,26],outlier:33,output:0,output_dir:4,outsid:[8,40],outstand:20,over:[2,4,13,16,26,28,32,34,35,49],overal:[10,34,40,46],overhead:25,overlap:[25,34,35,36],overli:16,overload:37,overrid:[2,5,25,50],overridden:4,overriden:5,overview:[8,16],overwrit:31,overwritten:25,own:[1,3,4],owner:20,ownership:20,oxt:[9,21,25],oxygen:[22,35,43,49,50],p_vinaparticl:49,pack:21,packag:[4,8,16],pad:[22,37],page:[2,8,20],pai:1,pair:[9,25,26,27,28,32,34,36,37,39,40,41,44,49,51],pairwis:[3,8,10,22,28,31,35,39],pairwise_energi:10,pairwisefunct:[40,41],pairwisefunctiontyp:40,pairwisescor:[8,35],paper:[43,44,47,49],paragraph:[1,8],parallel:26,paramet:[1,4,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,43,44,45,46,48,49,50,51,52],parameter_index:26,parametr:[3,32,35,36,49,50],parent:35,pars:[0,11,12],parser:12,part:[0,1,8,16,18,20,21,26,34,35,40,44],partial:29,particip:[36,44],particl:[3,25,26,32,41,43,44,45,47],particle_typ:49,particular:[8,10,20,26,31,32,34,49,51],partner:[39,40,41],pass:[13,16,21,25,26,28,29,32,34,44,45,49,50],past:[8,16,22,29],patent:20,path:[1,2,4,5,7,8,11,16,18,25,26,27,33,39,41,51],path_to_chemlib:15,path_to_dockerfile_dir:5,path_to_promod3_checkout:6,pattern:38,paus:14,pdb:[0,5,8,11,13,18,21,22,23,24,25,26,28,30,31,32,33,34,35,36,42,47],penal:[29,35],penalti:[29,35],penultim:3,peopl:16,pep:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],peptid:[3,21,23,25,26,28,35,36,47],peptide_sel:28,per:[4,8,10,12,16,21,27,31,34,35,39,40,41,44],percent:20,percentag:33,perfect:8,perfectli:8,perform:[0,10,16,18,19,20,25,28,31,32,33,34,35,37,40,44],period:25,periodic_dihedr:25,periodic_improp:25,permiss:[8,20],permut:10,perpetu:20,pertain:20,phase:25,phe:[49,51],phenix:33,phenylalanin:49,phi:[21,22,26,27,32,34,41,47,50,51],phi_bin:[41,51],phi_handl:47,philippsen:38,phipsisampl:34,phosphoru:49,phosphoserin:35,phrase:8,pick:[31,34],pictur:8,piec:[8,28],pipelin:[0,3,14],pivot:[31,32,34],pivot_on:[31,32],pivot_thre:[31,32],pivot_two:[31,32],place:[1,2,4,8,11,13,16,20,26],plain:[0,13],plan:16,plane:33,platform:[18,25],playground:7,pleas:[2,8,16,28,31,32,35,53],plot:27,plt:27,plu:[8,13,15,26,44,49],pluribu:28,pm3_csc:16,pm3_openmm_cpu_threads:[18,25,35],pm3_runtime_profiling_level:14,pm3argpars:[0,11,12],pm3argumentpars:[0,11,13],pm_action:[1,4,8],pm_action_init:8,pm_bin:1,pnas:38,png:27,pocket:28,pocket_view:28,point:[2,8,13,15,21,26,28,34,35,40,49,51],pointer:[2,8,37],polar:[49,50],polar_direct:49,polici:8,pop:[16,31,34,40],popul:[2,16],port_str_db:26,portabl:[4,17,25,26,27],portable_binary_seri:37,portable_file:4,portablebinarydatasink:37,portablebinarydatasourc:37,pos_end:28,pos_on:28,pos_start:28,pos_two:28,posit:[3,8,9],possibl:[0,3,8,10,13,16,20,22,25,26,27,28,29,31,32,34,35,36,37,39,40,41,44,46,49,51],post:13,postprocess:36,pot:25,pot_:32,potenti:[10,23,25,26,28,31,32,35,36,37,38,41,49],power:[7,20],pqhpg:0,practic:[4,8,25,26],pre:[8,16],pre_commit:[8,16],preceed:36,precis:[2,31,35],precomput:23,pred:40,predefin:[4,18,25,35,39,41],predict:[13,26,28,35,38,40,41],prefactor:49,prefer:[2,4,20,26,51,52],prefilt:35,prefix:[1,4,8,11],prepar:[8,20,35],present:[22,28,32,36,49,50,51],prev_aa:34,prevent:[1,8],previous:[25,26,31,36,40],primary_rot_angl:22,principl:[3,34,40],print:[1,2,5,20,22,23,25,26,31,32,33,35,42],printstatist:26,printsummari:14,prior:35,privat:[1,37],pro:[21,27,49,51],probabilist:[26,50],probability_cutoff:50,probabl:[4,8,10,13,16,26,27,28,31,32,34,49,50,51],problem:[3,7,10,13,16,26,28,31,32,34,35,40,42,44,46,48,52],problemat:[3,5,28],proce:42,procedur:[10,28,34,36,50],process:[1,3,13,16,21,25,28,32,34,35,37,40,45,49,51],processor:5,produc:[0,1,2,4,8,10,26,29,33,35],product:[1,3,16,20],prof:[0,26,31],prof_dir:26,prof_path:26,profil:[0,3,12,13],profiledb:26,profilehandl:[13,26,28,31,35],prog:13,program:[4,5,8,12],project:[3,4,5,8,16],prolin:[22,33,49],promin:[0,20],promod3_mod:4,promod3_name:4,promod3_name_head:4,promod3_path:8,promod3_root:8,promod3_shared_data_path:[8,37],promod3_unittest:[1,4,8],promod:[5,7],promot:8,propag:[8,22],proper:[16,26,50],properli:[1,35,39,41,50],properti:[21,22,35,50,51],propos:[29,31,32,34,44],proposed_posit:34,proposestep:34,prot:[8,23,26,28,32,34,36,47],prot_rec:8,protein:[0,18,24,25,28],proteinogen:26,proton:[21,25,49,51],prototyp:19,provid:[0,1,2,3,4,5,7,8,13,16,20,21,22,23,25,26,28,29,31,32,33,34,35,36,37,40,48,49,50,51],prune:[10,52],pscoringfunct:49,pseudo:[34,35,39,41],psi:[21,22,26,27,32,34,41,47,50,51],psi_bin:[41,51],psi_handl:47,psipr:[13,26,28,40,41],psipred:26,psipred_confid:41,psipred_pr:28,psipred_predict:[26,28,35],psipred_st:41,psipredpredict:23,pssm:[0,13],publicli:20,pull:[5,8,16,18],punch:[1,3,30],pure:0,purpos:[8,10,20,35,51],purpose:20,push:16,pushverbositylevel:13,put:[1,4,8,11,13,35],pwd:5,py_run:[1,4,8],pyc:1,pylint:16,pylintrc:16,pymod:[4,8,16],pyplot:27,pytest:8,python3:8,python:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],python_root:2,pythonpath:8,qmean:2,qmeandisco:40,qualiti:35,quantum:38,queri:[26,28,51],query_idx:28,query_list:28,querylib:51,question:[3,27],quickli:[5,8,32],quit:[8,13],rackovski:38,radian:[9,22,25,27],radii:[33,43],radiu:[8,33,39,41,49],raihvhqfgdlsqgcestgphynplavph:0,rais:[0,9,10,13,21,22,25,26,27,28,29,31,32,33,34,35,36,39,40,41,44,45,49,50,51],rama_iffi:33,ramachandran:33,random:[10,22,24,27,31,32,34],random_se:31,randomized_frag:22,randomli:[27,34],rang:[8,9,21,22,23,25,26,27,28,29,32,34,35,39,40,41,51],rank:31,rapid:38,rare:8,rather:[5,7,8,11,16,34,51],raw:[7,18,25,26,27,30,31],rawmodel:[3,8],reach:[0,29,32],read:[0,8,11,13,16,25,26,27,29,36,37,39,41,48,51],readabl:[0,8,13,20,51],readdunbrackfil:48,reader:[16,18],readi:[2,5,51],readme:[2,8,48],real:[8,13,37],realli:[1,2,8,11,16],reappear:16,reason:[8,16,20,32,34,52],rebas:16,rebuild:[2,8],recalcul:27,receiv:20,recent:[3,16],recip:[3,6],recipi:20,recoginz:49,recogn:[0,13],recognis:[1,8,16],recognit:38,recommend:[2,5,8,20,25,35],reconstruct:[0,3,8,18,21,22,25,30,32,35],reconstructcbetaposit:22,reconstructcstemoxygen:22,reconstructor:[32,35,36],reconstructoxygenposit:22,reconstructsidechain:[0,8,35,36],reconstructtest:8,record:[1,35],recreat:16,redistribut:20,redo:28,reduc:[3,25,28,35,41],reduced_scor:37,reducedscor:[35,37],redund:[24,31],ref_backbon:[23,26],ref_fil:8,refactor:3,refer:[1,4,8,18,21,22,23,25,26,34],referenc:8,refin:28,refine_thresh:28,refresh:31,regard:[20,32,44],region:[0,25,28,29,32,34,35,45,50],regist:[4,8],regress:38,regularli:5,reinterpret_cast:37,reject:[31,32,34],rel:[4,5,9,10,26,28,32,41],relat:[4,8,13,26,28,37,38,49],relax:30,releas:2,relev:[2,3,4,7,25,28,36,49],reli:5,remain:[20,30,34,35],rememb:[1,8,34],remodel:[31,36],remodel_cutoff:36,remov:[2,3,10,22,25,26,29,31,33,35,36,40,47,49],removecoordin:26,removeterminalgap:35,renumb:[26,35],reorder:35,reordergap:35,repeat:28,replac:[3,20,21,22,34,35],replacefrag:22,report:[1,8,35],reportmolprobityscor:33,repositori:[1,4,8,16,53],repres:[10,20,21],represent:[22,23,25,26,27,37,39,41,49,51],reproduc:[3,20,35],reproduct:20,reproduction:20,repuls:49,request:[26,28,48,51],requir:[0,2,3,5,8,13,16,19,20,21,22,26,27,28,31,32,35,36,37,42,49,50,51],reread:26,res_depth:26,res_idx:[49,50],res_index:21,res_indic:[21,25,36],res_list:[21,25,32,36],res_num:21,resembl:[16,28],reserv:11,reset:[10,21,25,32,34,40,49],resid:5,residu:[0,3,8,9,21,22,23,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,42,44,45,47,49,50,51],residue_depth:26,residue_index:[45,49,50],residue_list:35,residuedepth:26,residuehandl:[9,21,22,26,29,31,32,33,34,35,49,50,51],residuehandlelist:21,residueview:35,resiz:[22,37],resnum:[21,22,29,31,35,36,40],resnum_on:40,resnum_rang:35,resnum_two:40,resolut:[22,32],resolv:[16,21,32],resolvecystein:44,resort:35,respect:[9,25,28,35],respons:[8,16,20],rest:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],restor:[22,31,34,40],restraint:[26,32],restrict:[8,16,29],restructuredtext:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],result:[0,2,8,10,20,25,27,28,31,32,33,34,35,36,38,44,51],resum:14,retain:20,reus:[35,36],review:[16,53],revis:20,reviv:16,rewrit:1,richardson:38,ridig:36,right:[1,2,8,13,20],rigid:[0,3],rigid_frame_cutoff:36,rigidblock:28,rij:43,ring:[3,30],ring_punch_detect:35,risk:20,rms:33,rmsd:[22,23,26,28,31,32],rmsd_cutoff:[26,31,32],rmsd_thresh:[26,28],rname:28,rnum:40,robot:38,role:13,root:[2,4,8,16],rosetta:41,rot:36,rot_constructor:47,rot_group:[47,50],rot_lib:50,rot_lib_entri:50,rota_out:33,rotam:[0,3,33,36,38,44,45],rotamer:[48,51],rotamer_group:[44,46,47],rotamer_id:47,rotamer_librari:[3,35,36,48],rotamer_model:36,rotamer_on:44,rotamer_res_indic:36,rotamer_two:44,rotamerconstructor:[3,47,49],rotamergraph:[36,46,47,52],rotamergroup:49,rotamerid:47,rotamerlib:[35,36,37,48,50,51],rotamerlibentri:[50,51],rotat:[9,22],rotatearoundomegators:22,rotatearoundphipsitors:22,rotatearoundphitors:22,rotatearoundpsitors:22,rotationaroundlin:9,roughli:24,round:51,routin:[1,18,31],royalti:20,rrm:36,rrmrotam:[44,49,50],rrmrotamergroup:[44,46,49,50],rst1:4,rst2:4,rst:[4,8,16],rsync:8,rule:[5,8,9,16],run:0,runaction:1,runexitstatustest:1,runmolprob:33,runmolprobityent:33,runnabl:8,runner:1,runtest:[1,8],runtim:[0,3,10,12],runtimeerror:[9,10,21,22,25,26,27,29,31,32,34,35,36,39,40,41,44,45,48,49,50,51],runtimeexcept:27,s_id:26,s_vinaparticl:49,safe:[2,8],said:4,same:[0,1,2,4,7,8,10,13,14,20,21,25,26,28,31,32,34,35,36,37,39,40,41,42,45,48,49,50,51],samiti:35,sampl:[0,3,8,22,23],sampled_frag:34,samplemontecarlo:[3,34],sampler:[3,23,24,26],samplerbas:34,sampling_start_index:34,sander:38,saniti:2,sanity_check:2,satisfi:49,save:[16,22,25,26,27,28,31,34,37,39,40,41,51],savebb:26,savecach:28,savefig:27,savepdb:[18,21,22,25,26,28,30,31,32,34,35,36,47],saveport:[25,26,27,37,39,41,51],sc_data:32,sc_rec:[32,36],sc_rec_test:36,sc_result:32,scale:22,scatter:27,scheme:[1,8,13,21,26,29,34],schenk:38,schmidt:38,schwede:[5,8,18,19,38,53],sci:38,scicor:[5,8,18,19,53],scicore:[8,53],scondari:35,scope:14,score:[0,3,8,13,23,26,28,29,30],score_contain:31,score_env:[31,34,42],score_threshold:44,score_vari:35,scorecontain:31,scorer:3,scorer_env:[28,31,34],scorerbas:34,scoring_weight:28,scoringgapextend:[29,35],scoringweight:[28,31,35],scratch:[26,34],scriptname:11,scriptpath:8,scwrl3:[36,42],scwrl3disulfidscor:[43,44],scwrl3pairwisescor:43,scwrl3rotamerconstructor:50,scwrl4:[0,36,38,44,47],scwrl4particletyp:49,scwrl4rotamerconstructor:[3,47,50],scwrlrotamerconstructor:3,seamlessli:16,search:[0,2,3,8,21,26,28,31,33,35,36,41,44,49,50],searchdb:[23,26],second:[8,10,22,25,26,28,31,32,35,39,40,41,43,44],secondari:[3,13,26,28,38,41],secondli:8,section:[1,4,7,17,20,53,54],see:[0,1,7,8,9,10,11,13,16,18,20,21,25,26,27,29,31,33,34,35,37,39,40,41,51],seed:[10,24,27,31,32,34],seem:16,segment:22,select:[3,10,26,28,34,35,36,47],selenium:35,self:[1,8,10,44,47,49],self_energi:[10,49],sell:20,send:11,sensibl:35,sent:20,seok:38,separ:[1,3,8,10,20,25,27,35,39,41,44],seq:[13,21,23,26,28,29,31,35,40,42],seq_idx_on:28,seq_idx_two:28,seq_one_idx:28,seq_sep:[39,41],seq_tpl:[31,35],seq_trg:[31,35],seq_two_idx:28,seqid:[24,26],seqprof:13,seqr:[0,21,23,26,29,34,35,36,40],seqres:[21,26,28,31,34,35,39,40,41],seqres_str:[21,32,36],seqsim:26,sequenc:[0,3,8,13,18,21,22,23],sequencefromchain:42,sequencehandl:[21,26,28,29,35,40],sequencelist:[21,35,40],sequenceprofil:26,sequenti:[22,35],ser:49,serial:[26,37],serializ:37,serin:49,serv:[1,13,26,28,31,34],servic:[16,20],set:[1,2,4,8,10,11,13,15,16,18,21,22,25,26,28,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51,52],setaa:22,setactivesubrotam:49,setallatomscoringkei:31,setaroundomegators:22,setaroundphipsitors:22,setaroundphitors:22,setaroundpsitors:22,setbackbonescoringkei:31,setbackrub:22,setboolprop:50,setc:22,setca:22,setcb:22,setcharg:25,setcpuplatformsupport:25,setdefault:25,setdisulfidconnect:25,setenergi:[39,41],setenviron:[21,32,36,40],setepsilon:25,setfraggerhandl:35,setframeenergi:[47,49],setfudgelj:25,setfudgeqq:25,setinitialenviron:[21,31,32,34,36,40,42],setinternalconnect:25,setinternalenergi:49,setinternalenergyprefactor:49,setinterpol:51,setmass:25,setn:22,setnonbondedcutoff:32,seto:22,setolc:22,setpeptideboundconnect:25,setphitors:22,setpo:21,setprob:49,setpsipredpredict:[35,40,41],setpsitors:22,setresidu:21,setscor:41,setsequ:22,setsequenceoffset:35,setsequenceprofil:35,setsequenceprofilescoreskei:31,setsigma:25,setstemrmsdskei:31,setstructureprofil:26,setstructureprofilescoreskei:31,settemperatur:49,setup:[0,2,5,8,13],setupdefaultallatomscor:[31,35],setupdefaultbackbonescor:[31,35],setupsystem:25,setweight:31,sever:[0,2,3,5,8,10,13,24,26,27,28,31,32,35,36,40,41,42,44,48,49,51,52],sg_pos_on:43,sg_pos_two:43,shake:34,shall:20,shanno:35,shapovalov2011:[38,48],shapovalov:38,shared_ptr:37,shebang:8,sheet:35,shelenkov:38,shell:[1,2,7,8,11],shift:[22,26,29],shiftctermin:29,shiftextens:29,ship:[5,48],shorten:35,shorter:35,shortest:31,shortli:8,should:[1,2,4,5,7,8,10,11,13,16,18,20,22,23,26,27,28,31,32,34,35,36,37,40,45,47,49],show:[1,8,13,14,31,34,47,50],showcas:[1,21,25,27],shown:[8,14,35],shrink:22,shrug:38,side:[8,35,38],sidechain_pymod:8,sidechain_reconstructor:35,sidechain_rst:8,sidechain_test_data:8,sidechain_test_orig:36,sidechain_test_rec:36,sidechain_unit_tests:8,sidechainparticl:50,sidechainreconstructiondata:[30,32],sidechainreconstructor:[25,30,32,35],sidenot:[26,36],sig1:51,sig2:51,sig3:51,sig4:51,sigma:25,silent:1,sim:25,similar:[1,2,13,16,23,26,28,40,41,51],similardihedr:51,similarli:[2,25,35],simpl:[0,9,22,26,34,35,39,40,41,49,51],simpler:[25,35],simplest:[5,8,30],simpli:[5,21,22,31,32,34,35,49,50,51],simplic:[23,26],simplif:13,simplifi:[3,22,25,26],simul:[10,25,31,32,34],sinc:[1,2,4,8,10,11,16,18,22,25,26,27,28,49],singl:[2,4,8,10,21,22,25,26,28,31,32,34,35,36,40,41,45,48,49,50,52],singleton:25,singular:3,sink:37,sit:8,site:[3,5,8,28],size:[8,21,22,26,27,28,32,34,37,39,40,41],sizeof:37,skip:[0,1,8,16,26,28,35,50],slide:28,slight:35,slightli:35,slow:37,slower:[18,25,26,27,35,39,41,51],small:[8,26,32,35,36],smaller:[22,26,28,32,41],smallest:47,smallish:[2,8],smart:16,smng:3,smooth:38,smtl:35,soding2005:[26,38],softsampl:34,softwar:[8,20,38,49],sol:47,sole:[1,16,20],soli:38,solis2006:[24,38],solut:[8,10,28,31,32,34,35,36,46,47],solv:[10,16,47,52],solvent:26,solventaccess:26,solver:3,some:[1,2,4,5,6,7,8,13,16,21,23,26,30,33,34,35,36,37,40,42,47,50,51],somedata:37,someth:[1,8,11,16,26],sometim:16,somewher:4,soon:[10,32,41,47,51],sort:[1,4,10,14,31,34,51],sound:[16,50],sourc:[1,2,4,8,13,16,18,19,20,26,28,31,32,33,35,37,51],source1:[4,16],source2:[4,16],source3:4,source4:4,source:1,source_chain_idx:35,source_mhandl:35,sources:[1,4,8],sp3:51,space:[3,10,28,34,38],span:35,sparticl:49,spatial:[8,28,42],spawn:[1,8],spdbv:35,spdbv_style:35,special:[1,2,4,8,20,25,34,49,50,51],specif:[1,3,8,20,25,26,27,28,31,34,38,40,47,48,49],specifi:[0,2,4,5,9,10,22,26,27,28,31,32,35,36,40,49,51],specimen:11,speed:[3,25,35,38],spent:[14,18],sphere:[43,49],sphinx:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],spin:38,spit:[29,34],split:42,sport:8,squar:26,src:[8,16],ss_agreement:41,ss_agreement_scor:37,ssagree:26,ssagreementscor:37,sse:2,sstream:37,stabil:38,stabl:[5,16],stack:16,stage:[1,2,4,8],stai:[1,8,10,16,34],standalon:7,standard:[2,8,12,13,16,21,27,37,41,51],start:[0,1,2,4],start_idx:31,start_resnum:[21,22,26,31,34,35,36,39,40,41],start_resnum_list:36,start_rnum:40,start_temperatur:[10,34],starter:1,startscop:14,stash:[16,31,34,40],state:[1,2,8,20,21,26,31,34,40,41,44,49,51],statement:20,staticruntimeprofil:14,statist:[14,26,38],statu:[1,8],std:37,stderr:1,stdout:1,steadili:[10,34],steepest:[32,35],stem:[9,22,25,26,29,31,32,34,35,36],stemcoord:9,stempairorient:9,step:[8,10,14,16,18,28,29,30,31,32,34],stereo:35,stereo_chemical_problem_backbon:35,stereochem:[3,35],steric:51,still:[8,14,25,26,35,37],stop:[1,8,14,28,29,32],stop_criterion:32,stoppag:20,storabl:26,storag:[8,21,25,39,41],store:[0,1,3,8,9,16,18,21,22,25,26,27,28,29,31,32,34,35,36,37,47],stori:8,str:[1,11,13,14,15,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,51],str_len:37,straight:16,strategi:51,stream:37,stretch:[21,26,31,34,35,40,41],strict:16,strictli:3,string:[0,3,11,13,26,27,29,37],stringstream:37,strip:[0,35],struc:5,struct:[5,26,37],struct_db:23,structral:[21,40],structur:[0,3,8,13],structural_db:31,structuralgap:[29,33],structuralgaplist:[29,35],structure_db:[26,28,31,35,37],structure_db_on:26,structure_db_two:26,structure_dir:26,structure_id:26,structure_path:26,structure_sourc:13,structuredb:[3,13,24,26,28,31,35,37],structuredbdatatyp:26,structureprofil:26,studer:38,stuff:[26,39],style:[35,40,41,49],sub:[8,26],sub_frag:22,sub_res_list:26,subdir:8,subfold:8,subject:[8,20],sublicens:20,submiss:20,submit:20,submodul:8,submodule1:16,subpart:28,subrotam:[0,3,44,47,49,50],subrotameroptim:[36,52],subsequ:[10,20,22,35],subset:[0,13,25,26,28,31,32,35,36],subst:26,subst_matrix:26,substitut:26,substweightmatrix:26,subtre:[4,8],succeed:29,success:[10,11,34],successfulli:5,sudo:7,suffici:26,suffix:11,sugar:6,suggest:[5,8,43],suit:[1,8,26],sulfur:[43,44,49,50],sum:[14,29,35,36,43,44,49],summari:[14,26],superpos:[22,26,28,31,32,34],superpose_stem:22,superposed_rmsd:[22,31],superposeonto:22,superposit:[3,28,31,34],superpost:28,supersed:20,supervis:1,support:[0,1,2,3,8,11,13,18,20,25,32,35],suppos:[16,34],sure:[2,7,8,13,16,26],surfac:26,surotam:49,surprisingli:50,surround:[25,26,32,36,39,41],symmetr:[26,40,51],symmetri:[39,41],sync:8,syntax:20,system:[1,2,4,8,16,20,23],t_sampler:27,tabl:26,tag:5,tail:22,tailor:[21,35],take:[8,10,21,26,27,28,31,32,34,35,37,41,44,50,52],taken:[0,21,25,32,34,35,50],talk:1,target:[0,1,2,4,8,13,18,26,28,30,31,32,34,35,40,49],target_chain_idx:35,target_mhandl:35,target_pdb:33,target_posit:28,target_sequ:26,task:[8,16,32,35,37,40],techniqu:[10,38],tell:[1,8,11,13,16,26],temperatur:[10,31,34,49],templat:[0,1,3,13,18,30,35,37,40],template:13,temporari:[26,35],temporarili:16,term:[8,20,26,49,51,52],termin:[0,1,9,11,18,20,21,22,25,29,31,32,34,35,36,50],terminal_len:34,terminal_seqr:34,termini:[0,3,29,34,35],terminu:[26,34,35],terms:20,test_:8,test_action_:1,test_action_do_awesom:1,test_action_help:1,test_awesome_featur:8,test_check_io:37,test_cod:8,test_doctest:8,test_foo:4,test_portable_binari:37,test_reconstruct_sidechain:8,test_sidechain_reconstruct:8,test_submodule1:16,test_suite_:4,test_suite_your_module_run:8,test_your_modul:16,testcas:[1,8],testcasenam:8,testexit0:1,testpmexist:1,testreconstruct:8,testutil:[1,8],text:[1,13,20,35],than:[4,8,13,14,16,21,22,26,28,31,32,33,35,36,41,44,50],thei:[2,5,8,16,21,22,25,26,27,28,31,32,33,34,35,44,49,50,51,53],them:[4,8,16,22,25,26,27,28,29,31,35,36,40,45],themselv:25,theoret:34,theori:[20,38],therefor:[5,8,22,24,26,28,32,34,35,51],thereof:[20,25],thi:[0,1,2,3,4,5,7,8,10,11,12,13,14,15,16,17,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,42,44,47,49,50,51,52,54],thing:[1,2,8,16,26,28,35,51],think:10,thoroughli:16,those:[0,1,2,4,8,10,13,16,20,25,28,31,35,36,37,39,41,47,50,51],though:[25,35,37],thr:49,thread:[18,25,35,38],three:[1,4,16,21,22,27,28,31,33,34,38,41,49,51],threonin:49,thresh:[22,49,51],threshold:[10,26,28,32,35,36,40,51],through:[1,8,9,20,22,26,29,35,39,41],throughout:[13,16,24,25],thrown:26,thu:[5,11,49],tidi:16,tightli:16,time:[1,5,8,13,14,16,18,28,35],timer:14,tini:[16,35],titl:27,title:20,tlc:[21,49],tlc_an:21,tlctorotid:[47,49],tmp_buf:37,todens:22,toentiti:[18,21,22,25,26,32,34,36],toframeresidu:49,togeth:[8,16,26,44],too:[13,16,31,32,35,37],tool:[3,4,23,37,42,47],toolbox:16,top:[2,6,8,14,15,16,32,35],topic:[1,8,16],topolog:[25,32],torrmrotam:49,torsion:[0,13,21,22,23,24,26],torsion_angl:47,torsion_bin:41,torsion_plot:27,torsion_sampl:[22,26,31,32,34,35,37],torsion_sampler_coil:[28,37],torsion_sampler_extend:[28,37],torsion_sampler_hel:37,torsion_sampler_helix:28,torsion_sampler_list:26,torsion_scor:37,torsionprob:26,torsionsampl:[22,24,26,27,28,31,32,34,35,37,41],torsionscor:[35,37],tort:20,total:[10,14,26,28],touch:[1,8,25,32],toward:[0,3,8,13,26,29,32,35,39,41,47,49,50,52],tpl:[0,30,31,35],tpr:[49,51],trace:35,track:[3,11,20,30],trade:20,trademark:20,tradition:11,trail:0,train:[24,31,35],trajectori:[28,34],tran:[22,49,51],trans:51,transfer:20,transform:[9,20,22,28,34,35,51],translat:[4,8,20,26,49,51],translate:4,transomegators:22,treat:[3,8,25,35,36,37,51],treatment:50,tree:[1,4,8,10,16,46,47],treepack:3,treesolv:[10,36,47],trg:[0,13,31,35],tri:[10,28,29,35,44,51],triangl:28,trick:[1,7,16],trigger:[1,4,8,48],tripeptid:27,tripl:11,triplet:23,trott2010:[38,49],trott:38,trp:[49,51],trustworthi:16,tryptophan:49,ttccpsivarsnfnvcrlpgtpea:[31,35],ttccpsivarsnfnvcrlpgtpeaicatgytciiipgatcpgdyan:35,ttccpsivarsnfnvcrlpgtpeaicatytgciiipgatcpgdyan:[31,35],tupl:[9,10,11,22,25,26,28,29,33,35,36,44],turn:[0,1,11,14,16,35],tutori:8,tweak:35,twice:[14,40],two:[1,7,8,10,16,21,22,25,26,28,29,31,32,35,36,37,39,40,41,43,44,47,49,51],txt:[1,2,4,8,16,20],type:[0,1,8,9,10,11,13,14,20,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,47,48,49,50],typedef:37,typenam:37,typic:[22,28,34,47,51],tyr:[49,51],tyrosin:49,uint32_t:37,uint:37,ultra:26,uncertain:8,uncharg:50,unclos:35,undefin:25,under:[4,8,20],undergo:[28,32,34,36],underli:[29,31,49],underscor:1,understand:16,understood:0,undo:10,unexpect:2,unfavor:[22,32],unfavour:[32,34,44],unfortun:16,unhandl:[0,13],uniba:[5,8,18,19,53],uniform:32,union:20,uniqu:[0,13,28,31,34,51],unittest:[1,8,16],univers:[8,53],unix:16,unknown:25,unless:[13,20,21,22,25,31,39,41],unlik:47,unrecognis:11,unset:[21,25,36],unsupport:[13,37],until:[8,10,28,32,35,40,50],untouch:22,untrack:1,unum:28,unus:16,upat:5,updat:[5,7,8,16,21,28,29,31,32,35,36,40,42],update:[3,25],updatedistribut:27,updateposit:[25,32],upon:[26,32,34],upper:28,urei:25,urey_bradley_angl:25,usabl:16,usag:[0,3,10,13,24,26,31,32,36],use:[0,4,20,25,26,27,31,35,39,41,51],use_amber_ff:35,use_bbdep_lib:36,use_frm:36,use_full_extend:35,use_scoring_extend:35,used:[31,35],useful:[21,25,36],user:[1,5,8,28,53],userlevel:1,usr:[2,5,7,8],usual:[1,2,8,13,14,16,31,35,39],usualli:[2,4,8,16,22,35],utilis:[8,16],v_size:37,val:[27,49],valid:[0,10,16,22,26,29,34,35,36,48,51],valin:49,valu:[2,10,11,13,21,22,25,26,28,31,34,35,37,39,40,41,44,47,49,50,51,52],valueerror:[28,35],vanish:40,varadarajan:38,vari:[4,37],variabl:[1,2,8,14,18,25,33,35,37],variant:[25,31],variou:[1,2,4,16,30],vec3:[9,21,22,26,32,33,43,44,49],vec3list:[28,49],vector:[25,27,28,31,37,49],verbal:20,verbos:1,veri:[1,8,11,16,25,28,35,37],verif:13,verifi:[1,11,16],version:[2,3,5,8,16,20,26,35,37,48,49],vertic:28,via:[1,5,8,13,15,25],view:[13,16,27,35,40],vina:[3,38],vinaparticletyp:[49,50],vinarotamerconstructor:50,virtual:8,visibl:36,vision:38,visual:18,volum:5,wai:[1,2,4,5,8,16,22,23,25,31,41,47,49],wait:8,walk:[1,8],want:[1,2,3,8,15,16,22,26,28,31,32,35,40,49,50,51,52,53],warn:[3,8,16,35],warranti:20,warranties:20,watch:8,web:[2,8],weight:[3,26,28,31,34,35,39,41],weird:[28,32,47],well:[0,4,16,21,27,28,29,31,35,37,41,47,50,51],went:[0,8],were:[16,26,31,35],wester:38,wether:10,what:[1,8,11,13,16,23,26,36,40],when:[1,3,4,5,8,10,13,14,21,22,25,26,27,28,29,31,34,35,36,37,38,40,41,44,47,48,49,50,51],whenev:[8,21,31,40],where:[0,1,3,4,5,8,10,11,13,14,16,20,21,22,25,26,27,31,35,37,39,40,41,48,49,50,51],wherea:26,wherev:20,whether:[3,5,8,10,11,13,20,22,25,26,31,32,34,36,39,40,41,49,50,51],which:[0,1,2,4,8,9,11,12,13,16,18,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,50,51],whistl:8,whitespac:0,who:[10,47],whole:[1,2,8,16,20,22,26,35,49],whom:20,why:[1,16],width:[10,37,47],wild:4,window:28,window_length:28,wise:4,wish:[2,17,27,35],with_aa:31,with_db:31,within:[2,3,4,8,14,16,20,21,25,28,29,33,35,36,39,41,51],without:[0,1,3,4,8,11,13,20,25,29,32,35,40,51],wolfson:[28,38],won:[0,35,36,50],word:4,work:[1,2,4,5,7,8,14,16,18,20,25,29,35,37,50],worldwid:20,worst:16,worth:53,would:[1,2,8,11,22,26,27,44,49],wrap:26,wrapper:[1,4,8,15,35],write:0,writebasetyp:37,writemagicnumb:37,writetypes:37,writeversionnumb:37,written:[8,20,37],wrong:[2,13],wwpdb:5,www:20,xlabel:27,xlim:27,xml:8,xxx:[22,49],xxx_num_atoms:21,xxx_num_hydrogens:21,year:1,yet:[26,31,35],ylabel:27,ylim:27,you:[0,1,2,3,4,5,7,8,10,11,13,14,15,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,37,39,40,41,47,48,49,50,51,52,53],your:[1,2,4,5],your_modul:[8,16],yourself:[2,8,10,16,35,50],yyyi:20,zero:[0,26,28,35,51],zhou2005:[26,38],zhou:38,zip:[26,47]},titles:["ProMod3 Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],acid:[21,25,27],action:[0,1,4,5,8],actiontestcas:1,algorithm:28,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angle:27,api:1,app:7,argument:13,atom:[21,32,39],availabl:7,backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entry:51,environ:40,evaluat:44,everyth:11,exampl:[31,37],execut:[1,5],exisit:37,extender:29,featur:[8,26],file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],image:5,install:2,integrat:1,introduct:[4,11,13],issue:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:51,novo:[28,34],object:[24,34,45],optimiz:52,ost:25,other:43,output:1,own:[5,8],pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,5,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,registri:5,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,using:[2,37],vina:49,write:8,your:8}})
\ No newline at end of file
+Search.setIndex({docnames:["actions/index","actions/index_dev","buildsystem","changelog","cmake/index","container/docker","container/index","container/singularity","contributing","core/geometry","core/graph_minimizer","core/helper","core/index","core/pm3argparse","core/runtime_profiling","core/setcompoundschemlib","dev_setup","developers","gettingstarted","index","license","loop/all_atom","loop/backbone","loop/index","loop/load_loop_objects","loop/mm_system_creation","loop/structure_db","loop/torsion_sampler","modelling/algorithms","modelling/gap_handling","modelling/index","modelling/loop_candidates","modelling/loop_closing","modelling/model_checking","modelling/monte_carlo","modelling/pipeline","modelling/sidechain_reconstruction","portableIO","references","scoring/all_atom_scorers","scoring/backbone_score_env","scoring/backbone_scorers","scoring/index","scoring/other_scoring_functions","sidechain/disulfid","sidechain/frame","sidechain/graph","sidechain/index","sidechain/loading","sidechain/rotamer","sidechain/rotamer_constructor","sidechain/rotamer_lib","sidechain/subrotamer_optimizer","user_contributions","users"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":1,sphinx:56},filenames:["actions/index.rst","actions/index_dev.rst","buildsystem.rst","changelog.rst","cmake/index.rst","container/docker.rst","container/index.rst","container/singularity.rst","contributing.rst","core/geometry.rst","core/graph_minimizer.rst","core/helper.rst","core/index.rst","core/pm3argparse.rst","core/runtime_profiling.rst","core/setcompoundschemlib.rst","dev_setup.rst","developers.rst","gettingstarted.rst","index.rst","license.rst","loop/all_atom.rst","loop/backbone.rst","loop/index.rst","loop/load_loop_objects.rst","loop/mm_system_creation.rst","loop/structure_db.rst","loop/torsion_sampler.rst","modelling/algorithms.rst","modelling/gap_handling.rst","modelling/index.rst","modelling/loop_candidates.rst","modelling/loop_closing.rst","modelling/model_checking.rst","modelling/monte_carlo.rst","modelling/pipeline.rst","modelling/sidechain_reconstruction.rst","portableIO.rst","references.rst","scoring/all_atom_scorers.rst","scoring/backbone_score_env.rst","scoring/backbone_scorers.rst","scoring/index.rst","scoring/other_scoring_functions.rst","sidechain/disulfid.rst","sidechain/frame.rst","sidechain/graph.rst","sidechain/index.rst","sidechain/loading.rst","sidechain/rotamer.rst","sidechain/rotamer_constructor.rst","sidechain/rotamer_lib.rst","sidechain/subrotamer_optimizer.rst","user_contributions.rst","users.rst"],objects:{"":{"--backbone-independent":[0,6,1,"cmdoption-i"],"--energy_function":[0,6,1,"cmdoption-f"],"--keep-sidechains":[0,6,1,"cmdoption-k"],"--no-disulfids":[0,6,1,"cmdoption-n"],"--no-subrotamer-optimization":[0,6,1,"cmdoption-s"],"--rigid-rotamers":[0,6,1,"cmdoption-r"],"-f":[0,6,1,"cmdoption-f"],"-i":[0,6,1,"cmdoption-i"],"-k":[0,6,1,"cmdoption-k"],"-n":[0,6,1,"cmdoption-n"],"-r":[0,6,1,"cmdoption-r"],"-s":[0,6,1,"cmdoption-s"],"command:add_doc_dependency":[4,0,1,""],"command:add_doc_source":[4,0,1,""],"command:convert_module_data":[4,0,1,""],"command:module":[4,0,1,""],"command:pm_action":[4,0,1,""],"command:promod3_unittest":[4,0,1,""],"command:pymod":[4,0,1,""],test_actions:[1,2,0,"-"]},"promod3.core":{ConstructAtomPos:[9,1,1,""],ConstructCBetaPos:[9,1,1,""],ConstructCTerminalOxygens:[9,1,1,""],EvaluateGromacsPosRule:[9,1,1,""],GraphMinimizer:[10,3,1,""],RotationAroundLine:[9,1,1,""],StaticRuntimeProfiler:[14,3,1,""],StemCoords:[9,3,1,""],StemPairOrientation:[9,3,1,""],helper:[11,2,0,"-"],pm3argparse:[13,2,0,"-"]},"promod3.core.GraphMinimizer":{AStarSolve:[10,4,1,""],AddEdge:[10,4,1,""],AddNode:[10,4,1,""],ApplyDEE:[10,4,1,""],ApplyEdgeDecomposition:[10,4,1,""],MCSolve:[10,4,1,""],NaiveSolve:[10,4,1,""],Prune:[10,4,1,""],Reset:[10,4,1,""],TreeSolve:[10,4,1,""]},"promod3.core.StaticRuntimeProfiler":{Clear:[14,4,1,""],IsEnabled:[14,4,1,""],PrintSummary:[14,4,1,""],Start:[14,4,1,""],StartScoped:[14,4,1,""],Stop:[14,4,1,""]},"promod3.core.StemCoords":{c_coord:[9,5,1,""],ca_coord:[9,5,1,""],n_coord:[9,5,1,""]},"promod3.core.StemPairOrientation":{angle_four:[9,5,1,""],angle_one:[9,5,1,""],angle_three:[9,5,1,""],angle_two:[9,5,1,""],distance:[9,5,1,""]},"promod3.core.helper":{FileExists:[11,1,1,""],FileExtension:[11,1,1,""],FileGzip:[11,1,1,""],MsgErrorAndExit:[11,1,1,""]},"promod3.core.pm3argparse":{PM3ArgumentParser:[13,3,1,""]},"promod3.core.pm3argparse.PM3ArgumentParser":{AddAlignment:[13,4,1,""],AddFragments:[13,4,1,""],AddProfile:[13,4,1,""],AddStructure:[13,4,1,""],AssembleParser:[13,4,1,""],Parse:[13,4,1,""],__init__:[13,4,1,""],action:[13,5,1,""]},"promod3.loop":{AllAtomEnv:[21,3,1,""],AllAtomEnvPositions:[21,3,1,""],AllAtomPositions:[21,3,1,""],AminoAcidAtom:[21,3,1,""],AminoAcidHydrogen:[21,3,1,""],AminoAcidLookup:[21,3,1,""],BackboneList:[22,3,1,""],CoordInfo:[26,3,1,""],ForcefieldAminoAcid:[25,3,1,""],ForcefieldBondInfo:[25,3,1,""],ForcefieldConnectivity:[25,3,1,""],ForcefieldHarmonicAngleInfo:[25,3,1,""],ForcefieldHarmonicImproperInfo:[25,3,1,""],ForcefieldLJPairInfo:[25,3,1,""],ForcefieldLookup:[25,3,1,""],ForcefieldPeriodicDihedralInfo:[25,3,1,""],ForcefieldUreyBradleyAngleInfo:[25,3,1,""],FragDB:[26,3,1,""],Fragger:[26,3,1,""],FraggerMap:[26,3,1,""],FragmentInfo:[26,3,1,""],LoadFragDB:[24,4,1,""],LoadStructureDB:[24,4,1,""],LoadTorsionSampler:[24,4,1,""],LoadTorsionSamplerCoil:[24,4,1,""],LoadTorsionSamplerExtended:[24,4,1,""],LoadTorsionSamplerHelical:[24,4,1,""],MmSystemCreator:[25,3,1,""],PsipredPrediction:[26,3,1,""],StructureDB:[26,3,1,""],StructureDBDataType:[26,3,1,""],TorsionSampler:[27,3,1,""]},"promod3.loop.AllAtomEnv":{ClearEnvironment:[21,4,1,""],GetAllAtomPositions:[21,4,1,""],GetEnvironment:[21,4,1,""],GetSeqres:[21,4,1,""],SetEnvironment:[21,4,1,""],SetInitialEnvironment:[21,4,1,""]},"promod3.loop.AllAtomEnvPositions":{all_pos:[21,5,1,""],res_indices:[21,5,1,""]},"promod3.loop.AllAtomPositions":{AllAtomPositions:[21,4,1,""],ClearPos:[21,4,1,""],ClearResidue:[21,4,1,""],Copy:[21,4,1,""],Extract:[21,4,1,""],ExtractBackbone:[21,4,1,""],GetAA:[21,4,1,""],GetFirstIndex:[21,4,1,""],GetIndex:[21,4,1,""],GetLastIndex:[21,4,1,""],GetNumAtoms:[21,4,1,""],GetNumResidues:[21,4,1,""],GetOmegaTorsion:[21,4,1,""],GetPhiTorsion:[21,4,1,""],GetPos:[21,4,1,""],GetPsiTorsion:[21,4,1,""],GetSequence:[21,4,1,""],InsertInto:[21,4,1,""],IsAllSet:[21,4,1,""],IsAnySet:[21,4,1,""],IsSet:[21,4,1,""],SetPos:[21,4,1,""],SetResidue:[21,4,1,""],ToEntity:[21,4,1,""]},"promod3.loop.AminoAcidLookup":{GetAA:[21,4,1,""],GetAAA:[21,4,1,""],GetAAH:[21,4,1,""],GetAnchorAtomIndex:[21,4,1,""],GetAtomName:[21,4,1,""],GetAtomNameAmber:[21,4,1,""],GetAtomNameCharmm:[21,4,1,""],GetElement:[21,4,1,""],GetH1Index:[21,4,1,""],GetH2Index:[21,4,1,""],GetH3Index:[21,4,1,""],GetHNIndex:[21,4,1,""],GetHydrogenIndex:[21,4,1,""],GetIndex:[21,4,1,""],GetMaxNumAtoms:[21,4,1,""],GetMaxNumHydrogens:[21,4,1,""],GetNumAtoms:[21,4,1,""],GetNumHydrogens:[21,4,1,""],GetOLC:[21,4,1,""]},"promod3.loop.BackboneList":{ApplyTransform:[22,4,1,""],BackboneList:[22,4,1,""],CARMSD:[22,4,1,""],Copy:[22,4,1,""],Extract:[22,4,1,""],GetAA:[22,4,1,""],GetBounds:[22,4,1,""],GetC:[22,4,1,""],GetCA:[22,4,1,""],GetCB:[22,4,1,""],GetN:[22,4,1,""],GetO:[22,4,1,""],GetOLC:[22,4,1,""],GetOmegaTorsion:[22,4,1,""],GetPhiTorsion:[22,4,1,""],GetPsiTorsion:[22,4,1,""],GetSequence:[22,4,1,""],GetTransform:[22,4,1,""],InsertInto:[22,4,1,""],MinCADistance:[22,4,1,""],RMSD:[22,4,1,""],ReconstructCBetaPositions:[22,4,1,""],ReconstructCStemOxygen:[22,4,1,""],ReconstructOxygenPositions:[22,4,1,""],ReplaceFragment:[22,4,1,""],RotateAroundOmegaTorsion:[22,4,1,""],RotateAroundPhiPsiTorsion:[22,4,1,""],RotateAroundPhiTorsion:[22,4,1,""],RotateAroundPsiTorsion:[22,4,1,""],Set:[22,4,1,""],SetAA:[22,4,1,""],SetAroundOmegaTorsion:[22,4,1,""],SetAroundPhiPsiTorsion:[22,4,1,""],SetAroundPhiTorsion:[22,4,1,""],SetAroundPsiTorsion:[22,4,1,""],SetBackrub:[22,4,1,""],SetC:[22,4,1,""],SetCA:[22,4,1,""],SetCB:[22,4,1,""],SetN:[22,4,1,""],SetO:[22,4,1,""],SetOLC:[22,4,1,""],SetSequence:[22,4,1,""],SuperposeOnto:[22,4,1,""],ToDensity:[22,4,1,""],ToEntity:[22,4,1,""],TransOmegaTorsions:[22,4,1,""],__len__:[22,4,1,""],append:[22,4,1,""],clear:[22,4,1,""],empty:[22,4,1,""],resize:[22,4,1,""]},"promod3.loop.CoordInfo":{chain_name:[26,5,1,""],id:[26,5,1,""],offset:[26,5,1,""],shift:[26,5,1,""],size:[26,5,1,""],start_resnum:[26,5,1,""]},"promod3.loop.ForcefieldBondInfo":{bond_length:[25,5,1,""],force_constant:[25,5,1,""],index_one:[25,5,1,""],index_two:[25,5,1,""]},"promod3.loop.ForcefieldConnectivity":{harmonic_angles:[25,5,1,""],harmonic_bonds:[25,5,1,""],harmonic_impropers:[25,5,1,""],lj_pairs:[25,5,1,""],periodic_dihedrals:[25,5,1,""],periodic_impropers:[25,5,1,""],urey_bradley_angles:[25,5,1,""]},"promod3.loop.ForcefieldHarmonicAngleInfo":{angle:[25,5,1,""],force_constant:[25,5,1,""],index_one:[25,5,1,""],index_three:[25,5,1,""],index_two:[25,5,1,""]},"promod3.loop.ForcefieldHarmonicImproperInfo":{angle:[25,5,1,""],force_constant:[25,5,1,""],index_four:[25,5,1,""],index_one:[25,5,1,""],index_three:[25,5,1,""],index_two:[25,5,1,""]},"promod3.loop.ForcefieldLJPairInfo":{epsilon:[25,5,1,""],index_one:[25,5,1,""],index_two:[25,5,1,""],sigma:[25,5,1,""]},"promod3.loop.ForcefieldLookup":{GetAA:[25,4,1,""],GetCharges:[25,4,1,""],GetDefault:[25,4,1,""],GetDisulfidConnectivity:[25,4,1,""],GetEpsilons:[25,4,1,""],GetFudgeLJ:[25,4,1,""],GetFudgeQQ:[25,4,1,""],GetHeavyIndex:[25,4,1,""],GetHydrogenIndex:[25,4,1,""],GetInternalConnectivity:[25,4,1,""],GetMasses:[25,4,1,""],GetNumAtoms:[25,4,1,""],GetOXTIndex:[25,4,1,""],GetPeptideBoundConnectivity:[25,4,1,""],GetSigmas:[25,4,1,""],Load:[25,4,1,""],LoadCHARMM:[25,4,1,""],LoadPortable:[25,4,1,""],Save:[25,4,1,""],SavePortable:[25,4,1,""],SetCharges:[25,4,1,""],SetDefault:[25,4,1,""],SetDisulfidConnectivity:[25,4,1,""],SetEpsilons:[25,4,1,""],SetFudgeLJ:[25,4,1,""],SetFudgeQQ:[25,4,1,""],SetInternalConnectivity:[25,4,1,""],SetMasses:[25,4,1,""],SetPeptideBoundConnectivity:[25,4,1,""],SetSigmas:[25,4,1,""]},"promod3.loop.ForcefieldPeriodicDihedralInfo":{force_constant:[25,5,1,""],index_four:[25,5,1,""],index_one:[25,5,1,""],index_three:[25,5,1,""],index_two:[25,5,1,""],multiplicity:[25,5,1,""],phase:[25,5,1,""]},"promod3.loop.ForcefieldUreyBradleyAngleInfo":{angle:[25,5,1,""],angle_force_constant:[25,5,1,""],bond_force_constant:[25,5,1,""],bond_length:[25,5,1,""],index_one:[25,5,1,""],index_three:[25,5,1,""],index_two:[25,5,1,""]},"promod3.loop.FragDB":{AddFragments:[26,4,1,""],GetAngularBinSize:[26,4,1,""],GetDistBinSize:[26,4,1,""],GetNumFragments:[26,4,1,""],GetNumStemPairs:[26,4,1,""],HasFragLength:[26,4,1,""],Load:[26,4,1,""],LoadPortable:[26,4,1,""],MaxFragLength:[26,4,1,""],PrintStatistics:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SearchDB:[26,4,1,""]},"promod3.loop.Fragger":{AddSSAgreeParameters:[26,4,1,""],AddSeqIDParameters:[26,4,1,""],AddSeqSimParameters:[26,4,1,""],AddSequenceProfileParameters:[26,4,1,""],AddStructureProfileParameters:[26,4,1,""],AddTorsionProbabilityParameters:[26,4,1,""],Fill:[26,4,1,""],GetFragmentInfo:[26,4,1,""],GetScore:[26,4,1,""],__getitem__:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.FraggerMap":{Contains:[26,4,1,""],Load:[26,4,1,""],LoadBB:[26,4,1,""],Save:[26,4,1,""],SaveBB:[26,4,1,""],__getitem__:[26,4,1,""],__setitem__:[26,4,1,""]},"promod3.loop.FragmentInfo":{chain_index:[26,5,1,""],length:[26,5,1,""],offset:[26,5,1,""]},"promod3.loop.MmSystemCreator":{ExtractLoopPositions:[25,4,1,""],GetCpuPlatformSupport:[25,4,1,""],GetDisulfidBridges:[25,4,1,""],GetForcefieldAminoAcids:[25,4,1,""],GetIndexing:[25,4,1,""],GetLoopLengths:[25,4,1,""],GetLoopStartIndices:[25,4,1,""],GetNumLoopResidues:[25,4,1,""],GetNumResidues:[25,4,1,""],GetSimulation:[25,4,1,""],SetCpuPlatformSupport:[25,4,1,""],SetupSystem:[25,4,1,""],UpdatePositions:[25,4,1,""]},"promod3.loop.PsipredPrediction":{Add:[26,4,1,""],Extract:[26,4,1,""],FromHHM:[26,4,1,""],FromHoriz:[26,4,1,""],GetConfidence:[26,4,1,""],GetConfidences:[26,4,1,""],GetPrediction:[26,4,1,""],GetPredictions:[26,4,1,""],PsipredPrediction:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.StructureDB":{AddCoordinates:[26,4,1,""],GenerateStructureProfile:[26,4,1,""],GetBackboneList:[26,4,1,""],GetCoordIdx:[26,4,1,""],GetCoordInfo:[26,4,1,""],GetDSSPStates:[26,4,1,""],GetDihedralAngles:[26,4,1,""],GetNumCoords:[26,4,1,""],GetResidueDepths:[26,4,1,""],GetSequence:[26,4,1,""],GetSequenceProfile:[26,4,1,""],GetSolventAccessibilitites:[26,4,1,""],GetStructureProfile:[26,4,1,""],GetSubDB:[26,4,1,""],HasData:[26,4,1,""],Load:[26,4,1,""],LoadPortable:[26,4,1,""],PrintStatistics:[26,4,1,""],RemoveCoordinates:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SetStructureProfile:[26,4,1,""]},"promod3.loop.TorsionSampler":{Draw:[27,4,1,""],DrawPhiGivenPsi:[27,4,1,""],DrawPsiGivenPhi:[27,4,1,""],ExtractStatistics:[27,4,1,""],GetBinSize:[27,4,1,""],GetBinsPerDimension:[27,4,1,""],GetHistogramIndex:[27,4,1,""],GetHistogramIndices:[27,4,1,""],GetPhiProbabilityGivenPsi:[27,4,1,""],GetProbability:[27,4,1,""],GetPsiProbabilityGivenPhi:[27,4,1,""],Load:[27,4,1,""],LoadPortable:[27,4,1,""],Save:[27,4,1,""],SavePortable:[27,4,1,""],UpdateDistributions:[27,4,1,""]},"promod3.modelling":{AddModellingIssue:[35,1,1,""],AllAtomRelaxer:[32,3,1,""],BackboneRelaxer:[32,3,1,""],BuildFromRawModel:[35,1,1,""],BuildRawModel:[35,1,1,""],BuildSidechains:[35,1,1,""],CCD:[32,3,1,""],CCDCloser:[34,3,1,""],CTerminalCloser:[34,3,1,""],CheckFinalModel:[35,1,1,""],ClearGaps:[29,1,1,""],CloseGaps:[35,1,1,""],CloseLargeDeletions:[35,1,1,""],CloseSmallDeletions:[35,1,1,""],CloserBase:[34,3,1,""],CoolerBase:[34,3,1,""],CountEnclosedGaps:[29,1,1,""],CountEnclosedInsertions:[29,1,1,""],DeNovoCloser:[34,3,1,""],DeleteGapCols:[35,1,1,""],DirtyCCDCloser:[34,3,1,""],ExponentialCooler:[34,3,1,""],FillLoopsByDatabase:[35,1,1,""],FillLoopsByMonteCarlo:[35,1,1,""],FilterCandidates:[33,1,1,""],FilterCandidatesWithSC:[33,1,1,""],FindMotifs:[28,4,1,""],FraggerHandle:[28,3,1,""],FragmentSampler:[34,3,1,""],FullGapExtender:[29,3,1,""],GapExtender:[29,3,1,""],GenerateDeNovoTrajectories:[28,1,1,""],GetRingPunches:[33,1,1,""],GetRings:[33,1,1,""],HasRingPunches:[33,1,1,""],InsertLoop:[35,1,1,""],InsertLoopClearGaps:[29,1,1,""],IsAllAtomScoringSetUp:[35,1,1,""],IsBackboneScoringSetUp:[35,1,1,""],KIC:[32,3,1,""],KICCloser:[34,3,1,""],LinearScorer:[34,3,1,""],LoopCandidates:[31,3,1,""],MergeGaps:[29,1,1,""],MergeGapsByDistance:[35,1,1,""],MergeMHandle:[35,1,1,""],MinimizeModelEnergy:[35,1,1,""],ModelTermini:[35,1,1,""],ModellingHandle:[35,3,1,""],ModellingIssue:[35,3,1,""],MotifMatch:[28,3,1,""],MotifQuery:[28,3,1,""],NTerminalCloser:[34,3,1,""],PhiPsiSampler:[34,3,1,""],PullTerminalDeletions:[35,1,1,""],ReconstructSidechains:[36,1,1,""],RemoveTerminalGaps:[35,1,1,""],ReorderGaps:[35,1,1,""],ReportMolProbityScores:[33,1,1,""],RigidBlocks:[28,4,1,""],RunMolProbity:[33,1,1,""],RunMolProbityEntity:[33,1,1,""],SampleMonteCarlo:[34,1,1,""],SamplerBase:[34,3,1,""],ScoreContainer:[31,3,1,""],ScorerBase:[34,3,1,""],ScoringGapExtender:[29,3,1,""],ScoringWeights:[31,3,1,""],SetFraggerHandles:[35,1,1,""],SetPsipredPredictions:[35,1,1,""],SetSequenceProfiles:[35,1,1,""],SetupDefaultAllAtomScoring:[35,1,1,""],SetupDefaultBackboneScoring:[35,1,1,""],ShiftExtension:[29,3,1,""],SidechainReconstructionData:[36,3,1,""],SidechainReconstructor:[36,3,1,""],SoftSampler:[34,3,1,""],StructuralGap:[29,3,1,""],StructuralGapList:[29,3,1,""]},"promod3.modelling.AllAtomRelaxer":{GetSystemCreator:[32,4,1,""],Run:[32,4,1,""],UpdatePositions:[32,4,1,""]},"promod3.modelling.BackboneRelaxer":{AddCARestraint:[32,4,1,""],AddCBRestraint:[32,4,1,""],AddCRestraint:[32,4,1,""],AddNRestraint:[32,4,1,""],AddORestraint:[32,4,1,""],GetNonBondedCutoff:[32,4,1,""],Run:[32,4,1,""],SetNonBondedCutoff:[32,4,1,""]},"promod3.modelling.CCD":{CCD:[32,4,1,""],Close:[32,4,1,""]},"promod3.modelling.CCDCloser":{Close:[34,4,1,""]},"promod3.modelling.CTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.CloserBase":{Close:[34,4,1,""]},"promod3.modelling.CoolerBase":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.DeNovoCloser":{Close:[34,4,1,""]},"promod3.modelling.DirtyCCDCloser":{Close:[34,4,1,""]},"promod3.modelling.ExponentialCooler":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.FraggerHandle":{Get:[28,4,1,""],GetList:[28,4,1,""],LoadCached:[28,4,1,""],SaveCached:[28,4,1,""]},"promod3.modelling.FragmentSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.FullGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.GapExtender":{Extend:[29,4,1,""]},"promod3.modelling.KIC":{Close:[32,4,1,""],KIC:[32,4,1,""]},"promod3.modelling.KICCloser":{Close:[34,4,1,""]},"promod3.modelling.LinearScorer":{GetScore:[34,4,1,""]},"promod3.modelling.LoopCandidates":{Add:[31,4,1,""],AddFragmentInfo:[31,4,1,""],ApplyCCD:[31,4,1,""],ApplyKIC:[31,4,1,""],CalculateAllAtomScores:[31,4,1,""],CalculateBackboneScores:[31,4,1,""],CalculateSequenceProfileScores:[31,4,1,""],CalculateStemRMSDs:[31,4,1,""],CalculateStructureProfileScores:[31,4,1,""],Extract:[31,4,1,""],FillFromDatabase:[31,4,1,""],FillFromMonteCarloSampler:[31,4,1,""],GetClusteredCandidates:[31,4,1,""],GetClusters:[31,4,1,""],GetFragmentInfo:[31,4,1,""],GetLargestCluster:[31,4,1,""],GetSequence:[31,4,1,""],HasFragmentInfos:[31,4,1,""],Remove:[31,4,1,""]},"promod3.modelling.ModellingHandle":{Copy:[35,4,1,""],all_atom_scorer:[35,5,1,""],all_atom_scorer_env:[35,5,1,""],all_atom_sidechain_env:[35,5,1,""],backbone_scorer:[35,5,1,""],backbone_scorer_env:[35,5,1,""],fragger_handles:[35,5,1,""],gaps:[35,5,1,""],model:[35,5,1,""],modelling_issues:[35,5,1,""],profiles:[35,5,1,""],psipred_predictions:[35,5,1,""],seqres:[35,5,1,""],sidechain_reconstructor:[35,5,1,""]},"promod3.modelling.ModellingIssue":{Severity:[35,3,1,""],is_major:[35,4,1,""],residue_list:[35,5,1,""],severity:[35,5,1,""],text:[35,5,1,""]},"promod3.modelling.ModellingIssue.Severity":{MAJOR:[35,5,1,""],MINOR:[35,5,1,""]},"promod3.modelling.MotifMatch":{alignment:[28,5,1,""],mat:[28,5,1,""],query_idx:[28,5,1,""]},"promod3.modelling.MotifQuery":{GetIdentifiers:[28,4,1,""],GetN:[28,4,1,""],GetPositions:[28,4,1,""],Load:[28,4,1,""],Save:[28,4,1,""]},"promod3.modelling.NTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.PhiPsiSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.SamplerBase":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.ScoreContainer":{Contains:[31,4,1,""],Copy:[31,4,1,""],Extend:[31,4,1,""],Extract:[31,4,1,""],Get:[31,4,1,""],GetNumCandidates:[31,4,1,""],IsEmpty:[31,4,1,""],LinearCombine:[31,4,1,""],Set:[31,4,1,""]},"promod3.modelling.ScorerBase":{GetScore:[34,4,1,""]},"promod3.modelling.ScoringGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.ScoringWeights":{GetAllAtomScoringKeys:[31,4,1,""],GetAllAtomWeights:[31,4,1,""],GetBackboneScoringKeys:[31,4,1,""],GetBackboneWeights:[31,4,1,""],GetSequenceProfileScoresKey:[31,4,1,""],GetStemRMSDsKey:[31,4,1,""],GetStructureProfileScoresKey:[31,4,1,""],GetWeights:[31,4,1,""],SetAllAtomScoringKeys:[31,4,1,""],SetBackboneScoringKeys:[31,4,1,""],SetSequenceProfileScoresKey:[31,4,1,""],SetStemRMSDsKey:[31,4,1,""],SetStructureProfileScoresKey:[31,4,1,""],SetWeights:[31,4,1,""]},"promod3.modelling.ShiftExtension":{Extend:[29,4,1,""]},"promod3.modelling.SidechainReconstructionData":{disulfid_bridges:[36,5,1,""],env_pos:[36,5,1,""],is_c_ter:[36,5,1,""],is_n_ter:[36,5,1,""],loop_lengths:[36,5,1,""],loop_start_indices:[36,5,1,""],rotamer_res_indices:[36,5,1,""]},"promod3.modelling.SidechainReconstructor":{AttachEnvironment:[36,4,1,""],Reconstruct:[36,4,1,""]},"promod3.modelling.SoftSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.StructuralGap":{Copy:[29,4,1,""],ExtendAtCTerm:[29,4,1,""],ExtendAtNTerm:[29,4,1,""],GetChain:[29,4,1,""],GetChainIndex:[29,4,1,""],GetChainName:[29,4,1,""],GetLength:[29,4,1,""],IsCTerminal:[29,4,1,""],IsNTerminal:[29,4,1,""],IsTerminal:[29,4,1,""],ShiftCTerminal:[29,4,1,""],after:[29,5,1,""],before:[29,5,1,""],full_seq:[29,5,1,""],length:[29,5,1,""],seq:[29,5,1,""]},"promod3.scoring":{AllAtomClashScorer:[39,3,1,""],AllAtomInteractionScorer:[39,3,1,""],AllAtomOverallScorer:[39,3,1,""],AllAtomPackingScorer:[39,3,1,""],AllAtomScorer:[39,3,1,""],BackboneOverallScorer:[41,3,1,""],BackboneScoreEnv:[40,3,1,""],BackboneScorer:[41,3,1,""],CBPackingScorer:[41,3,1,""],CBetaScorer:[41,3,1,""],ClashScorer:[41,3,1,""],ConstraintFunction:[40,3,1,""],ContactFunction:[40,3,1,""],DiscoContainer:[40,3,1,""],HBondScorer:[41,3,1,""],LoadAllAtomInteractionScorer:[39,1,1,""],LoadAllAtomPackingScorer:[39,1,1,""],LoadCBPackingScorer:[41,1,1,""],LoadCBetaScorer:[41,1,1,""],LoadDefaultAllAtomOverallScorer:[39,1,1,""],LoadDefaultBackboneOverallScorer:[41,1,1,""],LoadHBondScorer:[41,1,1,""],LoadReducedScorer:[41,1,1,""],LoadSSAgreementScorer:[41,1,1,""],LoadTorsionScorer:[41,1,1,""],PairwiseFunction:[40,3,1,""],PairwiseFunctionType:[40,3,1,""],PairwiseScorer:[41,3,1,""],ReducedScorer:[41,3,1,""],SCWRL3DisulfidScore:[43,4,1,""],SCWRL3PairwiseScore:[43,4,1,""],SSAgreementScorer:[41,3,1,""],TorsionScorer:[41,3,1,""]},"promod3.scoring.AllAtomClashScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""]},"promod3.scoring.AllAtomInteractionScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""],Load:[39,4,1,""],LoadPortable:[39,4,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomOverallScorer":{AttachEnvironment:[39,4,1,""],CalculateLinearCombination:[39,4,1,""],Contains:[39,4,1,""],Get:[39,4,1,""],__getitem__:[39,4,1,""],__setitem__:[39,4,1,""]},"promod3.scoring.AllAtomPackingScorer":{DoNormalize:[39,4,1,""],Load:[39,4,1,""],LoadPortable:[39,4,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomScorer":{AttachEnvironment:[39,4,1,""],CalculateScore:[39,4,1,""],CalculateScoreProfile:[39,4,1,""]},"promod3.scoring.BackboneOverallScorer":{AttachEnvironment:[41,4,1,""],Calculate:[41,4,1,""],CalculateLinearCombination:[41,4,1,""],Contains:[41,4,1,""],Get:[41,4,1,""],__getitem__:[41,4,1,""],__setitem__:[41,4,1,""]},"promod3.scoring.BackboneScoreEnv":{AddPairwiseFunction:[40,4,1,""],ApplyPairwiseFunction:[40,4,1,""],ClearEnvironment:[40,4,1,""],Copy:[40,4,1,""],GetSeqres:[40,4,1,""],Pop:[40,4,1,""],SetEnvironment:[40,4,1,""],SetInitialEnvironment:[40,4,1,""],SetPsipredPrediction:[40,4,1,""],Stash:[40,4,1,""]},"promod3.scoring.BackboneScorer":{AttachEnvironment:[41,4,1,""],CalculateScore:[41,4,1,""],CalculateScoreProfile:[41,4,1,""]},"promod3.scoring.CBPackingScorer":{DoNormalize:[41,4,1,""],Load:[41,4,1,""],LoadPortable:[41,4,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.CBetaScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,4,1,""],LoadPortable:[41,4,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.ClashScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.DiscoContainer":{AddStructuralInfo:[40,1,1,""],AttachConstraints:[40,1,1,""]},"promod3.scoring.HBondScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,4,1,""],LoadPortable:[41,4,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.PairwiseFunction":{Score:[40,4,1,""]},"promod3.scoring.PairwiseScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.ReducedScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,4,1,""],LoadPortable:[41,4,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.SSAgreementScorer":{DoNormalize:[41,4,1,""],Load:[41,4,1,""],LoadPortable:[41,4,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetScore:[41,4,1,""]},"promod3.scoring.TorsionScorer":{DoNormalize:[41,4,1,""],Load:[41,4,1,""],LoadPortable:[41,4,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.sidechain":{AAToRotID:[49,4,1,""],BBDepRotamerLib:[51,3,1,""],CreateSCWRL3Particle:[49,4,1,""],CreateSCWRL4Particle:[49,4,1,""],CreateVINAParticle:[49,4,1,""],DihedralConfiguration:[51,3,1,""],DisulfidScore:[44,4,1,""],FRMRotamer:[49,3,1,""],FRMRotamerGroup:[49,3,1,""],Frame:[45,3,1,""],FrameResidue:[45,3,1,""],GetDihedralConfiguration:[51,4,1,""],GetRotamericConfiguration:[51,4,1,""],LoadBBDepLib:[48,4,1,""],LoadLib:[48,4,1,""],PScoringFunction:[49,3,1,""],Particle:[49,3,1,""],RRMRotamer:[49,3,1,""],RRMRotamerGroup:[49,3,1,""],ReadDunbrackFile:[48,4,1,""],ResolveCysteins:[44,4,1,""],RotamerConstructor:[50,3,1,""],RotamerGraph:[46,3,1,""],RotamerID:[49,3,1,""],RotamerLib:[51,3,1,""],RotamerLibEntry:[51,3,1,""],SCWRL3RotamerConstructor:[50,3,1,""],SCWRL4ParticleType:[49,3,1,""],SCWRL4RotamerConstructor:[50,3,1,""],SubrotamerOptimizer:[52,4,1,""],TLCToRotID:[49,4,1,""],VINAParticleType:[49,3,1,""],VINARotamerConstructor:[50,3,1,""]},"promod3.sidechain.BBDepRotamerLib":{AddRotamer:[51,4,1,""],Load:[51,4,1,""],LoadPortable:[51,4,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""],SetInterpolate:[51,4,1,""]},"promod3.sidechain.FRMRotamer":{AddFrameEnergy:[49,4,1,""],AddSubrotamerDefinition:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetActiveSubrotamer:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetNumSubrotamers:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],GetSubrotamerDefinition:[49,4,1,""],GetTemperature:[49,4,1,""],SetActiveSubrotamer:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],SetTemperature:[49,4,1,""],ToFrameResidue:[49,4,1,""],ToRRMRotamer:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FrameResidue":{__getitem__:[45,4,1,""],__len__:[45,4,1,""]},"promod3.sidechain.Particle":{GetCollisionDistance:[49,4,1,""],GetName:[49,4,1,""],GetPos:[49,4,1,""],GetScoringFunction:[49,4,1,""],PairwiseScore:[49,4,1,""]},"promod3.sidechain.RRMRotamer":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],ToFrameResidue:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructBackboneFrameResidue:[50,4,1,""],ConstructRRMRotamerGroup:[50,4,1,""],ConstructSidechainFrameResidue:[50,4,1,""]},"promod3.sidechain.RotamerGraph":{CreateFromFRMList:[46,4,1,""],CreateFromRRMList:[46,4,1,""]},"promod3.sidechain.RotamerLib":{AddRotamer:[51,4,1,""],Load:[51,4,1,""],LoadPortable:[51,4,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""]},"promod3.sidechain.RotamerLibEntry":{FromResidue:[51,4,1,""],IsSimilar:[51,4,1,""],SimilarDihedral:[51,4,1,""],chi1:[51,5,1,""],chi2:[51,5,1,""],chi3:[51,5,1,""],chi4:[51,5,1,""],probability:[51,5,1,""],sig1:[51,5,1,""],sig2:[51,5,1,""],sig3:[51,5,1,""],sig4:[51,5,1,""]},"promod3.sidechain.SCWRL3RotamerConstructor":{AssignInternalEnergies:[50,4,1,""]},"promod3.sidechain.SCWRL4RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFrameResidue:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""]},"promod3.sidechain.VINARotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFRMRotamerHeuristic:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""],ConstructRRMRotamerHeuristic:[50,4,1,""]},"test_actions.ActionTestCase":{RunAction:[1,4,1,""],RunExitStatusTest:[1,4,1,""],pm_action:[1,5,1,""],pm_bin:[1,5,1,""],testPMExists:[1,4,1,""]},promod3:{SetCompoundsChemlib:[15,1,1,""],core:[12,2,0,"-"],loop:[23,2,0,"-"],modelling:[30,2,0,"-"],scoring:[42,2,0,"-"],sidechain:[47,2,0,"-"]},test_actions:{ActionTestCase:[1,3,1,""]}},objnames:{"0":["cmake","command","CMake command"],"1":["py","function","Python function"],"2":["py","module","Python module"],"3":["py","class","Python class"],"4":["py","method","Python method"],"5":["py","attribute","Python attribute"],"6":["std","cmdoption","program option"]},objtypes:{"0":"cmake:command","1":"py:function","2":"py:module","3":"py:class","4":"py:method","5":"py:attribute","6":"std:cmdoption"},terms:{"0288eced23a9a541a88005a7ed30b8f019e06226":3,"10a":36,"1ake":28,"1aki":26,"1crn":[21,23,25,26,30,31,32,34,35,36,42,47],"1crn_cut":[30,31,35],"1crna":[26,31],"1e2q":28,"1ey":8,"1eye_rec":8,"1ko5":28,"20a":36,"2iyw":28,"2jlp":0,"30a":36,"3x3":9,"655a":26,"abstract":[34,50],"boolean":[11,13,35],"break":[3,4,8,16],"byte":[10,37],"case":[0,1,5,8,13,16,22,26,27,28,29,32,34,35,36,37,41,44,47,49,50,51],"catch":26,"char":[22,37],"class":[0,1,3,5,8,9,10,12,13,14,17,20,23,25,28,30,32,34,35,37,42,45,46,49,50,51],"const":37,"default":[0,1,2,3,4,5,8,10,13,14,15,18,21,22,25,26,27,28,30,31,32,34,36,39,41,47,49,50],"enum":[26,49],"export":[8,21],"final":[8,18,26,28,30,31,35,40,42,44,46,47,49],"float":[9,10,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,49,50,51,52],"function":[0,1,3,8,10,13,14,15,16,17,19,21,22,25,26,28,30,31,32,33,34,35,37,38,39,41,42,44,46,47,51,54],"import":[0,1,5,7,8,11,13,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,42,47,49,50],"int":[1,9,10,11,14,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,45,49,50,51,52],"long":35,"new":[1,3,7,8,13,16,17,21,22,25,26,29,31,32,34,35,36,37,38,47,49],"null":26,"public":[8,37,49],"return":[1,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,45,48,49,50,51],"s\u00f6ding":38,"short":[8,16,35,37],"static":[8,14,21,25,26,27,28,31,36,37,39,41,46,48,51],"super":47,"switch":[8,16,40],"throw":[1,37,47,48],"true":[1,11,13,14,21,22,23,25,26,28,29,31,32,33,34,35,36,37,39,41,44,47,50],"try":[1,8,18,29,35,37,51],"void":37,"while":[1,4,8,14,20,21,25,35,37,49],AND:[20,39,41,50],Added:3,Adding:[3,4],And:26,But:[1,4,8,16,35,50],CYS:[25,36,49,51],FOR:20,For:[1,2,5,8,12,13,16,18,20,21,25,26,28,31,34,35,36,37,40,41,44,49,50,51],HIS:[21,25,49,51],Has:4,IDs:49,ILE:[27,49],Into:[30,54],Its:[4,16,19],LYS:49,NOT:5,Not:20,One:[16,21,22,26,28,35,40,44,49,52],RMS:33,Res:[21,31,34,35,39,40,41],That:[0,1,4,8,11,13,16,26,28,41],Thats:52,The:[0,2,3,4,8,10,11,13,14,17,18,19,20,23,24,25,28,29,30,32,33,34,37,38,39,40,41,42,43,44,46,47,48,52,54],Then:[4,8,11,35],There:[1,4,5,8,10,13,16,25,26,27,34,39,41,48,49],These:[1,2,4,26,28,29,34,35],USE:20,Use:[0,4,25,26,27,35,39,41,51],Used:[31,35],Useful:[21,25,36],Uses:[31,35],Using:[4,17,25,54],Will:35,With:[8,30,35,51],__doc__:[11,13],__getitem__:[26,39,41,45,49],__init__:[1,8,13,16],__len__:[22,26,45,49],__main__:[1,8],__name__:[1,8],__setitem__:[26,39,41],_data:37,_name:4,_run:[1,4],_xml:4,a3m:[0,13],a3mtoprofil:[0,13],aa1:41,aa2:41,aa_aft:26,aa_befor:26,aa_clash:[35,39],aa_interact:[35,39],aa_pack:[35,39],aa_packing_scor:37,aa_relax_test:32,aa_res_idx:50,aa_scor:37,aa_with_rotam:47,aaa1:39,aaa2:39,aaa:[21,39],aaaaaaaa:22,aaaaggggggggggggggggggggaaaaaa:35,aafrequ:26,aafrequenciesstruct:26,aah:21,aatorotid:49,abcd:35,abcdef:35,abcdefghi:35,abcdefghij:35,abcdefghijklmnopqrstuvwxyz0123456789abcdefghijklmnopqrstuvwxyz:35,abil:16,abl:[2,8,35],abort:[8,10,32,35],about:[1,4,8,10,26,28,35],abov:[0,1,5,8,13,16,20,22,29,31,35,37,49,51],absolut:[4,5,34],academ:8,accept:[10,13,20,31,32,34,35,36,37],acceptor:[41,49,50],access:[4,5,8,21,22,26,27,31,35,39,40,41,49],accessor:26,accord:[0,5,10,16,21,22,25,26,27,28,29,31,34,35,36,39,44,47,49,50,51],accordingli:[26,40],account:[8,53],accumul:28,accur:28,accuraci:[0,28,35,38],achiev:[10,16],acid:[22,23,24,26,32,35,36,41,43,46,47,49,51],acknowledg:8,across:[1,51],act:[20,32],acta:38,action:[3,7,13,16,17,18,19,32,54],action_nam:16,action_unit_test:1,actiontest:1,actiontestcas:8,activ:[13,14,16,35,44,49,52],active_internal_energi:52,actual:[3,8,13,16,22,26,28,34,35,36,40,41,42,50,51],actual_posit:34,actual_step:34,adapt:[8,25,26,32,34,35,38],add:[1,2,4,6,8,10,13,18,20,21,26,27,28,31,32,35,36,39,40,41,44,47,49,50,53],add_argu:11,add_custom_target:8,add_doc_depend:4,add_doc_sourc:[4,8],add_flag:28,add_subdirectori:8,addalign:13,addcarestraint:32,addcbrestraint:32,addcoordin:26,addcrestraint:32,added:[0,4,8,10,13,21,22,26,28,29,31,33,35,36,39,40,41,49,50,51],addedg:10,addendum:20,addfrag:[13,26],addfragmentinfo:31,addframeenergi:49,addharmonicangl:25,addharmonicbond:25,addharmonicimprop:25,adding:[0,2,4,8,13,14,16,26,45],addit:[3,4,11,13,14,16,20,22,23,25,26,33,35,37],addition:[1,4,16,21,25,26,28],addljpair:25,addmodellingissu:35,addnod:10,addnrestraint:32,addorestraint:32,addpairwisefunct:40,addperiodicdihedr:25,addperiodicimprop:25,addprofil:13,addresidu:28,address:37,addrotam:51,addseqidparamet:26,addseqsimparamet:[23,26],addsequenceprofileparamet:26,addssagreeparamet:26,addstructur:13,addstructuralinfo:40,addstructureprofileparamet:26,addsubrotamerdefinit:49,addtorsionprobabilityparamet:26,addureybradleyangl:25,admir:8,advanc:28,advantag:25,advic:[8,16],advis:20,affect:[8,22,35,49,50],after:[1,2,4,5,8,10,13,16,21,22,25,26,27,29,31,32,34,35,37,40,51],after_c_stem:22,afterward:[8,26,35],again:[2,3,8,26,28,50],against:[20,28,39],agg:27,agglom:31,ago:1,agre:20,agreement:[13,20,26,28,41],agress:[2,10],aim:19,ala:[22,27,32,47,49,50,51],ala_cb:21,ala_h1:21,ala_h:21,alanin:[3,49],alg:[23,26,35],algorithm:[3,10,19,22,23,26,30,31,32,34,35,38,42,43,46,47,49,54],alia:29,align:[0,3,13,18,26,28,30,38,40],alignedcuboid:22,alignmenthandl:[28,35,40],alignmentlist:[0,13,35],all:[0,1,2,3,4,7,8,10,13,14,16,18,19,20,22,23,25,26,27,28,29,30,31,33,34,35,36,37,40,41,42,44,45,47,48,49,50,51,52,54],all_atom:[21,22,25,49],all_atom_env:21,all_atom_po:[21,50],all_atom_scor:35,all_atom_scorer_env:35,all_atom_sidechain_env:35,all_po:[21,25,32],all_scor:31,allatom:[32,35,36],allatomclashscor:[35,42],allatomenv:[23,32,35,36,39],allatomenvposit:[23,36],allatominteractionscor:[35,37,42],allatomoverallscor:[31,35,42],allatompackingscor:[35,37,42],allatomposit:[23,25,49,50],allatomrelax:[25,32],allatomscor:42,alleg:20,alloc:26,allow:[0,2,3,5,8,11,16,22,26,27,28,31,34,35,37,39,41,46,51],allow_multitempl:13,allow_prepro_ci:22,almost:[4,32,35],aln:[0,28,30,31,35,40],aln_preprocess:35,aln_sourc:13,alon:[11,20],along:[1,8,20],alongsid:20,alot:8,alpha:[9,22,41,47],alpha_bin:41,alreadi:[1,4,8,10,16,22,25,26,28,31,35,36,39,40,41,49,50,51,52],also:[1,2,4,8,11,16,20,26,27,28,31,32,33,34,35,36,44,45,46,50,51],alter:[31,34],altern:[4,5,8,31,34,35,48,50],alwai:[0,1,8,16,29,34,35,37],amber:[21,35],ambig:51,ambigu:[0,13,51],amino:[22,23,24,26,32,35,36,41,43,46,47,49,51],aminoacid:[21,22,25,27,41,49,51],aminoacidatom:[21,39],aminoacidhydrogen:21,aminoacidlookup:[21,25],among:31,amount:[3,18,28,51],analog:28,analysi:[32,33,38],analyt:[31,51],anchor:[9,21,35],ancient:15,angl:[0,9,21,22,23,25,26,31,32,33,34,35,41,47,50,51,54],angle_bin:41,angle_bin_s:26,angle_force_const:25,angle_four:9,angle_on:9,angle_thre:9,angle_two:9,angstrom:[26,32],ani:[0,1,4,5,8,10,13,14,15,18,20,21,22,25,26,27,28,29,31,33,34,35,36,37,39,40,41,45,47,49,50],anneal:[10,31,34],annot:20,announc:[1,8],anoth:[4,14,22,29,32,35,36,44],anymor:[3,10,28,35],anyon:[8,16],anyth:[0,2,5,8,13,14,15,28,31,32,36,39,41],anywai:8,anywher:16,apach:[3,20],apart:[1,31,35,36,39,41],api:[8,17],appear:20,append:[0,13,22,26,27,28,35,47],appendix:20,appli:[3,7,10,11,15,16,20,22,26,28,29,31,32,34,35,36,38,40,44,47,49,51],applic:[1,20,32,50],applyccd:31,applyde:10,applyedgedecomposit:10,applyk:31,applyonresidu:[47,49],applypairwisefunct:[40,41],applysd:25,applyselfenergythresh:[47,49],applytransform:[22,28],approach:[0,2,10,26,28,35,37,44,47,50],appropri:[10,20,27,35,37,50],approx:35,approxim:25,arbitrari:[3,7,21,26,44],arbitrarili:34,archiv:20,arendal:38,arg:[1,4,13,49],arg_ca:21,arg_hd3:21,arg_sorted_scor:31,arginin:49,argpars:13,argument:[0,1,2,4,11,12,34,40],argumentpars:13,argv:13,aris:20,around:[1,4,8,9,16,22,31,32,35,39,40,41,51],arrai:[0,8,37],arrang:28,artifici:26,ascend:29,ask:8,asn:[49,51],asn_c:21,asn_hb2:21,asp:[21,49,51],asp_ha:21,asp_o:21,asparagin:49,aspart:[49,51],ass:34,assembl:13,assemblepars:13,assert:20,assertequ:8,assess:[39,40],assign:[3,10,22,26,31,34,39,41,50,52],assigninternalenergi:50,assignsecstruct:35,associ:[20,26,29,45],assum:[1,4,5,8,20,25,26,32,35,37,40,41,44,50],assur:44,astar:3,astarsolv:10,atom:[3,8,9,22,23,25,26,28,30,31,33,35,36,40,41,42,44,45,49,50,51,54],atom_idx:[21,25],atom_nam:[21,25],atomhandl:50,atomseq:35,atp:28,atp_at:28,atp_idx:28,atp_list:28,atp_r:28,atp_sel:28,atp_view:28,attach:[0,4,8,13,20,21,25,28,29,31,35,36,39,40,41,42],attach_view:13,attachconstraint:40,attachenviron:[31,32,34,36,39,41,42],attachview:[30,31,35],attent:[1,16],attribut:[8,13,20,26,35,36,51],author:20,authorship:20,autodock:[38,49],autom:[2,4],automat:[1,8,10,11,14,16,26,30,31,37,50,51],automatis:8,avaibl:50,avail:[1,2,3,5,8,15,16,18,20,25,26,31,34,35,40,47,49],availab:20,availabl:8,averag:[31,40,44],avg:26,avg_sampling_per_posit:28,avoid:[0,3,6,11,13,15,26,28,32,34],awai:[16,36],awar:[0,3,8,35,50],awesom:[1,8],axi:[9,22],back:[1,16,25,34],backbon:[0,3,7,9,18,21,22,26,27,28,29,30,31,34,35,36,38,42,45,47,48,49,50,54],backbone_scor:35,backbone_scorer_env:35,backbonelist:[7,18,21,23,26,28,29,31,32,34,35,40],backboneoverallscor:[28,31,34,35,42],backbonerelax:[32,35],backbonescor:[8,42],backbonescoreenv:[8,28,31,34,35,41,42],backbonescoreenvlisten:8,background:[2,36],backrub:[22,38],backward:[2,3,37],bad:[25,35],bare:26,base:[0,3,4,5,9,11,13,19,20,22,23,27,28,31,32,34,35,37,38,40,42,47,49,50,51],base_target:4,baseclass:47,basel:[8,53],bashrc:8,basi:[4,8,16,20,28,32,34,48],basic:[1,2,8,11,16,27,34,35,47,51],bb_dep_lib:37,bb_list:[7,18,21,22,23,26,29,31,32,34,35,40],bb_list_on:28,bb_list_two:28,bb_score:31,bbdeprotamerlib:[35,36,37,48,50,51],bcde:35,becaus:[8,16,21,28,35,40],becom:[10,35,51],been:[2,3,10,16,20,24,26,31,32,35,39,41,44,51],befor:[0,1,4,7,8,13,16,22,25,26,27,29,31,32,34,35,36,37,50],begin:[1,8,21,22,28,34,40],behalf:20,behav:[1,51],behaviour:[0,13,39,40,49,50,51],behind:8,being:[3,5,8,10,21,26,28,31,34,35,44,51],believ:53,bell:8,belong:[3,4,16,21,22,26,29,31,34,35,36,39,40,41,45,49,50],belov:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:37,categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[8,14,15,17,18,20,54],cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,6,7,8,11,13,14,15,16,17,18,19,20,21,22,26,27,33,35,47,49,53],codetest:[4,8],coil:[24,28],collect:[11,14,21,28,40],collis:49,column:[26,28,35],combin:[20,25,26,27,28,31,34,35,38,39,41,44,49,51],come:[1,3,4,8,11,13,35,36,42,46,51],command:[0,1,7,8,11,12,16,18,54],commandlin:13,comment:[16,20],commerci:[8,20],commit:[3,8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib:50,compar:[3,8,22,23,26,31,32,51],comparison:[35,38,51],compat:[2,3,16,25,37],compensatori:22,compil:[1,2,3,4,8,14,16,18,20,37,54],complain:1,complaint:16,complet:[14,16,22,25,32,34,35,36,51],complex:[8,16,36,44,49,52],compli:20,complianc:20,complib_dir_contain:[5,7],complib_dir_localhost:[5,7],compon:[5,7,10,15,26,33,41,50],compound:[3,15,50],compoundlib:[5,50],compress:[11,26],comput:[3,8,19,20,31,33,38,39,41],concaten:21,concept:8,concern:8,condit:[8,20,27],conf:[2,8],confid:[26,41],config:[4,8],config_head:4,configur:[2,8,10,16,20,31,47],conflict:16,conform:[26,32,34,38,46,51],connect:[4,5,7,10,16,21,25,26,31],connectivi:5,conop:[5,21,22,25,27,41,49,50],conquer:8,consecut:[26,27,35,41],consequenti:20,conserv:[18,29],consid:[0,4,8,10,13,14,16,21,22,26,27,28,31,32,34,35,36,39,40,41,44,47,49,50,51,53],consider_all_nod:10,consider_hydrogen:49,consider_ligand:36,consist:[3,8,20,21,25,28,29,31,32,34,35,36,37,40,44,49,51],conspicu:20,constant:[3,25,32,39,41,52],constitut:20,constraint:[13,26,32,34,40],constraintfunct:40,constru:20,construct:[0,3,9,21,22,26,28,29,34,35,37,42,43,45,49,50,51],constructatompo:9,constructbackboneframeresidu:[47,50],constructcbetapo:9,constructcterminaloxygen:9,constructetd:10,constructframeresidu:50,constructframeresidueheurist:50,constructfrmrotamergroup:[47,50],constructfrmrotamerheurist:50,constructor:[21,25,28,29,32,34,37,40,41,47,49,54],constructrrmrotamergroup:50,constructrrmrotamerheurist:50,constructsidechainframeresidu:50,contact:[40,53],contactfunct:40,contain:[0,1,2,3,4,5,7,8,9,11,13,16,18,19,20,21,22,24,25,26,27,28,31,34,35,36,39,40,41,42,44,45,47,49,50,51,54],content:[8,12,17,20,23,26,42,47,54],contigu:[25,36,37],continu:[1,21,29,32,47],contract:20,contrast:45,contribut:[4,10,16,17,19,20,54],contributor:20,contributori:20,control:[0,3,8,10,20,31,34,36,40,49,50,51,52],conveni:[1,8,18,28,31,34,35,42,49,50,51],convent:[1,49],converg:[28,31,32,34],convers:[20,37],convert:[4,5,22,25,26,27,35,37,39,41,51,52],convert_module_data:4,convertbasetyp:37,cooler:[3,30,31],coolerbas:34,cooling_factor:[10,34],coord:[26,31],coord_idx:26,coordin:[3,9,26,28,31,32,34,35,38,39,47],coordinfo:26,cope:16,copi:[2,3,4,8,16,18,20,21,22,28,29,31,34,35,40],copyright:20,copyright_cmak:20,core:[0,8,9,10,11,13,14,19,35,37,46,53,54],correct:[5,25,50],correctli:35,correspond:[0,10,16,21,22,25,26,27,28,31,37,49,50,51],corrupt:[21,40],could:[1,4,5,8,13,16,25,26,35],couldn:35,count:[14,28,29,34,35,39,41],countenclosedgap:29,countenclosedinsert:29,counter:[28,34],counterclaim:20,counterpart:[31,41,50],coupl:[1,8,16,35],cours:8,coutsia:38,coutsias2005:[32,38],coval:49,cover:[0,1,8,12,13,14,21,25,28,30,34,35],coverag:[0,3,35],cparticl:49,cpp:4,cpr:[49,51],cpu:[18,25,35],cpu_platform_support:25,crambin:[26,31,34],crash:47,creat:[2,4,5,7,8,9,10,13,16,17,21,22,23,26,27,28,30,34,35,39,41,47,48,49,50,51],createalign:[31,35],createemptyview:28,createentityfromview:[28,36,47],createfromfrmlist:[46,47],createfromrrmlist:46,createfullview:[30,31,35],createscwrl3particl:49,createscwrl4particl:49,createsequ:[26,31,35],createvinaparticl:49,creation:[25,32,49],creator:[25,32],criteria:36,criterion:[10,34],criterium:31,croak:16,cross:[20,28],crucial:8,crude:[0,35],cryst:38,cterminalclos:34,cumul:50,current:[2,4,5,8,10,14,16,21,22,25,26,31,34,35,37,40,41,42,49,50,52],custom:[8,26,34,35,36,37,48,49],customari:20,cutoff:[24,25,31,32,36,39,41],cycl:29,cyclic:[31,32,38],cyd:[49,51],cyh:[49,51],cys_hb3:21,cys_sg:21,cystein:[25,36,44,47,49],d_bin:41,dai:11,damag:20,dampen:25,danc:38,dare:4,dat:[26,37],data1:4,data2:4,data:[0,1,3,4,8,16,17,21,23,24,25,28,29,30,31,32,34,35,36,40,42,47,49,54],data_:37,data_gener:[3,37,48],data_to_stor:26,data_typ:26,databas:[0,9,23,24,28,31,35],databs:26,datatyp:26,date:[5,7,16,20],davi:38,davis2006:[22,38],dbg:8,dcmake_install_prefix:2,deactiv:10,dead:[10,38],deal:[35,36],debug:[8,10,21],decent:15,decid:[3,8,32,50],decis:27,declar:[4,8,16],decod:13,decompos:[3,10],decomposit:[10,28,46],decreas:34,dedic:[4,8,16],dee:10,deep:[22,35],def:[1,8,21,35],def_angl:21,defend:20,defin:[1,4,8,9,13,14,15,20,21,22,23,24,25,28,29,31,32,34,35,36,37,39,40,41,44,49,50,51],definem:8,definit:[8,20,26,27,31,41,49],degre:[22,26,27],delet:[0,2,8,22,35,49],deletegapcol:35,deliber:20,deliv:[1,26,34,35],delta_scor:34,demand:35,demonstr:26,denovoclos:34,densiti:[22,32,38],dep1:4,dep2:4,dep:4,depend:[0,3,4,8,10,13,18,22,25,26,27,28,31,35,36,37,38,39,40,41,47,48,49,54],dependency1:4,dependency2:4,depends_on:4,depth:[26,38],deriv:[1,20,26,38,43,44],descend:35,descent:[31,32,38],describ:[0,4,7,8,10,11,17,20,21,22,26,28,29,30,32,33,37,39,41,44,47,48,49,50,51,54],descript:[0,5,13,16,20,34,35,51],descriptor:[26,28],descsrib:10,design:[1,3,19,20],desir:[9,18,25,26,31,32,34,35,39,40,41],despit:3,detail:[0,3,9,13,16,20,25,26,27,31,33,34,35,39,41,48,49,51],detect:[0,11,28,30,38,44],determin:[8,11,20,25,26,31,34,40,41],determinist:28,deuterium:[35,50],develop:[1,3,8,16,19,53],deviat:[22,33,34,51],devot:12,dict:[4,28,31,33,34,39,41],dictionari:[4,5,13,15,33,38],did:[8,26,31,35],didn:[7,28],didnt:5,diff:10,differ:[1,2,4,7,8,10,15,16,20,21,26,28,29,31,35,39,41,47,49,51],differenti:49,dihedr:[7,9,18,22,23,25,26,32,34,35,41,50,51,54],dihedral_angl:22,dihedral_bin:41,dihedral_idx:51,dihedral_pair:27,dihedralconfigur:51,dill:38,dimens:27,dimension:38,dir:[4,8,18],direct:[8,20,22,24,26,41,49,50],directli:[8,10,18,26,31,35,36,40,44,49,51,53],directori:[1,2,4,5,7,8,17,26,48],dirti:1,dirtyccdclos:34,disabl:[1,16,35],disable_doctest:2,disable_document:2,disable_linkcheck:2,discard:26,disclaim:20,discocontain:40,disconnect:3,discret:[28,39,41],discuss:[20,26],disk:[8,25,28,39,41,51],displai:[7,11,13,14,20],displaystyl:10,dissimilar:28,dist:41,dist_bin:41,dist_bin_s:26,distanc:[7,9,22,26,28,31,35,36,39,40,41,43,49],distance_thresh:28,distant:40,distinct:[21,28,36,51],distinguish:[3,23,25,37,39,41,51],distribut:[1,8,20,25,26,27,34,37,39,41,48,51],disulfid:[0,25,32,36,43,47,49,51,54],disulfid_bridg:[25,36],disulfid_score_thresh:36,disulfidscor:[36,44],dive:[16,35],diverg:8,divers:[26,28],dng:18,do_it:[39,41],doc:[2,4,8,16,20],dock:38,docker:[3,6,7,54],dockerfil:[5,7],docstr:13,doctest:[2,8,16],document:[1,2,7,16,20,26,53],doe:[1,3,4,8,9,10,11,13,15,16,20,22,26,30,31,34,35,37,40,48],doesn:[8,16,29,32,34,35,51],doesnt:51,doexternalscor:[39,41],doing:[1,5,16,28],dointernalscor:[39,41],domain:28,domin:10,don:[2,10,20,31,35,50],done:[1,8,11,13,16,23,25,27,31,34,35,37],donor:[41,49,50],donorm:[39,41],dont:[0,34],dont_write_bytecod:1,dost_root:2,doubl:28,doubt:13,down:[13,22,26,28,34],download:5,dpm3_runtime_profiling_level:14,draw:[22,27,34],drawback:8,drawn:[27,34],drawphigivenpsi:27,drawpsigivenphi:27,drop:[3,8],dssp:[3,26,41],dssp_state:41,due:[0,26,31,32,35,44],dump:[28,51],dunbrack:[3,38,48],duplic:6,dure:[1,3,21,32,35,37,45,51],dynam:51,dynamicspatialorgan:3,e_cut:10,e_thresh:[10,35],e_tresh:10,each:[0,7,8,10,13,14,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,41],earli:3,earlier:2,easi:8,easier:[1,8,20],easili:[4,16,35],echo:8,edg:[10,28],edge_idx:10,editor:1,editori:20,editxc:28,educ:8,effect:[4,8,10,25,36,44],effici:[21,28,34,38,42],egg:26,eigen3_include_dir:2,eigen:[2,3],either:[0,7,8,13,16,18,20,21,22,27,29,31,32,34,35,36,37,39,40,41,45,49,51],elabor:[8,20],electron:20,electrostat:[25,32],element:[1,10,21,22,26,28,31,33,37,40,44,50],elimin:[10,38],els:[8,16,36,37],emerg:1,empir:[43,44],emploi:16,empti:[8,11,13,22,26,28,31,35,49],enabl:[1,2,3,11,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,52],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,28,33,35,42,47],entityhandl:[13,21,22,26,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,31,32,33,36,41,47,50],entrypoint:5,enumer:[8,10,21,25,26,28,31,35,40,47,49,50,51],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39,41,42,54],epsilon:[10,25,36,52],equal:[28,34,39,41,44,50],equidist:51,equip:5,equival:[28,35,39,41],error:[0,11,13,14,26,32,35,37],especi:28,estim:[10,28,33,34,35,38,41,44,49,50,51],etc:[1,3,8,16,22,26,31,40],evalu:[4,8,32,35,39,40,41,46,47,49,51,54],evaluategromacsposrul:9,even:[2,8,10,20,22,25,29,35],event:[20,28],eventu:13,ever:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,51,52],everyth:[1,2,3,7,8,12,13,16,32,35,36,37,39,54],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,49],exampl:[0,1,2,3,8,11,13,16,17,18,20,21,23,25,26,27,28,30,32,34,35,36,42,47,48,49],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35],exclud:[8,20,26],exclus:[1,8,20,25],execut:[0,2,3,4,7,8,16,18,20,26,33,35],exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,31,32,33,34,35,37,39,40,41,48,49,51],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:[10,34],expect:[1,3,7,21,25,26,35,36,40,44,50,52],expens:26,experiment:35,explain:[1,8],explan:8,explicit:2,explicitli:20,explor:[5,38],exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28,30,31,35,41,46],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,29,35],extension_penalti:29,extent:26,extern:[3,4,5,8,34],external_script:[3,8],extra:[2,3,8,16,22,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:[22,28],eye:1,f_i:26,f_idx:40,f_vinaparticl:49,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,35,51],fall:32,fallback:51,fals:[1,8,10,11,13,22,25,26,29,31,34,35,36,44,47,49,50],fantast:8,far:[31,35],fast:[0,9,18,19,21,25,26,27,37,39,40,41,51],fasta:[0,13,30,35],faster:[10,25,26,32,33,40],fastest:[32,35],favor:33,favourit:1,featur:[16,17,23,28,31,35,37,38,53],fed:[4,16],fedora:8,fee:20,feed:[4,21,31],feel:[8,16],fellow:8,fetch:[13,16,18,28],few:[2,8,16,25,37,42],ff_aa:25,ff_aa_on:25,ff_aa_two:25,ff_ala:25,ff_arg:25,ff_asn:25,ff_asp:25,ff_cy:25,ff_cys2:25,ff_gln:25,ff_glu:25,ff_gly:25,ff_hisd:25,ff_hise:25,ff_ile:25,ff_leu:25,ff_lookup:[25,32,35],ff_lookup_charmm:37,ff_ly:25,ff_met:25,ff_phe:25,ff_pro:25,ff_ser:25,ff_thr:25,ff_trp:25,ff_tyr:25,ff_val:25,ff_xxx:25,fiddl:30,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,7,8,12,13,15,16,17,18,20,25,26,27,28,33,39,41,48,51],filecheck:16,fileexist:11,fileextens:11,filegzip:11,filenam:[0,8,11,13,25,26,27,28,37,39,41,48,51],filenotfound:33,fill:[4,8,13,16,23,26,29,30,31,33,35],fillfromdatabas:[31,35],fillfrommontecarlosampl:[31,35],fillloopsbydatabas:35,fillloopsbymontecarlo:35,filo:40,filtercandid:33,filtercandidateswithsc:33,final_model:[30,35],find:[3,4,7,8,10,16,21,23,28,31,32,35,44,46,48,51,53],findatom:28,findchain:42,findeigen3:20,finder:30,findmotif:28,findwithin:[8,28],fine:8,finish:52,fire:[1,7],first:[0,1,3,8,10,13,16,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,20,22,26,30,31,34,54],fix:[3,8,11,16,25,32,35,36,37,39,41],fix_cterm:32,fix_nterm:32,fix_surrounding_hydrogen:25,flag1:4,flag2:4,flag:[0,2,4,8,10,11,13,22,26,28,35,36,49,50],flanking_rot_angle_on:22,flanking_rot_angle_two:22,fletch:[26,47],fletcher:35,flexibl:[0,19,36,44,47,49,50,52],flip:51,flood:26,fluorin:49,flush:[1,16],fold:38,folder:[2,4,8,16,18,37],follow:[0,1,2,4,5,7,8,10,11,16,18,20,22,23,25,26,28,29,30,31,35,36,37,39,41,47,49,50,51],fontsiz:27,forbidden:8,forc:[25,32,35],force_const:[25,32],forcefield:[23,32,35],forcefieldaminoacid:25,forcefieldbondinfo:25,forcefieldconnect:25,forcefieldharmonicangleinfo:25,forcefieldharmonicimproperinfo:25,forcefieldljpairinfo:25,forcefieldlookup:[25,32,35,37],forcefieldperiodicdihedralinfo:25,forcefieldureybradleyangleinfo:25,forg:16,forget:[1,8],form:[14,20,24,25,26,30,35,40,51],formal:[31,32,49,51],format:[0,5,13,20,26,48],formula:33,forward:16,found:[1,3,4,8,11,13,16,19,21,23,26,28,31,32,33,34,35,36,44,46,49,51],foundat:1,four:[9,34],frac:10,fraction:[26,28,32,34],frag_db:[23,26,31,37],frag_length:[23,26,28],frag_map:26,frag_po:[23,26,28],frag_residu:[23,26],frag_seq:[23,26],frag_siz:26,fragdb:[23,24,26,31,35,37],fragger:[13,23,26,28,34,35],fragger_handl:[13,35],fragger_map:26,fraggerhandl:[0,13,26,28,35],fraggermap:[26,28],fragment:[0,3,9,13,22,23,24,28,31,32,34,35,38,47],fragment_db:35,fragment_handl:28,fragment_info:26,fragment_length:[26,28],fragmentinfo:[26,31],fragments_per_posit:28,fragmentsampl:34,frame:[3,16,35,36,46,47,49,50,52,54],frame_energi:49,frame_residu:[45,47],frameresidu:[45,49,50],framework:[8,19,38],free:[0,8,20,35,49,51],frequenc:[26,34],frm:36,frmrotam:[44,49,50,52],frmrotamergroup:[44,46,49,50],from:[0,1,2,3,4,5,6,7,8,9,10,11,13,16,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,46,47,49,50,51],fromhhm:26,fromhoriz:26,fromresidu:51,front:[1,11,16],fstream:37,fudg:25,fulfil:[26,51],full:[0,1,3,8,10,21,25,26,28,29,30,31,34,35,36,47,49,50],full_queri:28,full_seq:[29,31],fullgapextend:[29,35],fulli:[8,16,21,22,26,29,30,36],function_typ:40,functions_specific_to_your_act:8,fundament:37,funni:[2,8],further:[10,28,29,35,36,37,50],furthermor:[37,50],futur:[3,25,26],gamma:[40,41,44],gamma_bin:41,gap:[0,3,9,18,24,25,30,31,33,35,36,54],gapextend:[29,35],gapfre:26,gapless:[0,13],gather:[4,12,16,26,28,47,49,51],gauc:51,gauch:51,gauche_minu:51,gauche_plu:51,gaussian1:49,gaussian2:49,gciiipgatcpgdyan:[31,35],gener:[0,1,2,3,5,7,8,10,13,14,16,18,19,20,23,24,26,27,28,30,31,32,33,35,36,37,39,40,41,48,49,50,51,54],generatedenovotrajectori:28,generatestructureprofil:26,geom:[21,22,25,26,28,32,35,44,49],geometr:[3,9,23,28,31,38,44],geometri:[12,23,26,31,54],geoom:43,get:[0,1,2,8,16,19,21,22,23,25,26,28,30,31,32,33,34,35,36,37,39,40,41,44,47,48,51,52,54],getaa:[21,22,25],getaaa:21,getaah:21,getactivesubrotam:49,getallatomposit:[21,32,36],getallatomscoringkei:31,getallatomweight:31,getanchoratomindex:21,getangl:47,getangularbins:26,getatomcount:8,getatomnam:21,getatomnameamb:21,getatomnamecharmm:21,getaveragescor:31,getbackbonelist:[23,26],getbackbonescoringkei:31,getbackboneweight:31,getbins:27,getbinsperdimens:27,getbound:22,getc:22,getca:22,getcb:22,getchain:29,getchainindex:29,getchainnam:29,getchains:8,getcharg:25,getclust:31,getclusteredcandid:31,getcollisiondist:49,getconfid:26,getcoordidx:26,getcoordinfo:26,getcpuplatformsupport:25,getcreationd:5,getdefault:[25,32,35],getdefaultlib:5,getdihedralangl:26,getdihedralconfigur:51,getdistbins:26,getdisulfidbridg:25,getdisulfidconnect:25,getdsspstat:26,getel:21,getenviron:21,getenvsetdata:8,getepsilon:25,getfirstindex:21,getforcefieldaminoacid:25,getfragmentinfo:[26,31],getframeenergi:49,getfudgelj:25,getfudgeqq:25,geth1index:21,geth2index:21,geth3index:21,getheavyindex:25,gethistogramindex:[22,27],gethistogramindic:27,gethnindex:21,gethydrogenindex:[21,25],getidentifi:28,getindex:[21,25],getinternalconnect:25,getinternalenergi:49,getinternalenergyprefactor:49,getlargestclust:31,getlastindex:21,getlength:29,getlist:28,getlooplength:25,getloopstartindic:25,getmass:25,getmaxnumatom:21,getmaxnumhydrogen:21,getn:[22,28],getnam:[47,49],getnonbondedcutoff:32,getnum:31,getnumatom:[21,25],getnumb:31,getnumcandid:31,getnumchain:8,getnumcoord:26,getnumfrag:26,getnumhydrogen:21,getnumloopresidu:25,getnumresidu:[8,21,25],getnumstempair:26,getnumsubrotam:49,geto:22,getolc:[21,22],getomegators:[21,22],getoxtindex:25,getpeptideboundconnect:25,getphiprobabilitygivenpsi:27,getphitors:[21,22,47],getpo:[21,28,49],getposit:28,getpotentialenergi:25,getpredict:26,getprob:[27,49],getpsiprobabilitygivenphi:27,getpsitors:[21,22,47],getr:33,getresidu:28,getresiduedepth:26,getringpunch:33,getrotamericconfigur:51,getscor:[26,34],getscoringfunct:49,getselfenergi:49,getseqr:[21,40],getsequ:[21,22,26,31],getsequenceprofil:26,getsequenceprofilescoreskei:31,getsigma:25,getsimul:25,getsolventaccessibilitit:26,getstemrmsdskei:31,getstructureprofil:26,getstructureprofilescoreskei:31,getsubdb:26,getsubrotamerdefinit:49,getsystemcr:32,gettemperatur:[34,49],gettransform:22,getversionnumb:37,getweight:[28,31],gggg:35,ggggagggg:35,gggggggggggggggggggg:35,git:[1,4,8,17,18,19,53],gitignor:8,gitlab:[5,53],give:[4,8,16,20,23,28,31,34,35,49],given:[0,1,3,4,8,9,10,11,13,14,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51],glass:38,gln:[49,51],gln_ne2:21,global:[15,26,31,35,37],glu:[21,49,51],glu_oe1:21,glutam:49,glutamin:49,gly:[35,36,47,49,50],gly_n:21,glycin:[3,22,26,32,36,49],goal:[1,10,28,30],goe:[2,8,14,16,35,51],going:[8,9],goldfarb:35,goldstein1994:[10,38],goldstein:[10,38],good:[4,8,18,25,26,35],goodwil:20,got:2,govern:20,grain:8,grant:20,graph:[3,12,38,47,54],graph_initial_epsilon:36,graph_intial_epsilon:36,graph_max_complex:36,graphminim:[10,46],greatest:5,grep:2,grid:26,gromac:9,grossli:20,group:[4,14,24,26,27,28,41,44,45,46,47,50,52],group_definit:[27,41],group_idx:41,guarante:[26,28,31,34,36,37],gui:[8,27],guid:32,guidelin:[8,37],gzip:[0,5,11,13],haa:38,hand:[0,2,4,13],handl:[3,8,9,13,19,22,28,30,36,40,44,54],handler:28,happen:[1,8,25,28,29,34,35,49],hard:[43,49],hardwar:18,harmless:20,harmon:[25,32],harmonic_angl:25,harmonic_bond:25,harmonic_improp:25,has:[0,1,2,3,4,5,8,10,11,13,16,20,21,22,23,24,25,26,29,31,32,34,35,36,39,40,41,44,46,49,50,52],hasattr:35,hasdata:26,hasfraglength:26,hasfragmentinfo:31,hash:[3,26,28],hash_thresh:28,hash_tresh:28,hasringpunch:33,have:[0,2,4,5,7,8,10,13,14,16,18,20,21,22,25,26,28,29,31,33,34,35,36,37,39,40,41,44,46,47,50,51,52],hbond:[28,35,41,49,50],hbond_scor:37,hbondscor:[35,37,42],headach:8,header1:4,header2:4,header3:4,header4:4,header:[0,2,4,16,17],header_output_dir:4,headlin:8,heavi:[21,25,36,39,49,50],heavili:[26,47],helic:[22,24,25,28,35,41],helix:[7,18,22,34,47],hell:28,hello:37,hello_world:8,hellyeah:[7,18],help:[0,1,2,4,7,8,13,16,18,25,41],helpactiontest:1,helper:[4,12,16,17,21,25,31,36,37,54],hen:26,henc:[8,14,21,26,37],here:[0,1,2,4,8,11,13,14,16,18,19,21,22,25,26,27,28,30,31,32,34,35,37,39,41,44,48,51],herebi:20,herein:20,het:35,heurist:[3,35,50],heuristicprocessor:21,hg_po:49,hgfhvhefgdntngcmssgphfnpygkehgapvdenrhlg:0,hhblit:[0,13],hhm:[0,13,26,31],hhsearch:26,hide:[8,16],hierarch:[31,40],hierarchi:15,high:[3,8,16,28,30,35],high_resolut:22,higher:[31,40,41],highest:15,highli:[2,8],hint:13,histidin:[25,49],histogram:[27,34],histori:16,hit:[1,10,16,27,32],hmm:38,hold:[20,28],home:[4,5],homo:[0,13],homolog:[0,12,18,19,35,38],homologu:26,honor:35,honour:35,hook:[8,17],horiz:26,horribl:50,host:[4,7,8,16],hotfix:16,how:[1,16,17,20,26,31,34,35,38,40,48,54],howev:[5,20,26],hparticl:49,hpp:37,hsd:[49,51],hse:[49,51],html:[2,8,16],http:[8,18,19,20,53],hybrid:51,hydrogen:[3,21,22,25,35,38,41,49,50],hydrophob:49,hyphen:1,i_loop:[25,36],i_vinaparticl:49,id_:37,idea:[1,8,21,23,25,26,35,40,49,52],ideal:[22,32,52],ident:[3,26,27,28,41,51],identif:20,identifi:[0,3,13,14,20,26,28,31,35,36,39,41,49,50,51],ids:47,idx:[10,21,22,25,26,28,32,40,49],idx_ca_res_37:21,idxhandl:8,iff:[26,29,33],ifstream:37,ignor:[0,25,28,32,35],iii:20,illustr:26,imag:7,image_nam:5,imagehandl:22,imagin:8,imaginari:1,img:[7,22],immedi:[1,8,15,16],impact:[0,25,26],implement:[3,16,19,26,28,29,32,34,35,37,43,44,46,47,49,50,53],impli:20,implicit:2,improp:25,improv:[3,20,25,35,38,44],in_dir:4,in_fil:8,in_path:4,in_stream:37,in_stream_:37,inabl:20,inaccur:25,inaccurate_pot_energi:25,inact:52,inactive_internal_energi:52,incident:20,incl:[25,26,35],includ:[2,3,7,8,11,16,18,20,21,25,26,28,29,31,33,35,37,39,41,47],include_atom:28,include_ligand:35,inclus:[20,35],incompat:[31,32],incomplet:[35,48],inconsist:[10,13,21,22,25,26,29,31,32,36,40,49],inconveni:16,incorpor:20,increas:[0,10,28,31,32,35,50],increment:28,incur:20,indemn:20,indemnifi:20,independ:[0,3,25,36,48],index:[8,10,21,22,25,26,27,28,29,31,32,33,34,35,39,40,41,45,49,50,51],index_four:25,index_on:25,index_thre:25,index_two:25,indic:[8,10,11,13,20,21,22,25,26,27,28,29,31,32,35,36,40,44,47,49],indirect:20,individu:[7,20,39,41],inf:[10,32,35],infin:32,infinit:32,influenc:[13,28,40,50],info:[26,31,35,40],inform:[0,5,7,8,13,16,20,22,23,26,28,29,31,34,35,38,40,41,42,53],infring:20,inherit:[1,39,40,41,46],init:16,init_bb_list:34,init_frag:34,initi:[3,10,21,22,26,28,31,32,34,35,36,39,40,41,46,49,50,51],initial_bb:31,initial_epsilon:[10,52],initialis:1,inlin:37,inner:14,input:[0,1,3,13,16,18,25,26,27,28,32,34,35,36,39,40,41,44,48,52],insert:[21,22,29,31,34,35,52],insertinto:[21,22,31],insertloop:[29,35],insertloopcleargap:[29,31,35],insid:[1,4],insight:16,instal:[8,16,37,54],instanc:[3,8,13,24,25,37,53],instead:[0,1,2,3,4,8,11,26,28,29,31,34,35,50],institut:20,instruct:2,int16_t:37,int32_t:37,int_32_t:37,integ:[8,13,21,40],integr:[4,8,38],intend:[1,8,34,49],intent:26,intention:20,interact:[3,8,25,32,39,40,41,43,44,45,49],intercept:[39,41],interest:[1,10,25,26,34,37,49,51],interfac:[0,3,4,8,20,50],intermedi:8,intern:[0,1,3,4,5,8,16,21,24,25,26,27,28,31,32,34,35,36,37,38,39,40,41,46,49,50,52],internal_e_prefac:50,internal_e_prefactor:49,internal_energi:49,internet:8,interpl:51,interpol:[40,51],interpret:[8,11],intervent:8,intrins:2,introduc:[1,3,4,8,16,32,35],introduct:[12,17],invalid:[8,21,25,26,29,32,35,36,39,40,41,45,49,51],invalid_vinaparticl:49,invok:[2,4,8,15,16],involv:[16,30,44,49],iodin:49,ios:37,iostream:37,ipython:7,irrevoc:20,is_c_ter:[25,36],is_cter:25,is_hbond_acceptor:50,is_hbond_donor:50,is_major:35,is_n_ter:[25,36],is_nter:25,isallatomscoringsetup:[31,35],isallset:21,isanyset:21,isbackbonescoringsetup:35,isctermin:29,isempti:31,isen:14,isntermin:29,isoleucin:49,isset:21,issimilar:51,issourc:37,issu:[3,12,16,17,20,32,35,37],istermin:29,isvalid:47,item:[1,8,16,21,22,25,26,35,40],iter:[10,26,27,28,31,32,34,35,49],its:[0,1,2,4,5,8,11,16,20,25,26,30,31,33,34,35,41,48,49,50,51],itself:[3,4,8,16,26,34,36,37,39,41],januari:20,job:[8,26,34,35],johner:38,join:[8,21,23,26,31,32,34,36],jone:[38,49],jones1999:[26,38],journal:38,json:[0,13],jupyt:7,just:[1,2,8,13,15,16,23,25,26,28,29,31,35,50],kabsch1983:[26,38],kabsch:38,keep:[0,1,2,4,5,8,13,16,28,30,35,47],keep_non_converg:31,keep_sidechain:[8,36],kei:[0,13,26,28,31,34,35,39,40,41],kept:[8,16,25,31,32,36,45,49],kernel:[7,38],keyword:27,kic:[30,31,34],kicclos:34,kick:13,kill_electrostat:25,kind:[1,8,20],kinemat:32,know:[2,51],knowledg:51,known:[4,11,21,40,50],krivov2009:[10,38,47,49],krivov:38,kwarg:1,l_e:49,lab:48,label:[16,25],lack:35,languag:[4,20],larg:[5,27,32,35],larger:[10,14,22,26,28,35,50],largest:[28,31,44],last:[1,2,3,4,21,22,25,29,31,32,34,35,40,41,48],last_psi:22,later:[1,8,10,21,28,47],latest:[2,5,8],latter:[0,5,16,35],launcher:[4,8],law:20,lawsuit:20,layer:44,layout:[26,37],lbfg:35,lddt:7,leach1998:[10,38],leach:38,lead:[0,8,9,11,22,25,31,32,36,39,41,48],learn:28,least:[0,2,4,8,10,16,20,22,25,26,35,39,41,44],leav:1,left:[10,11,32],legal:[8,20],lemon:38,len:[22,23,25,26,28,31,35,36,41,47],length:[0,9,10,21,24,25,26,27,28,29,31,32,34,35,36,37,39,40,44],length_dep_weight:35,length_depend:31,lennard:49,less:[0,10,16,22,25,26,27,31,35,39,41,50,51],let:[1,8,22,26,28,31,47],letter:[3,5,21,22,26,27,34,49],leu:49,leu_h:21,leucin:49,level:[2,3,8,14,15,16,30,35],lexicograph:35,liabil:20,liabl:20,lib64:8,lib:[5,7,37],libexec:[4,8],libpromod3_nam:4,librari:[0,3,4,8,15,36,38,47,50,54],library1:4,library2:4,licenc:48,licens:[3,17,19],licensor:20,lies:26,life:16,ligand:[3,35,36,49,50],like:[0,1,4,8,16,35,37,48],limit:[0,3,20,26,32,35],line:[0,1,7,8,9,12,16,27,41,54],linear:[26,28,31,34,39,40,41],linear_weight:[31,34,39,41],linearcombin:31,linearscor:34,link:[0,2,4,8,16,20,21,25,26,28,34,36,39,40,41,42],link_cmd:4,linkcheck:[2,8,16],linker:[4,35],linker_length:35,list:[0,1,2,3,4,7,8,9,10,11,13,20,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,45,46,47,49,50,51,52],listen:8,literalinclud:8,litig:20,littl:[4,8,16,37],live:[4,8],lj_pair:25,load:[1,8,13,15,21,23,25,26,27,28,31,32,35,36,37,39,41,42,47,51,54],loadalign:[30,35],loadallatominteractionscor:39,loadallatompackingscor:39,loadamberforcefield:35,loadbb:26,loadbbdeplib:[0,36,47,48],loadcach:28,loadcbetascor:[31,34,41,42],loadcbpackingscor:41,loadcharmm:25,loadcharmmforcefield:35,loaddefaultallatomoverallscor:39,loaddefaultbackboneoverallscor:41,loadent:[0,13],loadfragdb:[23,24,31,35],loadhbondscor:41,loadlib:[0,36,48],loadpdb:[8,21,23,25,26,28,30,31,32,34,35,36,42,47],loadport:[25,26,27,37,39,41,51],loadreducedscor:41,loadsequenceprofil:[13,26,31],loadssagreementscor:41,loadstructuredb:[23,24,26,31,35],loadtorsionsampl:[22,24,27,34],loadtorsionsamplercoil:[24,31,35],loadtorsionsamplerextend:24,loadtorsionsamplerhel:24,loadtorsionscor:41,local:[2,5,7,25,26,27,39,41,51],localhost:7,locat:[2,3,4,5,10,22,24,26,28,29,37,39,41,49],log:[11,16,33,35,49,50],logic:0,loginfo:33,lone:49,lone_pair:49,longest:26,look:[5,8,11,16,22,26,36,40,50],lookup:[9,21,23,28,42],looooooong:10,loop:[0,3,7,8,13,18,19,21,24,26,27,28,29,30,33,35,36,37,38,39,40,41,50,54],loop_candid:31,loop_length:[25,26,31,36],loop_main:8,loop_po:25,loop_seq:31,loop_start_indic:[25,36],loopcandid:[28,30,33],loss:[16,20],lossi:26,lost:[1,16],lot:[1,8,13,16],low:[1,8,10,50],lower:[31,34,35,39,41],lowest:[31,34,49],lowest_energy_conform:34,lying:40,lysin:49,m_idx:28,m_vinaparticl:[49,50],machin:[25,26,27,37,39,41,51],macro:[4,8],macromolecul:38,made:[4,5,20,51],magic:[8,37],mai:[0,1,2,4,8,11,13,16,20,21,25,29,32,35],mail:20,main:[8,35,37,51],mainli:[21,34,49],maintain:[8,16],mainten:17,maintin:34,major:[16,35],make:[3,4,7,8,11,13,16,18,20,21,22,26,37,40,48,54],makefil:[2,8],makestat:51,malfunct:20,malici:16,man:[2,8],manag:[4,8,20,42],mani:[11,13,26,28,32,33,35,50],manipul:22,manner:[8,10,34],manual:[1,2,5,8,9,16,26,31,34,35,37,49],map:[0,13,21,22,26,28,33,36],mariani:38,mark:[4,20,50],mass:25,massiv:28,master:[8,16],mat3:9,mat4:[9,22,28,35],mat:28,match:[0,4,13,22,25,26,27,28,31,32,34,35,40,41],materi:[1,8],math:33,mathemat:[31,32],matplotlib:27,matric:38,matrix:[9,26,28],matter:[4,7,28,53],max:[9,10,21,29,33,35,36,41,51,52],max_alpha:41,max_beta:41,max_complex:[10,52],max_count:[39,41],max_d:41,max_dev:34,max_dist:[31,40],max_extens:35,max_gamma:41,max_iter:[28,31,35],max_iter_lbfg:35,max_iter_sd:35,max_length:29,max_loops_to_search:35,max_n:10,max_num_all_atom:35,max_p:50,max_prob:49,max_res_extens:35,max_step:32,max_to_show:14,max_triangle_edge_length:28,max_visited_nod:10,maxfraglength:26,maxim:[10,26,28,31,32,34,35,38,40,41],maximum:[10,26,31,32,34,49,50],mc_closer:34,mc_cooler:34,mc_num_loop:35,mc_sampler:34,mc_scorer:34,mc_step:[10,35],mcsolv:10,mean:[4,8,13,16,20,21,25,28,32,35,36],meaning:[26,31],meant:[18,21,26,33,35,50],measur:28,mechan:[18,20,31,32,34,35,40],meddl:[7,35],media:20,medium:20,meet:20,member:[8,13,31,35],memori:[10,26,35,37],mention:[1,2],merchant:20,mere:20,merg:[16,25,28,29,31,35,36,40,49],merge_dist:35,mergegap:29,mergegapsbydist:35,mergemhandl:35,mess:[8,16,40],messag:[12,13,37],messi:16,met:49,metal:49,methionin:[35,49],method:[0,1,10,13,21,25,26,27,32,35,36,37,50],metric:40,metropoli:[10,31,34],mhandl:[29,30,31,35],middl:16,might:[10,25,26,28,31,32,34,40,50,52],min:[31,41],min_alpha:41,min_beta:41,min_candid:31,min_d:41,min_dist:40,min_gamma:41,min_loops_requir:35,min_scor:31,min_terminal_anchor_s:35,min_triangle_edge_length:28,mincadist:22,mind:[1,8],minim:[3,12,18,22,25,26,31,32,35,39,40,41,46,47,54],minimizemodelenergi:35,minimum:[22,26,28,44],minor:[3,25,35],mirror:37,miser:14,mismatch:[21,35,40],miss:[0,11,13,25,35],mix:[0,4],mkdir:[2,8],mm_sy:[25,32],mm_sys_output:25,mm_system_cr:32,mmcif:[5,11],mmsystemcr:[25,32],mod:8,mode:[1,51],model:[1,3,7,8,12,13,14,19,21,25,26,29,32,34,36,40,41,42,45,46,49,50,52,53,54],model_termini:35,modelling_issu:35,modellinghandl:[3,29,31,35],modellingissu:35,modeltermini:35,modif:[20,35],modifi:[8,16,20,22,31,35],modified_crambin:31,modul:[1,3,11,12,15,16,17,18,23,24,30,37,44,47,49],modular:19,module_data:4,mol:[8,9,18,21,22,23,26,27,28,29,31,32,34,35,36,38,40,47,49,50,51,54],molck:7,molecular:[7,18,32,35],molprob:30,molprobity_bin:33,molprobity_execut:33,moment:8,monitor:1,monolith:8,mont:[0,3,10,28,31,34,35,46],montecarlo:3,mood:8,more:[1,2,4,7,8,10,13,14,16,20,28,35,44,49,53],most:[0,3,4,5,8,22,25,26,27,28,31,32,35,39,41,48,50],mostli:[4,16],motif:[3,30,38],motiffind:28,motifmatch:28,motifqueri:28,motion:[22,38],mount:[5,7],movabl:25,move:[2,3,8,16,25,31,32,34,35,37],movement:28,mpscore:33,msg:11,msgerrorandexit:11,msm:3,msse4:2,much:[10,26,35],multi:18,multipl:[0,2,3,4,8,13,14,18,25,28,31,35,36,39,41],multipli:[10,34],multitempl:13,multithread:38,must:[0,2,4,8,10,13,14,16,20,22,25,26,28,29,31,32,33,34,35,36,37,39,40,41,44,51],mutlipl:13,my_db_on:26,my_db_two:26,my_script:7,myclass:37,myclassptr:37,mytrg:0,n_a_vinaparticl:49,n_ad_vinaparticl:49,n_coord:9,n_d_vinaparticl:49,n_i:10,n_j:10,n_num:29,n_po:[9,22,41],n_stem:[9,23,26,29,31,32,34],n_stem_phi:34,n_ter:[32,50],n_vinaparticl:49,naivesolv:10,name:[0,1,3,4,5,7,8,11,13,14,20,21,25,26,27,29,31,33,35,44,48,49,51],name_pymod:4,namespac:[13,37],nan:[32,35,51],nativ:37,necessari:[8,22,34,40],necessarili:[20,52],need:[1,2,3,4,5,8,11,13,15,16,22,25,26,27,28,31,32,35,36,37,39,40,41,47,50],need_config_head:4,neg:[1,10,25,32,40],negelect:[0,35],neglect:[28,32,45,49,50],neglect_size_on:31,neglig:20,neighbor:[8,21,35],neighbour:[28,35,51],network:[22,44],never:[13,16,26,31,35,36,37,39,41],nevertheless:8,new_default:25,new_env_po:21,new_po:21,new_res_nam:49,new_siz:22,newli:[5,21,34],next:[1,8,16,22,27,28,29,37],next_aa:34,nglview:7,nice:8,nitrogen:[9,22,32,43,49,50],nobodi:1,node:10,node_idx:10,node_idx_on:10,node_idx_two:10,non:[0,4,10,13,16,20,24,25,27,28,29,31,32,35,37,47,48,50],non_rotamer:51,nonbonded_cutoff:[25,32],none:[13,26,28,33,34,35,36,49],nonredund:26,nonzero:51,norm:[28,41],normal:[20,39,41],normalis:40,notabl:26,note:[0,2,8,13,14,21,22,25,26,28,31,32,34,35,36,37,39,40,41,47,49,50],notebook:7,noth:[0,4,8,13,14,20,28,34,49],notic:[1,4,16,20],notwithstand:20,novel:[19,38],novo:[3,30,54],now:[3,8,14,16,18,22,26],nparticl:49,nterminalclos:34,null_model:31,num:[23,28,31,32,36],num_frag:[26,35],num_gap_extens:29,num_loop:31,num_residu:[21,25,34,36,39,40,41],num_residues_list:36,num_trajectori:28,number:[0,1,8,9,10,13,14,18,21,22,24,25,26,27,28,29,31,32,34,35,36,37,39,40,41,42,44,45,49,51],numer:35,numpi:[27,34],nussinov1991:[28,38],nussinov:[28,38],o_a_vinaparticl:[49,50],o_ad_vinaparticl:49,o_d_vinaparticl:49,o_po:22,o_vinaparticl:49,object:[0,3,8,13,14,20,21,22,23,25,26,27,28,30,31,32,35,36,37,39,41,44,46,47,49,50,54],oblig:20,observ:[10,26,28,32,50,52],obtain:[10,18,20,23,28,35],obviou:16,occupi:[45,50],occur:[21,28,35,40,41],ocparticl:49,odd:26,off:[1,8,14,35],offend:33,offer:[6,20,24,30,49,51],offset:[0,3,13,26,31,35],ofstream:37,often:[8,11,13,32],og_po:49,olc:22,old:[33,35],oligom:[0,13,30],oligomer:3,olson:38,omega:[21,22],omit:35,onc:[1,3,8,16,25,28,31,32,34,46,51,52],one:[0,1,2,4,5,6,8,9,10,13,14,15,16,20,21,22,25,26,28,29,31,32,34,35,36,39,40,41,44,49,50,51,52],one_letter_cod:[21,23,26,31,32,34,36],ones:[22,28,31,34,50,51],onli:[0,1,2,4,8,10,11,13,14,15,16,20,21,22,25,26,28,29,31,33,34,35,36,37,39,41,44,47,48,49,50],only_longest_stretch:26,onto:[1,22,26,28],oparticl:49,open:[13,25,26,27,37,39,41,51,53],openmm:[2,18,25,32],openstructur:[2,3,5,7,19,38],oper:[3,10,16,18,21,26,40],opt:[11,13,16],optim:[0,2,3,10,13,25,26,27,31,35,38,39,41,44,47,48,51,54],optimis:8,optimize_subrotam:[36,44],option:[0,2,3,5,7,13,26,31,32,35,51],order:[0,5,13,21,25,26,29,31,35,37,40],org:20,organ:[8,26,51],orient:[9,32,41],orig_indic:[31,33],origin:[5,7,9,13,16,20,22,26,31,34,35,40,52],orthogon:28,ost:[0,1,2,3,4,5,7,8,9,11,13,15,18,21,22,23,26,27,28,29,30,31,32,33,34,35,36,37,40,41,42,43,44,47,49,50,51,54],ost_double_precis:2,ost_ent:33,ost_librari:4,ost_root:[2,8],other:[0,1,2,3,4,8,10,14,16,20,21,22,31,32,35,36,39,41,42,49,50,51,52,53,54],other_index:22,other_particl:49,other_res_index:21,otherwis:[1,4,8,10,14,16,20,21,22,25,26,28,29,31,32,34,35,39,40,41,49,51],our:[4,5,8,16,26,28,31],out:[0,1,2,4,8,14,16,20,21,25,26,27,28,29,31,34,47,51],out_path:4,out_po:25,out_stream:37,out_stream_:37,outdat:[5,7],outer:[14,26],outlier:33,output:[0,5,8,11,13,25,27,28,32],output_dir:4,outsid:[8,40],outstand:20,over:[2,4,13,16,26,28,32,34,35,49],overal:[10,34,40,46],overhead:25,overlap:[25,34,35,36],overli:16,overload:37,overrid:[2,5,25,35,50],overridden:4,overriden:5,overview:[8,16],overwrit:31,overwritten:25,own:[1,3,4,16,17,20,25,26,35,48,49,50],owner:20,ownership:20,oxt:[9,21,25],oxygen:[22,35,43,49,50],p_vinaparticl:49,pack:21,packag:[4,8,16],pad:[22,37],page:[2,8,20],pai:1,pair:[9,10,25,26,27,28,32,34,36,37,39,40,41,44,49,51],pairwis:[3,8,10,22,28,31,35,39,41,42,43,44,46,47,49,50,52],pairwise_energi:10,pairwisefunct:[40,41],pairwisefunctiontyp:40,pairwisescor:[8,35,42,49],paper:[43,44,47,49],paragraph:[1,8],parallel:26,paramet:[1,4,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,43,44,45,46,48,49,50,51,52],parameter_index:26,parametr:[3,32,35,36,49,50],parent:35,pars:[0,11,12,25,26,27,39,41,51,54],parser:12,part:[0,1,8,16,18,20,21,26,34,35,40,44,46,47,49,54],parti:[16,17,20],partial:29,particip:[36,44],particl:[3,25,26,32,41,43,44,45,47,50],particle_typ:49,particular:[8,10,20,26,31,32,34,49,51],partner:[39,40,41],pass:[13,16,21,25,26,28,29,32,34,44,45,49,50],past:[8,16,22,29],patent:20,path:[1,2,4,5,7,8,11,16,18,25,26,27,33,39,41,51],path_to_chemlib:15,path_to_dockerfile_dir:5,path_to_promod3_checkout:6,pattern:38,paus:14,pdb:[0,5,7,8,11,13,18,21,22,23,24,25,26,28,30,31,32,33,34,35,36,42,47],penal:[29,35],penalti:[29,35],penultim:3,peopl:16,pep:[1,16],peptid:[3,21,23,25,26,28,35,36,47],peptide_sel:28,per:[4,8,10,12,16,21,27,31,34,35,39,40,41,44],percent:20,percentag:33,perfect:8,perfectli:8,perform:[0,10,16,18,19,20,25,28,31,32,33,34,35,37,40,44],period:25,periodic_dihedr:25,periodic_improp:25,permiss:[8,20],permut:10,perpetu:20,pertain:20,phase:25,phe:[49,51],phenix:33,phenylalanin:49,phi:[21,22,26,27,32,34,41,47,50,51],phi_bin:[41,51],phi_handl:47,philippsen:38,phipsisampl:34,phosphoru:49,phosphoserin:35,phrase:8,pick:[31,34],pictur:8,piec:[8,28],pipelin:[0,3,14,19,26,28,29,30,33,34,47,53,54],pivot:[31,32,34],pivot_on:[31,32],pivot_thre:[31,32],pivot_two:[31,32],place:[1,2,4,8,11,13,16,20,26],plain:[0,13],plan:16,plane:33,platform:[18,25],playground:7,pleas:[2,8,16,28,31,32,35,53],plot:27,plt:27,plu:[8,13,15,26,44,49],pluribu:28,pm3_csc:16,pm3_openmm_cpu_thread:[18,25,35],pm3_runtime_profiling_level:14,pm3argpars:[0,11,12,54],pm3argumentpars:[0,11,13],pm_action:[1,4,8],pm_action_init:8,pm_bin:1,pna:38,png:27,pocket:28,pocket_view:28,point:[2,8,13,15,21,26,28,34,35,40,49,51],pointer:[2,8,37],polar:[49,50],polar_direct:49,polici:8,pop:[16,31,34,40],popul:[2,16],port_str_db:26,portabl:[4,17,25,26,27,39,41,51],portable_binary_seri:37,portable_fil:4,portablebinarydatasink:37,portablebinarydatasourc:37,pos:[21,22,26,32,49],pos_end:28,pos_on:28,pos_start:28,pos_two:28,posit:[3,8,9,22,23,25,26,27,28,29,31,32,34,35,36,38,39,40,41,43,44,45,46,49,50,54],possibl:[0,3,8,10,13,16,20,22,25,26,27,28,29,31,32,34,35,36,37,39,40,41,44,46,49,51],post:13,postprocess:36,pot:25,pot_:32,potenti:[10,23,25,26,28,31,32,35,36,37,38,41,49],power:[7,20],pqhpg:0,practic:[4,8,25,26],pre:[8,16,35],pre_commit:[8,16],preceed:36,precis:[2,31,35],precomput:[23,54],pred:40,predefin:[4,18,25,35,39,41],predict:[13,26,28,35,38,40,41],prefactor:49,prefer:[2,4,20,26,51,52],prefilt:35,prefix:[1,4,8,11],prepar:[8,20,35],present:[22,28,32,36,49,50,51],prev_aa:34,prevent:[1,8],previous:[25,26,31,36,40],primary_rot_angl:22,principl:[3,34,40],print:[1,2,5,20,22,23,25,26,31,32,33,35,42],printstatist:26,printsummari:14,prior:35,privat:[1,37],pro:[21,27,49,51],probabilist:[26,50],probability_cutoff:50,probabl:[4,8,10,13,16,26,27,28,31,32,34,49,50,51],problem:[3,7,10,13,16,26,28,31,32,34,35,40,42,44,46,48,52],problemat:[3,5,28],proce:42,procedur:[10,28,34,36,50],process:[1,3,13,16,21,25,28,32,34,35,37,40,45,49,51],processor:5,produc:[0,1,2,4,8,10,26,29,33,35],product:[1,3,16,20],prof:[0,26,31],prof_dir:26,prof_path:26,profil:[0,3,12,13,26,28,31,35,38,54],profiledb:26,profilehandl:[13,26,28,31,35],prog:13,program:[4,5,8,12],project:[3,4,5,8,16],prolin:[22,33,49],promin:[0,20],promod3:[1,3,7,9,10,11,13,14,15,17,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],promod3_checkout:7,promod3_mod:4,promod3_nam:4,promod3_name_head:4,promod3_path:8,promod3_root:8,promod3_shared_data_path:[8,37],promod3_unittest:[1,4,8],promod:[5,7],promot:8,propag:[8,22],proper:[16,26,50],properli:[1,35,39,41,50],properti:[21,22,35,50,51],propos:[29,31,32,34,44],proposed_posit:34,proposestep:34,prot:[8,23,26,28,32,34,36,47],prot_rec:8,protein:[0,18,19,24,25,28,33,34,35,36,38,45,47,49,54],proteinogen:26,proton:[21,25,49,51],prototyp:19,provid:[0,1,2,3,4,5,7,8,13,16,20,21,22,23,25,26,28,29,31,32,33,34,35,36,37,40,48,49,50,51],prune:[10,52],pscoringfunct:49,pseudo:[34,35,39,41],psi:[21,22,26,27,32,34,41,47,50,51],psi_bin:[41,51],psi_handl:47,psipr:[13,26,28,40,41],psipred_confid:41,psipred_pr:28,psipred_predict:[26,28,35],psipred_st:41,psipredpredict:[23,28,35,40],pssm:[0,13],publicli:20,pull:[5,8,16,18],pullterminaldelet:35,punch:[1,3,30,35],pure:0,purpos:[8,10,20,35,51],push:16,pushverbositylevel:13,put:[1,4,8,11,13,35],pwd:5,py_run:[1,4,8],pyc:1,pylint:16,pylintrc:16,pymod:[4,8,16],pyplot:27,pytest:8,python3:8,python:[1,2,3,4,5,7,8,11,14,15,16,18,21,22,25,32,37,49,50],python_root:2,pythonpath:8,qmeandisco:40,qualiti:35,quantum:38,queri:[26,28,51],query_idx:28,query_list:28,querylib:51,question:[3,27],quick:17,quickli:[5,8,32],quit:[8,13],rackovski:38,radian:[9,22,25,27],radii:[33,43],radiu:[8,33,39,41,49],raihvhqfgdlsqgcestgphynplavph:0,rais:[0,9,10,13,21,22,25,26,27,28,29,31,32,33,34,35,36,39,40,41,44,45,49,50,51],rama_iffi:33,ramachandran:33,random:[10,22,24,27,31,32,34],random_se:31,randomized_frag:22,randomli:[27,34],rang:[8,9,21,22,23,25,26,27,28,29,32,34,35,39,40,41,51],rank:31,rapid:38,rare:8,rather:[5,7,8,11,16,34,51],raw:[7,18,25,26,27,30,31,37,39,41,44,51],rawmodel:[3,8],reach:[0,29,32],read:[0,8,11,13,16,25,26,27,29,36,37,39,41,48,51],readabl:[0,8,13,20,51],readdunbrackfil:48,reader:[16,18],readi:[2,5,51],readm:[2,8,48],real:[8,13,37],realli:[1,2,8,11,16],reappear:16,reason:[8,16,20,32,34,52],rebas:16,rebuild:[2,8],recalcul:27,receiv:20,recent:[3,16],recip:[3,6],recipi:20,recoginz:49,recogn:[0,13],recognis:[1,8,16],recognit:38,recommend:[2,5,8,20,25,35],reconstruct:[0,3,8,18,21,22,25,30,32,35,44,47,49,52,54],reconstructcbetaposit:22,reconstructcstemoxygen:22,reconstructor:[32,35,36],reconstructoxygenposit:22,reconstructsidechain:[0,8,35,36],reconstructtest:8,record:[1,35],recreat:16,redistribut:20,redo:28,reduc:[3,25,28,35,41],reduced_scor:37,reducedscor:[35,37,42],redund:[24,31],ref_backbon:[23,26],ref_fil:8,refactor:3,refer:[1,4,8,18,19,21,22,23,25,26,34],referenc:8,refin:28,refine_thresh:28,refresh:31,regard:[20,32,44],region:[0,25,28,29,32,34,35,45,50],regist:[4,8],regress:38,regularli:5,reinterpret_cast:37,reintroduc:3,reject:[31,32,34],rel:[4,5,9,10,26,28,32,41],relat:[4,8,13,26,28,37,38,49],relax:[30,35],releas:[2,5,8,16],relev:[2,3,4,7,25,28,36,49],reli:5,remain:[20,30,34,35],rememb:[1,8,34],remodel:[31,36],remodel_cutoff:36,remov:[2,3,10,22,25,26,29,31,33,35,36,40,47,49],removecoordin:26,removeterminalgap:35,renumb:[26,35],reorder:35,reordergap:35,repeat:28,replac:[3,20,21,22,34,35],replacefrag:22,report:[1,8,35],reportmolprobityscor:33,repositori:[1,4,8,16,53],repres:[10,20,21,23,26,27,28,29,40,41,44,45,46,47,50,52,54],represent:[22,23,25,26,27,37,39,41,49,51],reproduc:[3,20,35],reproduct:20,repuls:49,request:[26,28,48,51],requir:[0,2,3,5,8,13,16,19,20,21,22,26,27,28,31,32,35,36,37,42,49,50,51],reread:26,res:[9,21,22,25,28,31,32,36,40,49,50,51],res_depth:26,res_idx:[49,50],res_index:21,res_indic:[21,25,36],res_list:[21,25,32,36],res_num:21,resembl:[16,28],reserv:11,reset:[10,21,25,32,34,40,49],resid:5,residu:[0,3,8,9,21,22,23,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,42,44,45,47,49,50,51],residue_depth:26,residue_index:[45,49,50],residue_list:35,residuedepth:26,residuehandl:[9,21,22,26,29,31,32,33,34,35,49,50,51],residuehandlelist:21,residueview:35,resiz:[22,37],resnum:[21,22,29,31,35,36,40],resnum_on:40,resnum_rang:35,resnum_two:40,resolut:[22,32],resolv:[16,21,32,35],resolvecystein:44,resort:35,respect:[9,25,28,35],respons:[8,16,20],rest:[1,8,16,36],restor:[22,31,34,40],restraint:[26,32],restrict:[8,16,29],restructuredtext:[4,8],result:[0,2,8,10,20,25,27,28,31,32,33,34,35,36,38,44,51],resum:14,retain:[20,35],reus:[35,36],review:[16,53],revis:20,reviv:16,rewrit:1,richardson:38,ridig:36,right:[1,2,8,10,13,20],rigid:[0,3,30,32,34,36,46,47,49,51,52,54],rigid_frame_cutoff:36,rigidblock:28,rij:43,ring:[3,30,35],ring_punch_detect:35,risk:20,rmsd:[22,23,26,28,31,32],rmsd_cutoff:[26,31,32],rmsd_thresh:[26,28],rname:28,rnum:40,robot:38,role:13,root:[2,4,8,16],rosetta:41,rot:36,rot_constructor:47,rot_group:[47,50],rot_lib:50,rot_lib_entri:50,rota_out:33,rotam:[0,3,33,36,38,44,45,47,52,54],rotamer:[48,51],rotamer_group:[44,46,47],rotamer_id:47,rotamer_librari:[3,35,36,48],rotamer_model:36,rotamer_on:44,rotamer_res_indic:36,rotamer_two:44,rotamerconstructor:[3,47,49],rotamergraph:[36,46,47,52],rotamergroup:49,rotamerid:[47,50,51],rotamerlib:[35,36,37,48,50,51],rotamerlibentri:[50,51],rotat:[9,22],rotatearoundomegators:22,rotatearoundphipsitors:22,rotatearoundphitors:22,rotatearoundpsitors:22,rotationaroundlin:9,roughli:24,round:51,routin:[1,18,31],royalti:20,rrm:36,rrmrotam:[44,49,50],rrmrotamergroup:[44,46,49,50],rst1:4,rst2:4,rst:[4,8,16],rsync:8,rule:[5,8,9,16],run:[0,4,7,8,10,13,14,15,16,25,26,31,32,33,35,54],runact:1,runexitstatustest:1,runmolprob:33,runmolprobityent:33,runnabl:8,runner:1,runtest:[1,8],runtim:[0,3,10,12,35,50,54],runtimeerror:[9,10,21,22,25,26,27,29,31,32,34,35,36,39,40,41,44,45,48,49,50,51],runtimeexcept:27,s_id:26,s_vinaparticl:49,safe:[2,8],said:4,same:[0,1,2,4,7,8,10,13,14,20,21,25,26,28,31,32,34,35,36,37,39,40,41,42,45,48,49,50,51],samiti:35,sampl:[0,3,8,22,23,28,31,34,35,54],sampled_frag:34,samplemontecarlo:[3,34],sampler:[3,23,24,26,28,30,31,32,35],samplerbas:34,sampling_start_index:34,sander:38,saniti:2,sanity_check:2,satisfi:49,save:[16,22,25,26,27,28,31,34,37,39,40,41,51],savebb:26,savecach:28,savefig:27,savepdb:[7,18,21,22,25,26,28,30,31,32,34,35,36,47],saveport:[25,26,27,37,39,41,51],sc_data:32,sc_rec:[32,36],sc_rec_test:36,sc_result:32,scale:22,scatter:27,scheme:[1,8,13,21,26,29,34],schenk:38,schmidt:38,schwede:[5,8,18,19,38,53],sci:38,scicor:[5,8,18,19,53],scondari:35,scope:14,score:[0,3,8,13,19,23,26,28,29,30,33,34,35,36,37,38,39,41,44,47,54],score_contain:31,score_env:[31,34,42],score_threshold:44,score_vari:35,scorecontain:31,scorer:[3,17,28,30,31,35,40,42,54],scorer_env:[28,31,34],scorerbas:34,scoring_weight:28,scoringgapextend:[29,35],scoringweight:[28,31,35],scratch:[26,34],script:[2,3,4,7,11,13,16,17,18,26,28,37,48,54],scriptnam:11,scriptpath:8,scwrl3:[36,42,50],scwrl3disulfidscor:[43,44],scwrl3pairwisescor:43,scwrl3rotamerconstructor:50,scwrl4:[0,36,38,44,47,50],scwrl4particletyp:49,scwrl4rotamerconstructor:[3,47,50],scwrlrotamerconstructor:3,seamlessli:16,search:[0,2,3,8,21,26,28,31,33,35,36,41,44,49,50],searchdb:[23,26],second:[8,10,22,25,26,28,31,32,35,39,40,41,43,44],secondari:[3,13,26,28,38,41],secondli:8,section:[1,4,7,17,20,53,54],see:[0,1,3,7,8,9,10,11,13,16,18,20,21,25,26,27,29,31,33,34,35,37,39,40,41,51],seed:[10,24,27,31,32,34],seem:16,segment:22,select:[3,10,26,28,34,35,36,47],selenium:35,self:[1,8,10,44,47,49],self_energi:[10,49],sell:20,send:11,sensibl:35,sent:20,seok:38,separ:[1,3,8,10,20,25,27,35,39,41,44],seq:[13,21,23,26,28,29,31,35,40,42],seq_idx_on:28,seq_idx_two:28,seq_one_idx:28,seq_sep:[39,41],seq_tpl:[31,35],seq_trg:[31,35],seq_two_idx:28,seqid:[24,26],seqprof:13,seqr:[0,21,23,26,28,29,31,34,35,36,39,40,41],seqres_str:[21,32,36],seqsim:26,sequenc:[0,3,7,8,13,18,21,22,23,27,28,29,30,31,32,34,35,38,39,40,41],sequencefromchain:42,sequencehandl:[21,26,28,29,35,40],sequencelist:[21,35,40],sequenceprofil:26,sequenti:[22,35],ser:49,serial:[26,37],serializ:37,serin:49,serv:[1,13,26,28,31,34],servic:[16,20],set:[1,2,4,8,10,11,13,15,16,18,21,22,25,26,28,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51,52],setaa:22,setactivesubrotam:49,setallatomscoringkei:31,setaroundomegators:22,setaroundphipsitors:22,setaroundphitors:22,setaroundpsitors:22,setbackbonescoringkei:31,setbackrub:22,setboolprop:50,setc:22,setca:22,setcb:22,setcharg:25,setcompoundschemlib:[19,54],setcpuplatformsupport:25,setdefault:25,setdisulfidconnect:25,setenergi:[39,41],setenviron:[21,32,36,40],setepsilon:25,setfraggerhandl:35,setframeenergi:[47,49],setfudgelj:25,setfudgeqq:25,setinitialenviron:[21,31,32,34,36,40,42],setinternalconnect:25,setinternalenergi:49,setinternalenergyprefactor:49,setinterpol:51,setmass:25,setn:22,setnonbondedcutoff:32,seto:22,setolc:22,setpeptideboundconnect:25,setphitors:22,setpo:21,setprob:49,setpsipredpredict:[35,40,41],setpsitors:22,setresidu:21,setscor:41,setsequ:22,setsequenceoffset:35,setsequenceprofil:35,setsequenceprofilescoreskei:31,setsigma:25,setstemrmsdskei:31,setstructureprofil:26,setstructureprofilescoreskei:31,settemperatur:49,setup:[0,2,5,8,13,17,25,28,31,32,34,35,37,39,40,41,42],setupdefaultallatomscor:[31,35],setupdefaultbackbonescor:[31,35],setupsystem:25,setweight:31,sever:[0,2,3,5,8,10,13,24,26,27,28,31,32,35,36,40,41,42,44,48,49,51,52],sg_pos_on:43,sg_pos_two:43,shake:34,shall:20,shanno:35,shapovalov2011:[38,48],shapovalov:38,share:[5,7,12,17,20,25,37,53,54],shared_ptr:37,shebang:8,sheet:35,shelenkov:38,shell:[1,2,7,8,11],shift:[22,26,29,35],shiftctermin:29,shiftextens:29,ship:[5,48],shorten:35,shorter:35,shortest:31,shortli:8,should:[1,2,4,5,7,8,10,11,13,16,18,20,22,23,26,27,28,31,32,34,35,36,37,40,45,47,49],show:[1,8,13,14,31,34,47,50],show_fil:7,showcas:[1,21,25,27],shown:[8,14,35],shrink:22,shrug:38,side:[8,35,38],sidechain:[3,8,18,19,25,30,32,33,35,37,38,43,44,45,46,48,50,51,52,54],sidechain_pymod:8,sidechain_reconstructor:35,sidechain_rst:8,sidechain_test_data:8,sidechain_test_orig:36,sidechain_test_rec:36,sidechain_unit_test:8,sidechainparticl:50,sidechainreconstructiondata:[30,32],sidechainreconstructor:[25,30,32,35],sidenot:[26,36],sig1:51,sig2:51,sig3:51,sig4:51,sigma:25,silent:1,sim:25,similar:[1,2,13,16,23,26,28,40,41,51],similardihedr:51,similarli:[2,25,35],simpl:[0,9,22,26,34,35,39,40,41,49,51],simpler:[25,35],simplest:[5,8,30],simpli:[5,21,22,31,32,34,35,49,50,51],simplic:[23,26],simplif:13,simplifi:[3,22,25,26],simul:[10,25,31,32,34],sinc:[1,2,4,8,10,11,16,18,22,25,26,27,28,49],singl:[2,4,8,10,21,22,25,26,28,31,32,34,35,36,40,41,45,48,49,50,52],singleton:25,singular:[3,6,28,54],sink:37,sit:8,site:[3,5,8,28],size:[8,21,22,26,27,28,32,34,35,37,39,40,41],sizeof:37,skip:[0,1,8,16,26,28,35,50],slide:28,slight:35,slightli:35,slow:37,slower:[18,25,26,27,35,39,41,51],small:[8,26,32,35,36],smaller:[22,26,28,32,35,41],smallest:47,smallish:[2,8],smart:16,smng:3,smooth:38,smtl:35,snippet:7,soding2005:[26,38],softsampl:34,softwar:[8,20,38,49],sol:47,sole:[1,16,20],soli:38,solis2006:[24,38],solut:[8,10,28,31,32,34,35,36,46,47],solv:[10,16,47,52],solvent:26,solventaccess:26,solver:3,some:[1,2,4,5,6,7,8,13,16,21,23,26,30,33,34,35,36,37,40,42,47,50,51],somedata:37,someth:[1,8,11,16,26],sometim:16,somewher:4,soon:[10,32,41,47,51],sort:[1,4,10,14,31,34,51],sound:[16,50],sourc:[1,2,4,8,13,16,18,19,20,26,28,31,32,33,35,37,51],source1:[4,16],source2:[4,16],source3:4,source4:4,source_chain_idx:35,source_mhandl:35,sp3:51,space:[3,10,28,34,38],span:35,sparticl:49,spatial:[8,28,42],spawn:[1,8],spdbv:35,spdbv_style:35,special:[1,2,4,8,20,25,34,49,50,51],specif:[1,3,8,20,25,26,27,28,31,34,38,40,47,48,49,51],specifi:[0,2,4,5,9,10,22,26,27,28,31,32,35,36,40,49,51],specimen:11,speed:[3,25,35,38],spent:[14,18],sphere:[43,49],sphinx:[2,8],spin:38,spit:[29,34],split:42,sport:8,squar:26,src:[8,16],ss_agreement:41,ss_agreement_scor:37,ssagre:26,ssagreementscor:[37,42],sse:2,sstream:37,stabil:38,stabl:[5,16],stack:16,stage:[1,2,4,8,17,18,28,37,40,51],stai:[1,8,10,16,34],standalon:7,standard:[2,8,12,13,16,21,27,37,41,51],start:[0,1,2,4,7,10,14,16,17,19,21,22,25,26,28,29,31,32,34,35,36,40,41,42,54],start_idx:31,start_resnum:[21,22,26,31,34,35,36,39,40,41],start_resnum_list:36,start_rnum:40,start_temperatur:[10,34],starter:1,startscop:14,stash:[16,31,34,40],state:[1,2,8,20,21,26,31,34,40,41,44,49,51],statement:20,staticruntimeprofil:14,statist:[14,26,38],statu:[1,8],std:37,stderr:1,stdout:1,steadili:[10,34],steepest:[32,35],stem:[9,22,25,26,29,31,32,34,35,36],stemcoord:9,stempairorient:9,step:[3,8,10,14,16,18,19,28,29,30,31,32,34,40,44],stereo:35,stereo_chemical_problem_backbon:35,stereochem:[3,35],steric:51,still:[8,14,25,26,35,37],stop:[1,8,14,28,29,32],stop_criterion:32,stoppag:20,storabl:26,storag:[8,21,25,39,41],store:[0,1,3,7,8,9,16,18,21,22,25,26,27,28,29,31,32,34,35,36,37,47],stori:8,str:[1,11,13,14,15,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,51],str_len:37,straight:16,strategi:51,stream:37,stretch:[21,26,31,34,35,40,41],strict:16,strictli:3,string:[0,3,11,13,26,27,29,37],stringstream:37,strip:[0,35],struc:5,struct:[5,26,37],struct_db:23,structral:[21,40],structur:[0,3,8,13,17,18,19,21,22,23,24,25,27,28,29,30,31,33,34,35,36,37,38,40,41,42,47,49,50,52,54],structural_db:31,structuralgap:[29,33],structuralgaplist:[29,35],structure_db:[26,28,31,35,37],structure_db_on:26,structure_db_two:26,structure_dir:26,structure_id:26,structure_path:26,structure_sourc:13,structuredb:[3,13,24,26,28,31,35,37],structuredbdatatyp:26,structureprofil:26,studer:38,stuff:[26,39],style:[35,40,41,49],sub:[8,26],sub_frag:22,sub_res_list:26,subclass:[8,13],subdir:8,subfold:8,subject:[8,20],sublicens:20,submiss:20,submit:20,submodul:8,submodule1:16,subpart:28,subrotam:[0,3,44,47,49,50,54],subrotameroptim:[36,52],subsequ:[10,20,22,35],subset:[0,13,25,26,28,31,32,35,36],subst:26,subst_matrix:26,substitut:26,substweightmatrix:26,subtre:[4,8],succeed:29,success:[10,11,34],successfulli:5,sudo:7,suffici:26,suffix:11,sugar:6,suggest:[5,8,43],suit:[1,8,26],sulfur:[43,44,49,50],sum:[14,29,35,36,43,44,49],sum_:10,sum_i:10,sum_ie_:10,summari:[14,26],superpos:[22,26,28,31,32,34],superpose_stem:22,superposed_rmsd:[22,31],superposeonto:22,superposit:[3,28,31,34],superpost:28,supersed:20,supervis:1,support:[0,1,2,3,8,11,13,18,20,25,32,35],suppos:[16,34],sure:[2,7,8,13,16,26],surfac:26,surotam:49,surprisingli:50,surround:[25,26,32,36,39,41],symmetr:[26,40,51],symmetri:[39,41],sync:8,syntax:20,sys:[1,13,32],system:[1,2,4,8,16,20,23,26,32,42,54],t_sampler:27,tabl:26,tag:5,tail:22,tailor:[21,35],take:[8,10,21,26,27,28,31,32,34,35,37,41,44,50,52],taken:[0,21,25,32,34,50],talk:1,target:[0,1,2,4,8,13,18,26,28,30,31,32,34,35,40,49],target_chain_idx:35,target_mhandl:35,target_pdb:33,target_posit:28,target_sequ:26,task:[8,16,32,35,37,40],techniqu:[10,38],tell:[1,8,11,13,16,26],temperatur:[10,31,34,49],templat:[0,1,3,13,18,30,35,37,40],temporari:[26,35],temporarili:16,term:[8,20,26,49,51,52],termin:[0,1,9,11,18,20,21,22,25,29,31,32,34,35,36,50],terminal_len:34,terminal_seqr:34,termini:[0,3,29,34,35],terminu:[26,34,35],test:[2,7,12,16,17,18,25,26,33,37],test_:8,test_act:[8,17],test_action_:1,test_action_do_awesom:1,test_action_help:1,test_awesome_featur:8,test_check_io:37,test_cod:8,test_doctest:8,test_foo:4,test_portable_binari:37,test_reconstruct_sidechain:8,test_sidechain_reconstruct:8,test_submodule1:16,test_suite_:4,test_suite_your_module_run:8,test_your_modul:16,testcas:[1,8],testcasenam:8,testexit0:1,testpmexist:1,testreconstruct:8,testutil:[1,8],text:[1,13,20,35],than:[4,8,13,14,16,21,22,26,28,31,32,33,35,36,41,44,50],thats:[26,41],thei:[2,5,8,16,21,22,25,26,27,28,31,32,33,34,35,44,49,50,51,53],them:[4,8,16,22,25,26,27,28,29,31,35,36,40,45],themselv:25,theoret:34,theori:[20,38],therefor:[5,8,22,24,26,28,32,34,35,51],thereof:[20,25],thi:[0,1,2,3,4,5,7,8,10,11,12,13,14,15,16,17,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,42,44,47,49,50,51,52,54],thing:[1,2,8,16,26,28,35,51],think:10,third:[16,17,20,31,32],thoroughli:16,those:[0,1,2,4,8,10,13,16,20,25,28,31,35,36,37,39,41,47,50,51],though:[25,35,37],thr:49,thread:[18,25,35,38],three:[1,4,16,21,22,27,28,31,33,34,38,41,49,51],threonin:49,thresh:[22,49,51],threshold:[10,26,28,32,35,36,40,51],through:[1,8,9,20,22,26,29,35,39,41],throughout:[13,16,24,25],thrown:26,thu:[5,11,49],tidi:16,tightli:16,time:[1,5,8,13,14,16,18,28,35],timer:14,tini:[16,35],titl:[20,27],tlc:[21,49],tlc_an:21,tlctorotid:[47,49],tmp_buf:37,todens:22,toentiti:[7,18,21,22,25,26,32,34,36],toframeresidu:49,togeth:[8,16,26,44],too:[13,16,31,32,35,37],tool:[3,4,23,35,37,42,47],toolbox:16,top:[2,6,8,14,15,16,32,35],topic:[1,8,16],topolog:[25,32],torrmrotam:49,torsion:[0,13,21,22,23,24,26,28,31,32,34,35,41,47],torsion_angl:47,torsion_bin:41,torsion_plot:27,torsion_sampl:[22,26,31,32,34,35,37],torsion_sampler_coil:[28,37],torsion_sampler_extend:[28,37],torsion_sampler_hel:37,torsion_sampler_helix:28,torsion_sampler_list:26,torsion_scor:37,torsionprob:26,torsionsampl:[22,24,26,27,28,31,32,34,35,37,41],torsionscor:[35,37,42],tort:20,total:[10,14,26,28],touch:[1,8,25,32],toward:[0,3,8,13,26,29,32,35,39,41,47,49,50,52],tpl:[0,30,31,35],tpr:[49,51],trace:35,track:[3,11,20,30,35,47],trade:20,trademark:20,tradition:11,trail:0,train:[24,31,35],trajectori:[28,34],tran:[22,49,51],transfer:20,transform:[9,20,22,28,34,35,51],translat:[4,8,20,26,49,51],transomegators:22,treat:[3,8,25,35,36,37,51],treatment:50,tree:[1,4,8,10,16,46,47],treepack:3,treesolv:[10,36,47],trg:[0,13,31,35],tri:[10,28,29,35,44,51],triangl:28,trick:[1,7,16],trigger:[1,4,8,48],tripeptid:27,tripl:11,triplet:[23,28,34,41],trott2010:[38,49],trott:38,trp:[49,51],trustworthi:16,tryptophan:49,ttccpsivarsnfnvcrlpgtpea:[31,35],ttccpsivarsnfnvcrlpgtpeaicatgytciiipgatcpgdyan:35,ttccpsivarsnfnvcrlpgtpeaicatytgciiipgatcpgdyan:[31,35],tupl:[9,10,11,22,25,26,28,29,33,35,36,44],turn:[0,1,11,14,16,35],tutori:8,tweak:35,twice:[14,40],two:[1,7,8,10,16,21,22,25,26,28,29,31,32,35,36,37,39,40,41,43,44,47,49,51],txt:[1,2,4,8,16,20],type:[0,1,8,9,10,11,13,14,20,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,47,48,49,50,52],typedef:37,typenam:37,typic:[22,28,34,35,47,51],tyr:[49,51],tyrosin:49,uint32_t:37,uint:37,ultra:26,uncertain:8,uncharg:50,unclos:35,undefin:25,under:[4,8,20],undergo:[28,32,34,36],underli:[29,31,49],underscor:1,understand:16,understood:0,undo:10,unexpect:2,unfavor:[22,32],unfavour:[32,34,44],unfortun:16,unhandl:[0,13],uniba:[5,8,18,19,53],uniform:32,union:20,uniqu:[0,13,28,31,34,51],unit:[2,16,17,37],unittest:[1,8,16],univers:[8,53],unix:16,unknown:25,unless:[13,20,21,22,25,31,39,41],unlik:47,unrecognis:11,unset:[21,25,36],unsupport:[13,37],until:[8,10,28,32,35,40,50],untouch:22,untrack:1,unum:28,unus:16,upat:5,updat:[3,5,7,8,16,21,25,28,29,31,32,35,36,40,42],updatedistribut:27,updateposit:[25,32],upon:[26,32,34],upper:28,ups:3,urei:25,urey_bradley_angl:25,usabl:16,usag:[0,3,10,13,24,26,31,32,36],use:[0,2,3,4,5,8,10,13,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,37,47,48,49,50],use_amber_ff:35,use_bbdep_lib:36,use_frm:36,use_full_extend:35,use_scoring_extend:35,used:[0,2,3,4,8,9,10,11,13,14,15,16,18,21,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,42,45,47,48,49,50],useful:[1,3,8,10,11,22,26,28,30,31,32,35,50],user:[1,5,8,19,28,53],userlevel:1,uses:[5,8,10,22,25,27,28],using:[1,2,3,4,7,8,10,18,20,21,22,25,26,28,31,33,34,35,37,38,39,41,44,45,46,47,49,50,51,54],usr:[2,5,7,8],usual:[1,2,4,8,13,14,16,22,31,35,39],util:18,utilis:[8,16],v_size:37,val:[27,49],valid:[0,10,16,22,26,29,34,35,36,48,51],valin:49,valu:[2,10,11,13,21,22,25,26,28,31,34,35,37,39,40,41,44,47,49,50,51,52],valueerror:[28,35],vanish:40,varadarajan:38,vari:[4,37],variabl:[1,2,8,14,18,25,33,35,37],variant:[25,31],variou:[1,2,4,16,30],vec3:[9,21,22,26,32,33,43,44,49],vec3list:[28,49],vector:[25,27,28,31,37,49],verbal:20,verbos:1,veri:[1,8,11,16,25,28,35,37],verif:13,verifi:[1,11,16],version:[2,3,5,8,16,20,26,35,37,48,49],vertic:28,via:[1,5,8,13,15,25],view:[7,13,16,27,35,40],vina:[3,38,50],vinaparticletyp:[49,50],vinarotamerconstructor:50,virtual:8,visibl:36,vision:38,visual:18,volum:5,wai:[1,2,4,5,8,16,22,23,25,31,41,47,49],wait:8,walk:[1,8],want:[1,2,3,8,15,16,22,26,28,31,32,35,40,49,50,51,52,53],warn:[3,8,16,35],warranti:20,watch:8,web:[2,8],weight:[3,26,28,31,34,35,39,41],weird:[28,32,47],well:[0,4,16,21,27,28,29,31,35,37,41,47,50,51],went:[0,8],were:[16,26,31,35],wester:38,wether:10,what:[1,8,11,13,16,23,26,36,40],when:[1,3,4,5,8,10,13,14,21,22,25,26,27,28,29,31,34,35,36,37,38,40,41,44,47,48,49,50,51],whenev:[8,21,31,40],where:[0,1,3,4,5,8,10,11,13,14,16,20,21,22,25,26,27,31,35,37,39,40,41,48,49,50,51],wherea:26,wherev:20,whether:[3,5,8,10,11,13,20,22,25,26,31,32,34,35,36,39,40,41,49,50,51],which:[0,1,2,4,8,9,11,12,13,16,18,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,50,51],whistl:8,whitespac:0,who:[10,47],whole:[1,2,8,16,20,22,26,35,49],whom:20,why:[1,16],width:[10,37,47],wild:4,window:28,window_length:28,wise:4,wish:[2,17,27,35],with_aa:31,with_db:31,within:[2,3,4,8,14,16,20,21,25,28,29,33,35,36,39,41,51],without:[0,1,3,4,8,11,13,20,25,29,32,35,40,51],wolfson:[28,38],won:[0,35,36,50],word:4,work:[1,2,4,5,7,8,14,16,18,20,25,29,35,37,50],worldwid:20,worst:16,worth:53,would:[1,2,8,11,22,26,27,35,44,49],wrap:26,wrapper:[1,4,8,15,35],write:[0,17,20,26,27,32,37,39,41,51],writebasetyp:37,writemagicnumb:37,writetypes:37,writeversionnumb:37,written:[8,20,37],wrong:[2,13],wwpdb:5,www:20,x_1:10,x_2:10,x_i:10,x_j:10,x_n:10,xlabel:27,xlim:27,xml:8,xxx:[22,49],xxx_num_atom:21,xxx_num_hydrogen:21,year:1,yet:[26,31,35],ylabel:27,ylim:27,you:[0,1,2,3,4,5,7,8,10,11,13,14,15,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,37,39,40,41,47,48,49,50,51,52,53],your:[1,2,4,5,13,14,16,17,18,20,22,26,28,35,37,48],your_modul:[8,16],yourself:[2,8,10,16,35,50],yyyi:20,zero:[0,26,28,35,51],zhou2005:[26,38],zhou:38,zip:[26,47]},titles:["ProMod3 Actions","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3\u2019s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"xref py py-func docutils literal notranslate\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],For:[4,11,17,54],Into:32,The:[1,5,7,16,21,22,26,27,31,35,36,45,49,50,51],Using:[2,37],With:33,acid:[21,25,27],action:[0,1,4,5,8],actiontestcas:1,algorithm:28,align:35,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,app:7,argument:13,atom:[21,32,39],avail:7,backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:[1,5],exisit:37,extend:29,featur:[8,26],fiddl:35,file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:5,instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:51,novo:[28,34],object:[24,34,45],optim:52,ost:25,other:43,output:1,own:[5,8],pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,5,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,registri:5,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 1bddb4b5482b8452a671f9479457228e39a07bab..75517390cc3c8e174d9c62a7a7c63652fe6d36a7 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Disulfid Bond Evaluation — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Disulfid Bond Evaluation — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
<link rel="prev" title="Rotamer Graph" href="graph.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -50,12 +36,12 @@
<div class="section" id="disulfid-bond-evaluation">
<h1>Disulfid Bond Evaluation<a class="headerlink" href="#disulfid-bond-evaluation" title="Permalink to this headline">¶</a></h1>
<p>When calculating the pairwise interaction energy between two rotamers building
-a disulfid bond, one would get an unfavourable energy due to “clashes” between
+a disulfid bond, one would get an unfavourable energy due to “clashes” between
the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
disulfid bonds. The scoring module implements an empirically derived disulfid
-score (<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>) as defined in
-<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>. The paper proposes two rotamers to be in a disulfid
+score (<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>) as defined in
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>. The paper proposes two rotamers to be in a disulfid
bonded state, if the resulting disulfid score plus the self energies of the
involved rotamers is below 45. If there are several cysteines close together,
this problem gets another layer of complexity. One has to assure, that
@@ -64,83 +50,75 @@ of disulfid bonds is geometrically optimal. SCWRL4 proposes an approach,
that has also been implemented here.</p>
<dl class="method">
<dt id="promod3.sidechain.DisulfidScore">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">DisulfidScore</code><span class="sig-paren">(</span><em>rotamer_one</em>, <em>rotamer_two</em>, <em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>ca_pos_two</em>, <em>cb_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.DisulfidScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">DisulfidScore</code><span class="sig-paren">(</span><em class="sig-param">rotamer_one</em>, <em class="sig-param">rotamer_two</em>, <em class="sig-param">ca_pos_one</em>, <em class="sig-param">cb_pos_one</em>, <em class="sig-param">ca_pos_two</em>, <em class="sig-param">cb_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.DisulfidScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Directly extracts the positions of the gamma sulfurs from the rotamers by
-searching for particles with the name “SG”.
+searching for particles with the name “SG”.
The found positions are then passed to
-<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>.
-In case of <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> it expects exactly one gamma sulfur per
-rotamer. In case of <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> there can be an arbitrary number
+<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>.
+In case of <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> it expects exactly one gamma sulfur per
+rotamer. In case of <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> there can be an arbitrary number
of gamma sulfurs per rotamer (at least one), it then evaluates the score
for all possible combinations of gamma sulfurs and takes the minimum score.
To get a final DisulfidScore, it finally adds the self energies of the
rotamers to the result of the geometric expression.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
-<li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
-<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
-<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
-<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</p></li>
+<li><p><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</p></li>
+<li><p><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</p></li>
+<li><p><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</p></li>
+<li><p><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</p></li>
+<li><p><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if given rotamers do not contain
-exactly (in case of <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a>) or at least (in case of
-<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) one particle representing the gamma sulfur.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The result of the raw score plus the average
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if given rotamers do not contain
+exactly (in case of <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a>) or at least (in case of
+<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) one particle representing the gamma sulfur.</p>
+</dd>
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The result of the raw score plus the average
self energies of the input rotamers</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.ResolveCysteins">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ResolveCysteins</code><span class="sig-paren">(</span><em>rotamer_groups</em>, <em>ca_positions</em>, <em>cb_positions</em><span class="optional">[</span>, <em>score_threshold=45.0</em>, <em>optimize_subrotamers=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ResolveCysteins" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">ResolveCysteins</code><span class="sig-paren">(</span><em class="sig-param">rotamer_groups</em>, <em class="sig-param">ca_positions</em>, <em class="sig-param">cb_positions</em><span class="optional">[</span>, <em class="sig-param">score_threshold=45.0</em>, <em class="sig-param">optimize_subrotamers=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ResolveCysteins" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to optimize disulfid bond network. In a first step, all disulfid bonds
-get detected using <a class="reference internal" href="#promod3.sidechain.DisulfidScore" title="promod3.sidechain.DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">DisulfidScore()</span></code></a>. If the value between two rotamers is
-below <strong>score_threshold</strong>, they’re assumed to be bonded. The function then
+get detected using <a class="reference internal" href="#promod3.sidechain.DisulfidScore" title="promod3.sidechain.DisulfidScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">DisulfidScore()</span></code></a>. If the value between two rotamers is
+below <strong>score_threshold</strong>, they’re assumed to be bonded. The function then
tries to detect the largest possible set of disulfide bonds, with no
cysteine being part of more than one bond. If several largest sets are
possible, the one with the optimal sum of scores gets estimated.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of
-<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</li>
-<li><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
-<li><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
-<li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
-as a disulfid bond</li>
-<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</p></li>
+<li><p><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</p></li>
+<li><p><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</p></li>
+<li><p><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
+as a disulfid bond</p></li>
+<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
rotamer groups, the active subrotamers get
optimized. For every pair of rotamers
participating in a disulfid bond, the subrotamers
-with best <a class="reference internal" href="#promod3.sidechain.DisulfidScore" title="promod3.sidechain.DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">DisulfidScore()</span></code></a> get activated in
+with best <a class="reference internal" href="#promod3.sidechain.DisulfidScore" title="promod3.sidechain.DisulfidScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">DisulfidScore()</span></code></a> get activated in
the input <strong>rotamer_groups</strong>. This has an effect
-when the rotamers get applied on residues.</li>
+when the rotamers get applied on residues.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> objects with equal
-length. Both lists contain <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#tuple" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></a> objects with two elements.
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> objects with equal
+length. Both lists contain <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> objects with two elements.
The tuples in the first list describe the indices of cysteins
participating in disulfid bonds. The tuples in the second list
describe the optimal rotamers in the according rotamer groups.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -151,12 +129,46 @@ describe the optimal rotamers in the according rotamer groups.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="graph.html" title="previous chapter">Rotamer Graph</a></li>
<li>Next: <a href="loading.html" title="next chapter">Loading Rotamer Libraries</a></li>
</ul></li>
@@ -164,23 +176,24 @@ describe the optimal rotamers in the according rotamer groups.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/disulfid.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -189,11 +202,11 @@ describe the optimal rotamers in the according rotamer groups.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/disulfid.txt"
+ <a href="../_sources/sidechain/disulfid.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 553d9083a5e70fc95cc3e37391479c96dd820fc4..c9d5c91db3abb0803acb37180af1bcd14fa32216 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Frame - The Rigid Part — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Frame - The Rigid Part — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
<link rel="prev" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -61,66 +47,55 @@ belonging to the frame residue with the same residue index are neglected.</p>
<h2>The Frame Objects<a class="headerlink" href="#the-frame-objects" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.FrameResidue">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FrameResidue</code><span class="sig-paren">(</span><em>particles</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a>) – particles building frame residue</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Interaction energies between the constructed frame
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">FrameResidue</code><span class="sig-paren">(</span><em class="sig-param">particles</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a>) – particles building frame residue</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Interaction energies between the constructed frame
residue and any rotamer associated to the same
-residue index are neglected</li>
+residue index are neglected</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.FrameResidue.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of particles in <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of particles in <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FrameResidue.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> index</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> at position <strong>index</strong></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if index is invalid</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> index</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at position <strong>index</strong></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.Frame">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">Frame</code><span class="sig-paren">(</span><em>frame_residues</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame" title="Permalink to this definition">¶</a></dt>
-<dd><p>The <a class="reference internal" href="#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> object is used as a container for rigid particles, that
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">Frame</code><span class="sig-paren">(</span><em class="sig-param">frame_residues</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame" title="Permalink to this definition">¶</a></dt>
+<dd><p>The <a class="reference internal" href="#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> object is used as a container for rigid particles, that
can be passed to rotamer groups for calculating frame energies.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame_residues</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>) – residues building the frame.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>frame_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>) – residues building the frame.</p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -133,19 +108,45 @@ can be passed to rotamer groups for calculating frame energies.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Frame - The Rigid Part</a><ul>
-<li><a class="reference internal" href="#the-frame-objects">The Frame Objects</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="rotamer.html" title="previous chapter">Representing Sidechains - Rotamers & Co.</a></li>
<li>Next: <a href="rotamer_constructor.html" title="next chapter">Rotamer Constructor</a></li>
</ul></li>
@@ -153,23 +154,24 @@ can be passed to rotamer groups for calculating frame energies.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/frame.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -178,11 +180,11 @@ can be passed to rotamer groups for calculating frame energies.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/frame.txt"
+ <a href="../_sources/sidechain/frame.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index acd4f311bcee96a0804d6fe3623e80eb76225d98..cc392291aa2bec8486007c41713a5fe53d67fa72 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Rotamer Graph — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Rotamer Graph — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
<link rel="prev" title="Rotamer Library" href="rotamer_lib.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -53,32 +39,29 @@
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
overall solution has to be found. ProMod3 implements a
-<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.GraphMinimizer</span></code></a> that allows to find solutions using
+<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.core.GraphMinimizer</span></code></a> that allows to find solutions using
tree decomposition, A* and Monte Carlo algorithms.</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerGraph">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerGraph</code><a class="headerlink" href="#promod3.sidechain.RotamerGraph" title="Permalink to this definition">¶</a></dt>
-<dd><p>The <a class="reference internal" href="#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal"><span class="pre">RotamerGraph</span></code></a> objects inherits from
-<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.GraphMinimizer</span></code></a> and extends the minimizer by static
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerGraph</code><a class="headerlink" href="#promod3.sidechain.RotamerGraph" title="Permalink to this definition">¶</a></dt>
+<dd><p>The <a class="reference internal" href="#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a> objects inherits from
+<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.core.GraphMinimizer</span></code></a> and extends the minimizer by static
initialization functions.</p>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.sidechain.RotamerGraph.CreateFromRRMList">
-<em class="property">static </em><code class="descname">CreateFromRRMList</code><span class="sig-paren">(</span><em>rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromRRMList" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">CreateFromRRMList</code><span class="sig-paren">(</span><em class="sig-param">rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromRRMList" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.sidechain.RotamerGraph.CreateFromFRMList">
-<em class="property">static </em><code class="descname">CreateFromFRMList</code><span class="sig-paren">(</span><em>rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromFRMList" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> or <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>
+<em class="property">static </em><code class="sig-name descname">CreateFromFRMList</code><span class="sig-paren">(</span><em class="sig-param">rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromFRMList" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> or <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
objects representing the possible sidechain
-conformations for every amino acid position.</td>
-</tr>
-</tbody>
-</table>
+conformations for every amino acid position.</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -91,12 +74,46 @@ conformations for every amino acid position.</td>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="rotamer_lib.html" title="previous chapter">Rotamer Library</a></li>
<li>Next: <a href="disulfid.html" title="next chapter">Disulfid Bond Evaluation</a></li>
</ul></li>
@@ -104,23 +121,24 @@ conformations for every amino acid position.</td>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/graph.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -129,11 +147,11 @@ conformations for every amino acid position.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/graph.txt"
+ <a href="../_sources/sidechain/graph.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index c739e3252590010ad0b5d36b3650c3eb21132926..d74fe72a81522f2b4d1b1d248f32f1594f14d23b 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>sidechain - Sidechain Modelling — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>sidechain - Sidechain Modelling — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
<link rel="prev" title="Modelling Algorithms" href="../modelling/algorithms.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -48,9 +34,9 @@
<div class="body" role="main">
<div class="section" id="module-promod3.sidechain">
-<span id="sidechain-sidechain-modelling"></span><h1><a class="reference internal" href="#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> - Sidechain Modelling<a class="headerlink" href="#module-promod3.sidechain" title="Permalink to this headline">¶</a></h1>
+<span id="sidechain-sidechain-modelling"></span><h1><a class="reference internal" href="#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> - Sidechain Modelling<a class="headerlink" href="#module-promod3.sidechain" title="Permalink to this headline">¶</a></h1>
<p>Tools and algorithms to model sidechains given backbone coordinates. The full
-module is heavily based on SCWRL4 <a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a> . The according paper describes
+module is heavily based on SCWRL4 <a class="reference internal" href="../references.html#krivov2009" id="id1"><span>[krivov2009]</span></a> . The according paper describes
the modelling of sidechains using two different rotamer models. A rigid model,
as well as a flexible model. Both models are implemented in ProMod3 and can be
applied in flexible ways.</p>
@@ -59,8 +45,8 @@ algorithm using the functionality in the module. Note, that this code will crash
as soon as you have structures containing all the weirdness the PDB throws at
us. In this case, you should use the full fletched sidechain reconstruction
pipelines available in the modelling module.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">sidechain</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">sidechain</span>
<span class="c1"># load a protein</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
@@ -187,7 +173,41 @@ pipelines available in the modelling module.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
@@ -198,23 +218,24 @@ pipelines available in the modelling module.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/index.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -223,11 +244,11 @@ pipelines available in the modelling module.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/index.txt"
+ <a href="../_sources/sidechain/index.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index 610569f82a2a8cb0387f22b455ac4a1eaa28ee49..e5087c03d885199a9cd22308eaf01cef0aa2ef7d 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Loading Rotamer Libraries — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Loading Rotamer Libraries — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
<link rel="prev" title="Disulfid Bond Evaluation" href="disulfid.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -51,75 +37,71 @@
<h1>Loading Rotamer Libraries<a class="headerlink" href="#loading-rotamer-libraries" title="Permalink to this headline">¶</a></h1>
<p>There are several rotamer libraries that can be used in ProMod3 . ProMod3
is optimized for the use with backbone dependent rotamer libraries such
-as the 2010 library provided by the Dunbrack lab <a class="reference internal" href="../references.html#shapovalov2011" id="id1">[shapovalov2011]</a>.
+as the 2010 library provided by the Dunbrack lab <a class="reference internal" href="../references.html#shapovalov2011" id="id1"><span>[shapovalov2011]</span></a>.
You can request a licence <a class="reference external" href="http://dunbrack.fccc.edu/bbdep2010/">here</a>
and generate such a library as described in
extras/data_generation/rotamer_library/README. Alternatively, ProMod3
provides its own backbone dependent or backbone independent libraries
-that can be loaded with <a class="reference internal" href="#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal"><span class="pre">LoadBBDepLib()</span></code></a> / <a class="reference internal" href="#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal"><span class="pre">LoadLib()</span></code></a>.</p>
+that can be loaded with <a class="reference internal" href="#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadBBDepLib()</span></code></a> / <a class="reference internal" href="#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadLib()</span></code></a>.</p>
<dl class="method">
<dt id="promod3.sidechain.LoadBBDepLib">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadBBDepLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadBBDepLib" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">LoadBBDepLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadBBDepLib" title="Permalink to this definition">¶</a></dt>
<dd><p>A backbone dependent rotamer library shipped with ProMod3. You can find
details on how it is created in extras/data_generation/rotamer_library/README.
All scripts to build it are in the same directory as the README file and
build the basis for custom versions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested Library</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The requested Library</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.LoadLib">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadLib" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">LoadLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadLib" title="Permalink to this definition">¶</a></dt>
<dd><p>A backbone independent rotamer library shipped with ProMod3. You can find
details on how it is created in extras/data_generation/rotamer_library/README.
All scripts to build it are in the same directory as the README file and
build the basis for custom versions.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested library</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The requested library</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.ReadDunbrackFile">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ReadDunbrackFile</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ReadDunbrackFile" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">ReadDunbrackFile</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ReadDunbrackFile" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads a file as it is provided when you get a licence for the 2010 library of
the Dunbrack lab. It can only read the classic version, where all rotamers
are in a single file. Specific distributions of non-rotameric sidechains
cannot be read. You can find an example described in
extras/data_generation/rotamer_library/README</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – Name of the file</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Throws:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file does not exist, the format
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> – Name of the file</p>
+</dd>
+<dt class="field-even">Throws</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file does not exist, the format
is not valid or when the library is incomplete leading to problems
to make the library static. Most likely your input file is
-incomplete if the last problem gets triggered.</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The read library</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a></td>
-</tr>
-</tbody>
-</table>
+incomplete if the last problem gets triggered.</p>
+</dd>
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The read library</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -130,12 +112,46 @@ incomplete if the last problem gets triggered.</td>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="disulfid.html" title="previous chapter">Disulfid Bond Evaluation</a></li>
<li>Next: <a href="subrotamer_optimizer.html" title="next chapter">Subrotamer Optimization</a></li>
</ul></li>
@@ -143,23 +159,24 @@ incomplete if the last problem gets triggered.</td>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/loading.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -168,11 +185,11 @@ incomplete if the last problem gets triggered.</td>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/loading.txt"
+ <a href="../_sources/sidechain/loading.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 19ed06f65c3451f4b00e3cab7725cf5b5c1aa70c..0fbcb9adc832aace334453193da8dfb179e30b24 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Frame - The Rigid Part" href="frame.html" />
<link rel="prev" title="sidechain - Sidechain Modelling" href="index.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -49,13 +35,13 @@
<div class="section" id="representing-sidechains-rotamers-co">
<h1>Representing Sidechains - Rotamers & Co.<a class="headerlink" href="#representing-sidechains-rotamers-co" title="Permalink to this headline">¶</a></h1>
-<p>A rotamer represents an amino acid sidechain identified by a <a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>
-and is a set of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects.
-Two types of rotamers exist. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>.
+<p>A rotamer represents an amino acid sidechain identified by a <a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>
+and is a set of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects.
+Two types of rotamers exist. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>.
To gather all possible rotamers for one location,
-ProMod3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.
+ProMod3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>.
All parts of the structure that are kept rigid can be represented by
-a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> object.</p>
+a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> object.</p>
<div class="section" id="rotamerid">
<h2>RotamerID<a class="headerlink" href="#rotamerid" title="Permalink to this headline">¶</a></h2>
<p>The sidechain module has its own definition of amino acids to satisfy custom
@@ -64,83 +50,79 @@ As an example there are histidine in two possible protonation states,
that affect the hbond term or different versions of proline/cysteine.</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerID">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acids. Possible values:</p>
<table class="hlist"><tr><td><ul class="simple">
-<li>ARG - Arginine</li>
-<li>ASN - Asparagine</li>
-<li>ASP - Aspartate</li>
-<li>GLN - Glutamine</li>
-<li>GLU - Glutamate</li>
-<li>LYS - Lysine</li>
-<li>SER - Serine</li>
-<li>CYS - Cystein</li>
-<li>CYH - “free” Cystein</li>
-<li>CYD - disulfid bonded Cystein</li>
-<li>MET - Methionine</li>
-<li>TRP - Tryptophane</li>
-<li>TYR - Tyrosine</li>
-<li>THR - Threonine</li>
+<li><p>ARG - Arginine</p></li>
+<li><p>ASN - Asparagine</p></li>
+<li><p>ASP - Aspartate</p></li>
+<li><p>GLN - Glutamine</p></li>
+<li><p>GLU - Glutamate</p></li>
+<li><p>LYS - Lysine</p></li>
+<li><p>SER - Serine</p></li>
+<li><p>CYS - Cystein</p></li>
+<li><p>CYH - “free” Cystein</p></li>
+<li><p>CYD - disulfid bonded Cystein</p></li>
+<li><p>MET - Methionine</p></li>
+<li><p>TRP - Tryptophane</p></li>
+<li><p>TYR - Tyrosine</p></li>
+<li><p>THR - Threonine</p></li>
</ul>
</td><td><ul class="simple">
-<li>VAL - Valine</li>
-<li>ILE - Isoleucine</li>
-<li>LEU - Leucine</li>
-<li>PRO - Proline</li>
-<li>CPR - cis-Proline</li>
-<li>TPR - trans-Proline</li>
-<li>HIS - Histidine</li>
-<li>HSD - d-protonated Histidine</li>
-<li>HSE - e-protonated Histidine</li>
-<li>PHE - Phenylalanine</li>
-<li>GLY - Glycine</li>
-<li>ALA - Alanine</li>
-<li>XXX - Invalid</li>
+<li><p>VAL - Valine</p></li>
+<li><p>ILE - Isoleucine</p></li>
+<li><p>LEU - Leucine</p></li>
+<li><p>PRO - Proline</p></li>
+<li><p>CPR - cis-Proline</p></li>
+<li><p>TPR - trans-Proline</p></li>
+<li><p>HIS - Histidine</p></li>
+<li><p>HSD - d-protonated Histidine</p></li>
+<li><p>HSE - e-protonated Histidine</p></li>
+<li><p>PHE - Phenylalanine</p></li>
+<li><p>GLY - Glycine</p></li>
+<li><p>ALA - Alanine</p></li>
+<li><p>XXX - Invalid</p></li>
</ul>
</td></tr></table>
-<p>The RotamerID enum can be accessed either directly as <code class="docutils literal"><span class="pre">promod3.sidechain.ARG</span></code>
-or as <code class="docutils literal"><span class="pre">promod3.sidechain.RotamerID.ARG</span></code>.</p>
+<p>The RotamerID enum can be accessed either directly as <code class="docutils literal notranslate"><span class="pre">promod3.sidechain.ARG</span></code>
+or as <code class="docutils literal notranslate"><span class="pre">promod3.sidechain.RotamerID.ARG</span></code>.</p>
</dd></dl>
<div class="section" id="how-can-i-get-an-id">
<h3>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h3>
<p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
or from amino acid three letter codes.</p>
<dl class="method">
<dt id="promod3.sidechain.TLCToRotID">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">TLCToRotID</code><span class="sig-paren">(</span><em>tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">TLCToRotID</code><span class="sig-paren">(</span><em class="sig-param">tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
<dd><p>Directly translates the three letter code into a RotamerID. Following
exactly the naming convention defined above.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>tlc</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Three letter code of amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>tlc</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Three letter code of amino acid</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.AAToRotID">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">AAToRotID</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">AAToRotID</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
to generate special IDs this way
-(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
-defined in <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
-</tr>
-</tbody>
-</table>
+(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
+defined in <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</p>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -149,109 +131,101 @@ defined in <a class="reference external" href="https://www.openstructure.org/doc
<h2>The Smallest Building Block - The Particle<a class="headerlink" href="#the-smallest-building-block-the-particle" title="Permalink to this headline">¶</a></h2>
<p>Particles give raise to more complex objects such as rotamers and frame
residues. They contain all data required to calculate pairwise energies.
-For every energy function available in ProMod3, there’s a particle creation
+For every energy function available in ProMod3, there’s a particle creation
function.</p>
<dl class="class">
<dt id="promod3.sidechain.PScoringFunction">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">PScoringFunction</code><a class="headerlink" href="#promod3.sidechain.PScoringFunction" title="Permalink to this definition">¶</a></dt>
-<dd><p>The available scoring functions between <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects</p>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">PScoringFunction</code><a class="headerlink" href="#promod3.sidechain.PScoringFunction" title="Permalink to this definition">¶</a></dt>
+<dd><p>The available scoring functions between <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</p>
<ul class="simple">
-<li>SCWRL4 - <a class="reference internal" href="#scwrl4-scoring-function"><span class="std std-ref">The SCWRL4 scoring function</span></a></li>
-<li>SCWRL3 - <a class="reference internal" href="#scwrl3-scoring-function"><span class="std std-ref">The SCWRL3 scoring function</span></a></li>
-<li>VINA - <a class="reference internal" href="#vina-scoring-function"><span class="std std-ref">The VINA scoring function</span></a></li>
+<li><p>SCWRL4 - <a class="reference internal" href="#scwrl4-scoring-function"><span class="std std-ref">The SCWRL4 scoring function</span></a></p></li>
+<li><p>SCWRL3 - <a class="reference internal" href="#scwrl3-scoring-function"><span class="std std-ref">The SCWRL3 scoring function</span></a></p></li>
+<li><p>VINA - <a class="reference internal" href="#vina-scoring-function"><span class="std std-ref">The VINA scoring function</span></a></p></li>
</ul>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.Particle">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">Particle</code><a class="headerlink" href="#promod3.sidechain.Particle" title="Permalink to this definition">¶</a></dt>
-<dd><p>The particle class. There’s no constructor. You can either use the
-<a class="reference internal" href="rotamer_constructor.html#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> to create full <code class="xref py py-class docutils literal"><span class="pre">RotamerGroup</span></code> objects
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">Particle</code><a class="headerlink" href="#promod3.sidechain.Particle" title="Permalink to this definition">¶</a></dt>
+<dd><p>The particle class. There’s no constructor. You can either use the
+<a class="reference internal" href="rotamer_constructor.html#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> to create full <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGroup</span></code> objects
with all underlying particles or the energy function specific creation
functions.</p>
<dl class="method">
<dt id="promod3.sidechain.Particle.PairwiseScore">
-<code class="descname">PairwiseScore</code><span class="sig-paren">(</span><em>other_particle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.PairwiseScore" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">PairwiseScore</code><span class="sig-paren">(</span><em class="sig-param">other_particle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.PairwiseScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates score between the two particles</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other_particle</strong> (<a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a>) – The interacting particle</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The score</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if the scoring function
-parametrization of the two particles is inconsistent</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>other_particle</strong> (<a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a>) – The interacting particle</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The score</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the scoring function
+parametrization of the two particles is inconsistent</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetName">
-<code class="descname">GetName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetName" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The name of the particle, which corresponds to the
-atom name</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetName" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The name of the particle, which corresponds to the
+atom name</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetCollisionDistance">
-<code class="descname">GetCollisionDistance</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetCollisionDistance" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The “collision distance” all pairs of particles with
+<code class="sig-name descname">GetCollisionDistance</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetCollisionDistance" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The “collision distance” all pairs of particles with
their distance below the sum of their collision
distances are considered as interacting and thus
-evaluated by the underlying scoring function.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
-</tr>
-</tbody>
-</table>
+evaluated by the underlying scoring function.</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetPos">
-<code class="descname">GetPos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetPos" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The position of the particle</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetPos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetPos" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The position of the particle</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetScoringFunction">
-<code class="descname">GetScoringFunction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetScoringFunction" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The underlying scoring function</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.PScoringFunction" title="promod3.sidechain.PScoringFunction"><code class="xref py py-class docutils literal"><span class="pre">PScoringFunction</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetScoringFunction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetScoringFunction" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The underlying scoring function</p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.PScoringFunction" title="promod3.sidechain.PScoringFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PScoringFunction</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -260,57 +234,53 @@ evaluated by the underlying scoring function.</td>
<span id="scwrl4-scoring-function"></span><h3>The SCWRL4 scoring function<a class="headerlink" href="#the-scwrl4-scoring-function" title="Permalink to this headline">¶</a></h3>
<p>The SCWRL4 scoring function combines a Lennard-Jones style term with
a hydrogen bond term. Details can be found in the relevant publication
-<a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a>.</p>
+<a class="reference internal" href="../references.html#krivov2009" id="id1"><span>[krivov2009]</span></a>.</p>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4ParticleType">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4ParticleType</code><a class="headerlink" href="#promod3.sidechain.SCWRL4ParticleType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SCWRL4ParticleType</code><a class="headerlink" href="#promod3.sidechain.SCWRL4ParticleType" title="Permalink to this definition">¶</a></dt>
<dd><p>The SCWRL4 energy function differentiates between following particle types
that define the behaviour of the Lennard-Jones style term:</p>
<ul class="simple">
-<li>HParticle - represents hydrogen</li>
-<li>CParticle - default representation of a carbon</li>
-<li>CH1Particle - represents carbon bound to 1 hydrogen</li>
-<li>CH2Particle - represents carbon bound to 2 hydrogen</li>
-<li>CH3Particle - represents carbon bound to 3 hydrogen</li>
-<li>NParticle - represents nitrogen</li>
-<li>OParticle - default representation of oxygen</li>
-<li>OCParticle - represents carbonyl-oxygen for ASP/GLU</li>
-<li>SParticle - represents sulfur</li>
+<li><p>HParticle - represents hydrogen</p></li>
+<li><p>CParticle - default representation of a carbon</p></li>
+<li><p>CH1Particle - represents carbon bound to 1 hydrogen</p></li>
+<li><p>CH2Particle - represents carbon bound to 2 hydrogen</p></li>
+<li><p>CH3Particle - represents carbon bound to 3 hydrogen</p></li>
+<li><p>NParticle - represents nitrogen</p></li>
+<li><p>OParticle - default representation of oxygen</p></li>
+<li><p>OCParticle - represents carbonyl-oxygen for ASP/GLU</p></li>
+<li><p>SParticle - represents sulfur</p></li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.CreateSCWRL4Particle">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateSCWRL4Particle</code><span class="sig-paren">(</span><em>name</em>, <em>particle_type</em>, <em>pos</em><span class="optional">[</span>, <em>charge</em>, <em>lone_pairs=None</em>, <em>polar_direction=None</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL4Particle" title="Permalink to this definition">¶</a></dt>
-<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL4 scoring
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">CreateSCWRL4Particle</code><span class="sig-paren">(</span><em class="sig-param">name</em>, <em class="sig-param">particle_type</em>, <em class="sig-param">pos</em><span class="optional">[</span>, <em class="sig-param">charge</em>, <em class="sig-param">lone_pairs=None</em>, <em class="sig-param">polar_direction=None</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL4Particle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL4 scoring
function</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The name of the particle</li>
-<li><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
-<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
-bond term</li>
-<li><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
+<li><p><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<li><p><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
+bond term</p></li>
+<li><p><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
relevant for the hydrogen bond term. If set, the
particle is a potential hydrogen bond acceptor.
An example would be the Serine OG atom, where you can
represent the two lone pairs with vectors pointing
-from the OG position towards the lone pair centers.</li>
-<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+from the OG position towards the lone pair centers.</p></li>
+<li><p><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
relevant for the hydrogen bond term. If set, the
particle is a potential hydrogen bond donor. An
example would be the Serine HG hydrogen. The
<em>polar_direction</em> would be a vector
-estimated as follows: hg_pos-og_pos.</li>
+estimated as follows: hg_pos-og_pos.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -318,26 +288,22 @@ estimated as follows: hg_pos-og_pos.</li>
<span id="scwrl3-scoring-function"></span><h3>The SCWRL3 scoring function<a class="headerlink" href="#the-scwrl3-scoring-function" title="Permalink to this headline">¶</a></h3>
<p>The SCWRL3 scoring function implements a simple repulsion term that depends on
the hard-sphere radius of the involved particles.
-Details can be found in the relevant publication <a class="reference internal" href="../references.html#canutescu2003" id="id2">[canutescu2003]</a>.</p>
+Details can be found in the relevant publication <a class="reference internal" href="../references.html#canutescu2003" id="id2"><span>[canutescu2003]</span></a>.</p>
<dl class="method">
<dt id="promod3.sidechain.CreateSCWRL3Particle">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateSCWRL3Particle</code><span class="sig-paren">(</span><em>name</em>, <em>radius</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL3Particle" title="Permalink to this definition">¶</a></dt>
-<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL3 scoring
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">CreateSCWRL3Particle</code><span class="sig-paren">(</span><em class="sig-param">name</em>, <em class="sig-param">radius</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL3Particle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL3 scoring
function</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The name of the particle</li>
-<li><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
-repulsion term.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
+<li><p><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
+repulsion term.</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -345,56 +311,52 @@ repulsion term.</li>
<span id="vina-scoring-function"></span><h3>The VINA scoring function<a class="headerlink" href="#the-vina-scoring-function" title="Permalink to this headline">¶</a></h3>
<p>The VINA scoring function is a combination of scores that are named
gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
-software <a class="reference internal" href="../references.html#trott2010" id="id3">[trott2010]</a>. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+software <a class="reference internal" href="../references.html#trott2010" id="id3"><span>[trott2010]</span></a>. VINA only evaluates heavy atoms. Gaussian1, gaussian2
and repulsion are evaluated for all pairs of particles. Hydrophobic is only
-evaluated between C_VINAParticle <a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a> and hbond is
+evaluated between C_VINAParticle <a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a> and hbond is
evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
are intended to evaluate sidechain-sidechain interactions in proteins,
VINA is mainly targeted at interactions between sidechains and ligands.</p>
<p>The VINA scoring function differentiates between the following particle types:</p>
<dl class="class">
<dt id="promod3.sidechain.VINAParticleType">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINAParticleType</code><a class="headerlink" href="#promod3.sidechain.VINAParticleType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">VINAParticleType</code><a class="headerlink" href="#promod3.sidechain.VINAParticleType" title="Permalink to this definition">¶</a></dt>
<dd><ul class="simple">
-<li>O_D_VINAParticle - Oxygen that can be a hydrogen bond donor</li>
-<li>N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor</li>
-<li>O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor</li>
-<li>N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor</li>
-<li>O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor</li>
-<li>N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor</li>
-<li>O_VINAParticle - Oxygen</li>
-<li>N_VINAParticle - Nitrogen</li>
-<li>S_VINAParticle - Sulfur</li>
-<li>P_VINAParticle - Phosphorus</li>
-<li>C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom</li>
-<li>C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens</li>
-<li>F_VINAParticle - Fluorine</li>
-<li>Cl_VINAParticle - Chlorine</li>
-<li>Br_VINAParticle - Bromine</li>
-<li>I_VINAParticle - Iodine</li>
-<li>M_VINAParticle - Metals</li>
-<li>INVALID_VINAParticle - Invalid particle...</li>
+<li><p>O_D_VINAParticle - Oxygen that can be a hydrogen bond donor</p></li>
+<li><p>N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor</p></li>
+<li><p>O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor</p></li>
+<li><p>N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor</p></li>
+<li><p>O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor</p></li>
+<li><p>N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor</p></li>
+<li><p>O_VINAParticle - Oxygen</p></li>
+<li><p>N_VINAParticle - Nitrogen</p></li>
+<li><p>S_VINAParticle - Sulfur</p></li>
+<li><p>P_VINAParticle - Phosphorus</p></li>
+<li><p>C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom</p></li>
+<li><p>C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens</p></li>
+<li><p>F_VINAParticle - Fluorine</p></li>
+<li><p>Cl_VINAParticle - Chlorine</p></li>
+<li><p>Br_VINAParticle - Bromine</p></li>
+<li><p>I_VINAParticle - Iodine</p></li>
+<li><p>M_VINAParticle - Metals</p></li>
+<li><p>INVALID_VINAParticle - Invalid particle…</p></li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.CreateVINAParticle">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateVINAParticle</code><span class="sig-paren">(</span><em>name</em>, <em>particle_type</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateVINAParticle" title="Permalink to this definition">¶</a></dt>
-<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> that can evaluate the VINA scoring
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">CreateVINAParticle</code><span class="sig-paren">(</span><em class="sig-param">name</em>, <em class="sig-param">particle_type</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateVINAParticle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> that can evaluate the VINA scoring
function</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The name of the particle</li>
-<li><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
+<li><p><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -403,405 +365,336 @@ function</p>
<h2>Rotamers<a class="headerlink" href="#rotamers" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RRMRotamer">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RRMRotamer</code><span class="sig-paren">(</span><em class="sig-param">particles</em>, <em class="sig-param">probability</em>, <em class="sig-param">internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>The RRMRotamer represents a rotamer of the so called rigid rotamer model.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects</li>
-<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</p></li>
+<li><p><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
energy calculation, this directly controls the
-internal energy of that rotamer.</li>
-<li><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
+internal energy of that rotamer.</p></li>
+<li><p><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
as -log(<strong>probability</strong>/max_probability),
where max_probability is the maximum
rotamer probability of any rotamer in a
-particular <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>.</li>
+particular <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Access particle at specified index</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of particle of interest</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> at specified index</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if index is invalid</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of particle of interest</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at specified index</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of particles the rotamer contains</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of particles the rotamer contains</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.ApplyOnResidue">
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over every particle and searches for the according atom in
-<strong>res</strong>. If it’s present, the position gets reset to the particle position.
+<strong>res</strong>. If it’s present, the position gets reset to the particle position.
If not, a new atom gets added to <strong>res</strong>. No atoms are removed from <strong>res</strong>
in this process.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
-<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-<strong>res</strong></li>
-<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
-default value (“”)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+<strong>res</strong></p></li>
+<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
+default value (“”)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Set all sidechain atom positions for given residue to the positions of the
particles in the rotamer.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
-<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
+<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.ToFrameResidue">
-<code class="descname">ToFrameResidue</code><span class="sig-paren">(</span><em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Generates and returns a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> based on the internal
+<code class="sig-name descname">ToFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generates and returns a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> based on the internal
particles.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> constructor</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> constructor</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor">
-<code class="descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Prefactor used in internal energy calculation</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Prefactor used in internal energy calculation</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetInternalEnergy">
-<code class="descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Internal Energy if calculated, 0.0 otherwise</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Internal Energy if calculated, 0.0 otherwise</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetFrameEnergy">
-<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns frame energy. This energy can either be manually set or calculated
-using a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> and the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> this rotamer
+using a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> and the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> this rotamer
belongs to.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Frame energy if calculated, 0.0 otherwise</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Frame energy if calculated, 0.0 otherwise</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetSelfEnergy">
-<code class="descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Self energy consisting of internal plus frame energy</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Self energy consisting of internal plus frame energy</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetProbability">
-<code class="descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">probability of this rotamer</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>probability of this rotamer</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor">
-<code class="descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em>prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em class="sig-param">prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetInternalEnergy">
-<code class="descname">SetInternalEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetInternalEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy to be set</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetFrameEnergy">
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy to be set</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.AddFrameEnergy">
-<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy to be added</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy to be added</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetProbability">
-<code class="descname">SetProbability</code><span class="sig-paren">(</span><em>probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal probability to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetProbability</code><span class="sig-paren">(</span><em class="sig-param">probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal probability to be set</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.FRMRotamer">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>T</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">FRMRotamer</code><span class="sig-paren">(</span><em class="sig-param">particles</em>, <em class="sig-param">T</em>, <em class="sig-param">probability</em>, <em class="sig-param">internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>The FRMRotamer represents a rotamer of the so called flexible rotamer model,
where one rotamer gets represented by several subrotamers.
The idea is that all particles of all subrotamers are given at
initialization. Subrotamers are then defined by providing lists of indices.
One particle can be part of several subrotamers.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects</li>
-<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</p></li>
+<li><p><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
energy calculation, this directly controls the
-internal energy of that rotamer.</li>
-<li><strong>T</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Temperature factor, that is used to generate a final
+internal energy of that rotamer.</p></li>
+<li><p><strong>T</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Temperature factor, that is used to generate a final
energy given the subrotamers according to the formalism
-described in the SCWRL4 paper.</li>
-<li><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
+described in the SCWRL4 paper.</p></li>
+<li><p><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
as -log(<strong>probability</strong>/max_probability),
where max_probability is the maximum
rotamer probability of any rotamer in a
-particular <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.</li>
+particular <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>.</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Access particle at specified index</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of particle of interest</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> at specified index</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if index is invalid</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of particle of interest</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at specified index</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of particles the rotamer contains</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of particles the rotamer contains</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetNumSubrotamers">
-<code class="descname">GetNumSubrotamers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetNumSubrotamers" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of subrotamers</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetNumSubrotamers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetNumSubrotamers" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of subrotamers</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.ApplyOnResidue">
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over every particle of the active subrotamer and searches for the
-according atom in <strong>res</strong>. If it’s present, the position gets reset to the
+according atom in <strong>res</strong>. If it’s present, the position gets reset to the
particle position. If not, a new atom gets added to <strong>res</strong>.
No atoms are removed from <strong>res</strong> in this process.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
-<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-the sidechain</li>
-<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+the sidechain</p></li>
+<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Set all sidechain atom positions for given residue to the positions of the
particles in the active surotamer.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
-<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
+<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.ToFrameResidue">
-<code class="descname">ToFrameResidue</code><span class="sig-paren">(</span><em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Generates and returns a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> based on the internal
+<code class="sig-name descname">ToFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generates and returns a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> based on the internal
particles of the active subrotamer.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> constructor</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> constructor</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.ToRRMRotamer">
-<code class="descname">ToRRMRotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToRRMRotamer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Generates and returns a <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> based on the internal
+<code class="sig-name descname">ToRRMRotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToRRMRotamer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generates and returns a <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> based on the internal
particles of the active subrotamer. Following parameters of the
returned rotamer get set: probability (probability of the whole FRMRotamer),
internal_e_prefactor (prefactor of the whole FRMRotamer),
@@ -811,268 +704,216 @@ calculated), internal_energy (the internal energy of the whole FRMRotamer)</p>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetSubrotamerDefinition">
-<code class="descname">GetSubrotamerDefinition</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of subrotamer</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of particle indices belonging to this
-particular subrotamer</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if index is invalid</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSubrotamerDefinition</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of particle indices belonging to this
+particular subrotamer</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor">
-<code class="descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Prefactor used in internal energy calculation</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Prefactor used in internal energy calculation</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetInternalEnergy">
-<code class="descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Internal Energy if calculated, 0.0 otherwise</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Internal Energy if calculated, 0.0 otherwise</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetFrameEnergy">
-<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns frame energy. This energy can either be manually set or calculated
-using a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> and the <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a> this rotamer
+using a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> and the <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a> this rotamer
belongs to.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Frame energy if calculated, 0.0 otherwise</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Frame energy if calculated, 0.0 otherwise</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">GetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span></dt>
<dd><p>Returns frame energy of specified <strong>index</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of subrotamer you want the frame energy from</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Frame energy if calculated, 0.0 otherwise</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if index is invalid</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer you want the frame energy from</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Frame energy if calculated, 0.0 otherwise</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetSelfEnergy">
-<code class="descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Self energy consisting of internal plus frame energy</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Self energy consisting of internal plus frame energy</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetTemperature">
-<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The temperature factor for this rotamer</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>The temperature factor for this rotamer</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetProbability">
-<code class="descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Probability of this rotamer</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Probability of this rotamer</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor">
-<code class="descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em>prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em class="sig-param">prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetInternalEnergy">
-<code class="descname">SetInternalEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetInternalEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy to be set</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetFrameEnergy">
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be set</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>energy</em>, <em>index</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be set</li>
-<li><strong>index</strong> – Index of subrotamer</li>
+<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em>, <em class="sig-param">index</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be set</p></li>
+<li><p><strong>index</strong> – Index of subrotamer</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.AddFrameEnergy">
-<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be added</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be added</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>energy</em>, <em>index</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be added</li>
-<li><strong>index</strong> – Index of subrotamer</li>
+<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em>, <em class="sig-param">index</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be added</p></li>
+<li><p><strong>index</strong> – Index of subrotamer</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.AddSubrotamerDefinition">
-<code class="descname">AddSubrotamerDefinition</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of indices defining a subrotamer</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">AddSubrotamerDefinition</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of indices defining a subrotamer</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetActiveSubrotamer">
-<code class="descname">SetActiveSubrotamer</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetActiveSubrotamer</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>The provided <strong>idx</strong> relates to the subrotamer definitions added at the
rotamer buildup. This idx controls which subrotamer is used when
-<a class="reference internal" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="promod3.sidechain.FRMRotamer.ApplyOnResidue"><code class="xref py py-func docutils literal"><span class="pre">ApplyOnResidue()</span></code></a>, <a class="reference internal" href="#promod3.sidechain.FRMRotamer.ToFrameResidue" title="promod3.sidechain.FRMRotamer.ToFrameResidue"><code class="xref py py-func docutils literal"><span class="pre">ToFrameResidue()</span></code></a> or <a class="reference internal" href="#promod3.sidechain.FRMRotamer.ToRRMRotamer" title="promod3.sidechain.FRMRotamer.ToRRMRotamer"><code class="xref py py-func docutils literal"><span class="pre">ToRRMRotamer()</span></code></a>
+<a class="reference internal" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="promod3.sidechain.FRMRotamer.ApplyOnResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ApplyOnResidue()</span></code></a>, <a class="reference internal" href="#promod3.sidechain.FRMRotamer.ToFrameResidue" title="promod3.sidechain.FRMRotamer.ToFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ToFrameResidue()</span></code></a> or <a class="reference internal" href="#promod3.sidechain.FRMRotamer.ToRRMRotamer" title="promod3.sidechain.FRMRotamer.ToRRMRotamer"><code class="xref py py-func docutils literal notranslate"><span class="pre">ToRRMRotamer()</span></code></a>
gets called. By default, the value is 0 => first added subrotamer
definition gets used.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of subrotamer definition applied on residues</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer definition applied on residues</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetActiveSubrotamer">
-<code class="descname">GetActiveSubrotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">GetActiveSubrotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>Get the index of the active subrotamer</p>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetTemperature">
-<code class="descname">SetTemperature</code><span class="sig-paren">(</span><em>temperature</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>temperature</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Temperature factor for this rotamer</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetTemperature</code><span class="sig-paren">(</span><em class="sig-param">temperature</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Temperature factor for this rotamer</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetProbability">
-<code class="descname">SetProbability</code><span class="sig-paren">(</span><em>probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal probability to be set</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetProbability</code><span class="sig-paren">(</span><em class="sig-param">probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal probability to be set</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -1082,132 +923,110 @@ definition gets used.</p>
<h2>Rotamer Groups<a class="headerlink" href="#rotamer-groups" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RRMRotamerGroup">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
-<dd><p>The RRMRotamerGroup groups several <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects for the same
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">rotamers</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<dd><p>The RRMRotamerGroup groups several <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> objects for the same
residue position.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> objects</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
represents. This index is important when calculating
frame energies to neglect the interactions to frame
-particles of the same residue.</li>
+particles of the same residue.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of rotamers in group</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of rotamers in group</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> at given <em>index</em></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> at given <em>index</em></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.ApplyOnResidue">
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Calls ApplyOnResidue function on rotamer at position <em>index</em></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
-<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-the sidechain</li>
-<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</li>
-<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
-<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+the sidechain</p></li>
+<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</p></li>
+<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
+<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em> or when <em>index</em> or <em>res_idx</em> are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.Merge">
-<code class="descname">Merge</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
-<dd><p>Adds all rotamers in <em>other</em> to current <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Merge</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adds all rotamers in <em>other</em> to current <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a></p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.SetFrameEnergy">
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates sets the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.AddFrameEnergy">
-<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates adds the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh">
-<code class="descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em>thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em class="sig-param">thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches rotamer with lowest self energy <em>l_e</em> and deletes all
rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
</dd></dl>
@@ -1216,132 +1035,110 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<dl class="class">
<dt id="promod3.sidechain.FRMRotamerGroup">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
-<dd><p>The FRMRotamerGroup groups several <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects for the same
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">FRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">rotamers</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<dd><p>The FRMRotamerGroup groups several <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> objects for the same
residue position.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> objects</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
represents. This index is important when calculating
frame energies to neglect the interactions to frame
-particles of the same residue.</li>
+particles of the same residue.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.__len__">
-<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of rotamers in group</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p>Number of rotamers in group</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.__getitem__">
-<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> at given <em>index</em></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> at given <em>index</em></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.ApplyOnResidue">
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Calls ApplyOnResidue function on rotamer at position <em>index</em></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
-<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-the sidechain</li>
-<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</li>
-<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
-<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+the sidechain</p></li>
+<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</p></li>
+<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
+<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em> or when <em>index</em> or <em>res_idx</em> are invalid</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.Merge">
-<code class="descname">Merge</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
-<dd><p>Adds all rotamers in <em>other</em> to current <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">Merge</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adds all rotamers in <em>other</em> to current <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a></p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.SetFrameEnergy">
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates sets the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.AddFrameEnergy">
-<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates adds the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh">
-<code class="descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em>thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em class="sig-param">thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches rotamer with lowest self energy <em>l_e</em> and deletes all
rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
</dd></dl>
@@ -1358,54 +1155,70 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Representing Sidechains - Rotamers & Co.</a><ul>
-<li><a class="reference internal" href="#rotamerid">RotamerID</a><ul>
-<li><a class="reference internal" href="#how-can-i-get-an-id">How can I get an ID?</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a><ul>
-<li><a class="reference internal" href="#the-scwrl4-scoring-function">The SCWRL4 scoring function</a></li>
-<li><a class="reference internal" href="#the-scwrl3-scoring-function">The SCWRL3 scoring function</a></li>
-<li><a class="reference internal" href="#the-vina-scoring-function">The VINA scoring function</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
-<li><a class="reference internal" href="#rotamers">Rotamers</a></li>
-<li><a class="reference internal" href="#rotamer-groups">Rotamer Groups</a></li>
</ul>
-</li>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
<li>Next: <a href="frame.html" title="next chapter">Frame - The Rigid Part</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/rotamer.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -1414,11 +1227,11 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/rotamer.txt"
+ <a href="../_sources/sidechain/rotamer.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 7f0691781d8190af24b8f0195f2a805d20b982ea..3b3b1ea0dd9bb85bb8d9e3a829e65ed204d41441 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Rotamer Constructor — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Rotamer Constructor — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
<link rel="prev" title="Frame - The Rigid Part" href="frame.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -55,187 +41,171 @@ convenient functionality provided by ProMod3.</p>
<h2>The RotamerConstructor Baseclass<a class="headerlink" href="#the-rotamerconstructor-baseclass" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RotamerConstructor">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerConstructor</code><a class="headerlink" href="#promod3.sidechain.RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerConstructor</code><a class="headerlink" href="#promod3.sidechain.RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class that cannot be initialized from Python. It builds
an interface implemented by scoring function specific constructors
-(e.g. <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="promod3.sidechain.SCWRL4RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">SCWRL4RotamerConstructor</span></code></a>).</p>
+(e.g. <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="promod3.sidechain.SCWRL4RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4RotamerConstructor</span></code></a>).</p>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">
-<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib_entries</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib_entries</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib_entries</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib_entries</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>All functions are also avaible for their flexible rotamer model counterpart.
-=>ConstructFRMRotamerGroup(...) with the same parameters.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
-<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li>
-<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
-extract the required backbone atoms</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain.</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
-<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
+=>ConstructFRMRotamerGroup(…) with the same parameters.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</p></li>
+<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</p></li>
+<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
+extract the required backbone atoms</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain.</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
+<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
-representing the own backbone...</li>
-<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a> / <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – To search for rotamers</li>
-<li><strong>rot_lib_entries</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> objects to circumvent the
-direct use of a rotamer library</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi dihedral angle</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi dihedral angle</li>
-<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
-<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
-<li><strong>probability_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – For some rotamers, there might be many low
+representing the own backbone…</p></li>
+<li><p><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a> / <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>) – To search for rotamers</p></li>
+<li><p><strong>rot_lib_entries</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> objects to circumvent the
+direct use of a rotamer library</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi dihedral angle</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi dihedral angle</p></li>
+<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
+<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
+<li><p><strong>probability_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – For some rotamers, there might be many low
probability entries in the library.
The function adds single rotamers to the group until
the cumulative probability of the added rotamers is
-larger or equal <strong>probability_cutoff</strong>.</li>
+larger or equal <strong>probability_cutoff</strong>.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The rotamer group containing all constructed rotamers
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>The rotamer group containing all constructed rotamers
with internal energies assigned.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a></p>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> when not all required backbone
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required backbone
atoms are present in <strong>residue</strong> or not all required atom
positions are set in <strong>all_atom_pos</strong></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue">
-<code class="descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854 n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854 n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Constructs frame residues only containing backbone atoms (the ones that
-don’t show up in a rotamer).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
-<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
-<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
-extract the backbone positions</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
-<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
+don’t show up in a rotamer).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
+<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
+<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
+extract the backbone positions</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
+<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
-representing the own backbone...</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
-<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+representing the own backbone…</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
+<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> when not all required backbone
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required backbone
atoms are present in <strong>residue</strong> or not all required atom
positions are set in <strong>all_atom_pos</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">
-<code class="descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854 n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854 n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Constructs frame residues only containing sidechain atoms (the ones that
you observe in a rotamer).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
-<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
-<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
-extract the backbone positions</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
-<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
+<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
+<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
+extract the backbone positions</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
+<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
-representing the own backbone...</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
-<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+representing the own backbone…</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
+<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> when not all required sidechain
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required sidechain
atoms are present in <strong>residue</strong> or not all required sidechain
atom positions are set in <strong>all_atom_pos</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.AssignInternalEnergies">
-<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
<dd><p>Assigns an internal energy to every rotamer in <em>rot_group</em>, i.e. an energy
value before looking at any structural component of the energy function.
-The default implementation simply assigns 0.0 to every rotamer, it’s up
+The default implementation simply assigns 0.0 to every rotamer, it’s up
to the energy function specific constructors to override that behaviour.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
-<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
+<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -245,16 +215,14 @@ to be assigned</li>
<h2>Scoring Function Specific RotamerConstructors<a class="headerlink" href="#scoring-function-specific-rotamerconstructors" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SCWRL4RotamerConstructor</code><span class="sig-paren">(</span><em class="sig-param">cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>This object implements the full interface defined in
-<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
+<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
are parametrized according to the SCWRL4 method. They contain all heavy atoms,
but also the polar hydrogens.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
the cb atom. This flag also affects the construction
of frame residues and controls whether the cb atom
shows up in the backbone frame residues or sidechain
@@ -262,76 +230,67 @@ frame residues.
This is useful when you want to represent ALA or
GLY with actual rotamers, but be aware of increased
runtime. This flag can be set to False for most
-modeling applications and you just don’t generate
-any rotamers for ALA and GLY.</td>
-</tr>
-</tbody>
-</table>
+modeling applications and you just don’t generate
+any rotamers for ALA and GLY.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">
-<code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<code class="sig-name descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
This can be useful to mark a region occupied by a ligand. Note, that
-there won’t be any parametrization of hbonds in this function. All heavy
+there won’t be any parametrization of hbonds in this function. All heavy
atoms of the residue will be represented as carbons and hydrogens are
skipped.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
-construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">
-<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms based on the passed compounds library.
-This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal"><span class="pre">ConstructFrameResidue()</span></code></a>,
+This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ConstructFrameResidue()</span></code></a>,
which will be called by this function if the residue is not known by the given
compounds library.
Only non-hydrogen atoms are considered and by default added as uncharged
carbons. Special treatment is used for atoms known by the compounds library
in the following cases:</p>
<ul class="simple">
-<li>carbons, nitrogens, oxygens and sulfur particles use an appropriate type
-as in the <code class="xref py py-class docutils literal"><span class="pre">SidechainParticle</span></code> enumeration</li>
-<li>carbonyls are added as charged oxygen particles as hbond acceptors</li>
+<li><p>carbons, nitrogens, oxygens and sulfur particles use an appropriate type
+as in the <code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainParticle</span></code> enumeration</p></li>
+<li><p>carbonyls are added as charged oxygen particles as hbond acceptors</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
-construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
-<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
+<li><p><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies">
-<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
-<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.
+<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a>.
Takes the rotamer group and assigns every single rotamer its internal
energy based on the probabilistic approach used by SCWRL4.
=> -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
@@ -339,40 +298,34 @@ rotamer specific and max_p is the maximum probablity of any of the rotamers
in <strong>rot_group</strong>. If you construct a rotamer group by the
ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
is already called at construction and the energies are properly assigned.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
-<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
+<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.SCWRL3RotamerConstructor">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL3RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SCWRL3RotamerConstructor</code><span class="sig-paren">(</span><em class="sig-param">cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>This object implements the full interface defined in
-<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
+<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
are parametrized according to the SCWRL3 method. They contain only heavy atoms.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
the cb atom. This flag also affects the construction
of frame residues and controls whether the cb atom
shows up in the backbone frame residues or sidechain
@@ -380,15 +333,14 @@ frame residues.
This is useful when you want to represent ALA or
GLY with actual rotamers, but be aware of increased
runtime. This flag can be set to False for most
-modeling applications and you just don’t generate
-any rotamers for ALA and GLY.</td>
-</tr>
-</tbody>
-</table>
+modeling applications and you just don’t generate
+any rotamers for ALA and GLY.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">
-<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
-<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.
+<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a>.
Takes the rotamer group and assigns every single rotamer its internal
energy based on the probabilistic approach used by SCWRL3.
=> -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
@@ -396,40 +348,34 @@ rotamer specific and max_p is the maximum probablity of any of the rotamers
in <strong>rot_group</strong>. If you construct a rotamer group by the
ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
is already called at construction and the energies are properly assigned.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
-<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
+<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.VINARotamerConstructor">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINARotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">VINARotamerConstructor</code><span class="sig-paren">(</span><em class="sig-param">cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>This object implements the full interface defined in
-<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
+<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
are parametrized according to the VINA method. They contain only heavy atoms.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
the cb atom. This flag also affects the construction
of frame residues and controls whether the cb atom
shows up in the backbone frame residues or sidechain
@@ -437,15 +383,14 @@ frame residues.
This is useful when you want to represent ALA or
GLY with actual rotamers, but be aware of increased
runtime. This flag can be set to False for most
-modeling applications and you just don’t generate
-any rotamers for ALA and GLY.</td>
-</tr>
-</tbody>
-</table>
+modeling applications and you just don’t generate
+any rotamers for ALA and GLY.</p>
+</dd>
+</dl>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies">
-<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
-<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.
+<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a>.
Takes the rotamer group and assigns every single rotamer its internal
energy based on the probabilistic approach used by SCWRL3/SCWRL4.
=> -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
@@ -453,31 +398,27 @@ rotamer specific and max_p is the maximum probablity of any of the rotamers
in <strong>rot_group</strong>. If you construct a rotamer group by the
ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
is already called at construction and the energies are properly assigned.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
-<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
-<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
+<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
+<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
+<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
-<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>res</em>, <em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms. It is important that the residue has
proper bonds assigned, as they influence the atom typing procedure.
Furthermore, you need hydrogens to automatically estimate the correct
@@ -486,88 +427,80 @@ Alternatively you can assign generic properties to oxygens and nitrogens
to circumvent the requirement of hydrogens. This is further described for
the case of oxygen.</p>
<ul class="simple">
-<li>Carbon is assigned C_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a> if its only
+<li><p>Carbon is assigned C_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a> if its only
bound to other carbons or hydrogens (and deuterium). All other carbons are
-assigned C_P_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
-<li>In case of oxygen, the heuristic first checks for set generic properties.
-If the atom has the bool properties “is_hbond_acceptor” AND
-“is_hbond_donor” set, it decides between the according oxygen types
-in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
+assigned C_P_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
+<li><p>In case of oxygen, the heuristic first checks for set generic properties.
+If the atom has the bool properties “is_hbond_acceptor” AND
+“is_hbond_donor” set, it decides between the according oxygen types
+in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
every oxygen is assumed to be an hbond acceptor. But only an hbond donor
if its bound to a hydrogen (or deuterium). You can set the generic
-properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
-at.SetBoolProp(“is_hbond_donor”, False) and
-at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
-generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
-<li>In case of nitrogen, the heuristic again first checks for set generic
+properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
+at.SetBoolProp(“is_hbond_donor”, False) and
+at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
+generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
+<li><p>In case of nitrogen, the heuristic again first checks for set generic
properties.
-If the atom has the bool properties “is_hbond_acceptor” AND
-“is_hbond_donor” set, it decides between the according nitrogen types
-in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>. If not, nitrogen is expected to be an
+If the atom has the bool properties “is_hbond_acceptor” AND
+“is_hbond_donor” set, it decides between the according nitrogen types
+in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>. If not, nitrogen is expected to be an
hbond donor if it is bound to a hydrogen (or deuterium) and
an hbond acceptor if it is bound to less than 3 other atoms (sounds
-horrible but works surprisingly well).</li>
-<li>Atoms of elements [“MG”, “MN”, “ZN”, “CA”, “FE”] are assigned
-M_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
-<li>Atoms of elements [“S”, “P”, “F”, “CL”, “BR”, “I”] are assigned their
-corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
-<li>All other atoms are neglected and not added to the returned
-<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
+horrible but works surprisingly well).</p></li>
+<li><p>Atoms of elements [“MG”, “MN”, “ZN”, “CA”, “FE”] are assigned
+M_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
+<li><p>Atoms of elements [“S”, “P”, “F”, “CL”, “BR”, “I”] are assigned their
+corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
+<li><p>All other atoms are neglected and not added to the returned
+<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
-<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
-<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
+<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">
-<code class="descname">ConstructRRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> with the atom typing heuristic
-as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
-<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">ConstructRRMRotamerHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> with the atom typing heuristic
+as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">
-<code class="descname">ConstructFRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> with the atom typing heuristic
-as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method. The
-constructed <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> only contains one subrotamer that
+<code class="sig-name descname">ConstructFRMRotamerHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> with the atom typing heuristic
+as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method. The
+constructed <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> only contains one subrotamer that
contains the atoms from <em>residue</em>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
-<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></p>
+</dd>
+<dt class="field-even">Return type</dt>
+<dd class="field-even"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -582,20 +515,45 @@ contains the atoms from <em>residue</em>.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Rotamer Constructor</a><ul>
-<li><a class="reference internal" href="#the-rotamerconstructor-baseclass">The RotamerConstructor Baseclass</a></li>
-<li><a class="reference internal" href="#scoring-function-specific-rotamerconstructors">Scoring Function Specific RotamerConstructors</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="frame.html" title="previous chapter">Frame - The Rigid Part</a></li>
<li>Next: <a href="rotamer_lib.html" title="next chapter">Rotamer Library</a></li>
</ul></li>
@@ -603,23 +561,24 @@ contains the atoms from <em>residue</em>.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/rotamer_constructor.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -628,11 +587,11 @@ contains the atoms from <em>residue</em>.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/rotamer_constructor.txt"
+ <a href="../_sources/sidechain/rotamer_constructor.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index f428916047849ff61fa177b37a8f7ec471a74850..31ee974e5b03d01d997ac62c563bccc59ce18988 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Rotamer Library — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Rotamer Library — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Graph" href="graph.html" />
<link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -55,9 +41,9 @@ combinations of such dihedral angles are a result of steric properties and
can be gathered in rotamer libraries. Different libraries exist in the field
and their main difference is, whether the provided sidechain conformations
are dependent on their backbone or not. ProMod3 provides you with a
-<a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a> organizing rotamers for the different aminoacids
-in equidistant phi/psi bins, as well as a simple <a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>.
-Both libraries are containers for <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> and are optimized
+<a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a> organizing rotamers for the different aminoacids
+in equidistant phi/psi bins, as well as a simple <a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a>.
+Both libraries are containers for <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> and are optimized
for fast writing/loading from/to disk. Once initialized, the library is in a
dynamic mode where rotamers can be added.
No rotamers can be read at this stage. As soon as
@@ -67,103 +53,95 @@ mode you can get the rotamers out of it or dump it to disk.</p>
<h2>The Non Backbone Dependent Rotamer Library<a class="headerlink" href="#the-non-backbone-dependent-rotamer-library" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RotamerLib">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerLib</code><a class="headerlink" href="#promod3.sidechain.RotamerLib" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerLib</code><a class="headerlink" href="#promod3.sidechain.RotamerLib" title="Permalink to this definition">¶</a></dt>
<dd><p>Non backbone dependent rotamer library</p>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.sidechain.RotamerLib.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.RotamerLib.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.sidechain.RotamerLib.Save" title="promod3.sidechain.RotamerLib.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.sidechain.RotamerLib.SavePortable" title="promod3.sidechain.RotamerLib.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.sidechain.RotamerLib.Save" title="promod3.sidechain.RotamerLib.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.sidechain.RotamerLib.SavePortable" title="promod3.sidechain.RotamerLib.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A rotamer library</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A rotamer library</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.RotamerLib.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.AddRotamer">
-<code class="descname">AddRotamer</code><span class="sig-paren">(</span><em>id</em>, <em>rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
-<li><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</li>
+<code class="sig-name descname">AddRotamer</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</p></li>
+<li><p><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if the library is already static</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the library is already static</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.QueryLib">
-<code class="descname">QueryLib</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">QueryLib</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
<dd><p>The query function follows following strategies in case of
special <em>id</em> requests.</p>
<ul class="simple">
-<li>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</li>
-<li>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</li>
-<li>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</li>
-<li>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</li>
-<li>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</li>
-<li>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</li>
+<li><p>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</p></li>
+<li><p>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</p></li>
+<li><p>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</p></li>
+<li><p>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</p></li>
+<li><p>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</p></li>
+<li><p>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
-probability sorted by their probability</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
-found</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
+probability sorted by their probability</p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
+found</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.MakeStatic">
-<code class="descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
<dd><p>Once all rotamers are added, the library can be made static to become readable
and ready for io.</p>
</dd></dl>
@@ -175,95 +153,85 @@ and ready for io.</p>
<h2>The Backbone Dependent Rotamer Library<a class="headerlink" href="#the-backbone-dependent-rotamer-library" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.BBDepRotamerLib">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">BBDepRotamerLib</code><span class="sig-paren">(</span><em>phi_bins</em>, <em>psi_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">BBDepRotamerLib</code><span class="sig-paren">(</span><em class="sig-param">phi_bins</em>, <em class="sig-param">psi_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib" title="Permalink to this definition">¶</a></dt>
<dd><p>Backbone dependent rotamer library</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>phi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – number of bins for phi backbone dihedral</li>
-<li><strong>psi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – number of bins for psi backbone dihedral</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>phi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of bins for phi backbone dihedral</p></li>
+<li><p><strong>psi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of bins for psi backbone dihedral</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
-<dl class="staticmethod">
+</dd>
+</dl>
+<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.BBDepRotamerLib.LoadPortable">
-<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.Save" title="promod3.sidechain.BBDepRotamerLib.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
-reading) / portable file generated with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="promod3.sidechain.BBDepRotamerLib.SavePortable"><code class="xref py py-meth docutils literal"><span class="pre">SavePortable()</span></code></a> (slower but
+<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.Save" title="promod3.sidechain.BBDepRotamerLib.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
+reading) / portable file generated with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="promod3.sidechain.BBDepRotamerLib.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A rotamer library</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>A rotamer library</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.Save">
-<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Save" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.BBDepRotamerLib.SavePortable">
-<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.AddRotamer">
-<code class="descname">AddRotamer</code><span class="sig-paren">(</span><em>id</em>, <em>r1</em>, <em>r2</em>, <em>r3</em>, <em>r4</em>, <em>phi_bin</em>, <em>psi_bin</em>, <em>rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
-<li><strong>r1</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Configuration of chi1</li>
-<li><strong>r2</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Configuration of chi2</li>
-<li><strong>r3</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Configuration of chi3</li>
-<li><strong>r4</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Configuration of chi4</li>
-<li><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Phi backbone dihedral description</li>
-<li><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Psi backbone dihedral description</li>
-<li><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</li>
+<code class="sig-name descname">AddRotamer</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">r1</em>, <em class="sig-param">r2</em>, <em class="sig-param">r3</em>, <em class="sig-param">r4</em>, <em class="sig-param">phi_bin</em>, <em class="sig-param">psi_bin</em>, <em class="sig-param">rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</p></li>
+<li><p><strong>r1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi1</p></li>
+<li><p><strong>r2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi2</p></li>
+<li><p><strong>r3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi3</p></li>
+<li><p><strong>r4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi4</p></li>
+<li><p><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Phi backbone dihedral description</p></li>
+<li><p><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Psi backbone dihedral description</p></li>
+<li><p><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if an invalid backbone angle bin
+</dd>
+<dt class="field-even">Raises</dt>
+<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if an invalid backbone angle bin
is given or when the library is already static.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.QueryLib">
-<code class="descname">QueryLib</code><span class="sig-paren">(</span><em>id</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">QueryLib</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
<dd><p>The returned rotamers are either directly returned in the form as they are
added to the library or can be interpolated.
In the first option, <em>phi</em> and <em>psi</em> simply get transformed to the
@@ -273,76 +241,66 @@ according standard deviations of the rotamers get bilinearly interpolated
using the corresponding rotamers with same configuration from the
neighbouring bins. No interplation is applied to non-rotameric dihedral
angles (chi2 in ASP, ASN, HIS, PHE, TRP, TYR; chi3 in GLU, GLN).
-This behaviour can be controlled with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="promod3.sidechain.BBDepRotamerLib.SetInterpolate"><code class="xref py py-meth docutils literal"><span class="pre">SetInterpolate()</span></code></a>.
+This behaviour can be controlled with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="promod3.sidechain.BBDepRotamerLib.SetInterpolate"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetInterpolate()</span></code></a>.
The query function follows following strategies in case of
special <em>id</em> requests.</p>
<ul class="simple">
-<li>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</li>
-<li>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</li>
-<li>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</li>
-<li>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</li>
-<li>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</li>
-<li>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</li>
+<li><p>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</p></li>
+<li><p>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</p></li>
+<li><p>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</p></li>
+<li><p>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</p></li>
+<li><p>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</p></li>
+<li><p>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle in range [-pi,pi[</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle in range [-pi,pi[</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</p></li>
+<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle in range [-pi,pi[</p></li>
+<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle in range [-pi,pi[</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
probability for given phi/psi pair sorted by their probability</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
found</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.MakeStatic">
-<code class="descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
<dd><p>Once all rotamers are added, the library can be made static to become readable
and ready for io. Several things get checked during this process</p>
<ul class="simple">
-<li>For every phi/psi bin combination of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>,
-the same number of rotamers must have been added</li>
-<li>All configuration combinations of the added rotamers in one phi/psi bin
-of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must be unique</li>
-<li>The configuration combinations of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must
-be consistent across all phi/psi bins</li>
+<li><p>For every phi/psi bin combination of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>,
+the same number of rotamers must have been added</p></li>
+<li><p>All configuration combinations of the added rotamers in one phi/psi bin
+of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> must be unique</p></li>
+<li><p>The configuration combinations of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> must
+be consistent across all phi/psi bins</p></li>
</ul>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if one of the points above is
-not fulfilled</td>
-</tr>
-</tbody>
-</table>
+<dl class="field-list simple">
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the points above is
+not fulfilled</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.SetInterpolate">
-<code class="descname">SetInterpolate</code><span class="sig-paren">(</span><em>interpolate</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Controls behaviour when <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="promod3.sidechain.BBDepRotamerLib.QueryLib"><code class="xref py py-meth docutils literal"><span class="pre">QueryLib()</span></code></a>
-gets called</td>
-</tr>
-</tbody>
-</table>
+<code class="sig-name descname">SetInterpolate</code><span class="sig-paren">(</span><em class="sig-param">interpolate</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Controls behaviour when <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="promod3.sidechain.BBDepRotamerLib.QueryLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">QueryLib()</span></code></a>
+gets called</p>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -357,250 +315,225 @@ convenience functions. For analytical purposes they provide some comparison
functionalities.</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerLibEntry">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerLibEntry</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerLibEntry</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="class">
<dt>
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerLibEntry</code><span class="sig-paren">(</span><em>p</em>, <em>chi1</em>, <em>chi2</em>, <em>chi3</em>, <em>chi4</em>, <em>sig1</em>, <em>sig2</em>, <em>sig3</em>, <em>sig4</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>p</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of rotamer</li>
-<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Chi1 dihedral in range [-pi,pi[</li>
-<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Chi2 dihedral in range [-pi,pi[</li>
-<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Chi3 dihedral in range [-pi,pi[</li>
-<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Chi4 dihedral in range [-pi,pi[</li>
-<li><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation for Chi1 dihedral</li>
-<li><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation for Chi2 dihedral</li>
-<li><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation for Chi3 dihedral</li>
-<li><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation for Chi4 dihedral</li>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerLibEntry</code><span class="sig-paren">(</span><em class="sig-param">p</em>, <em class="sig-param">chi1</em>, <em class="sig-param">chi2</em>, <em class="sig-param">chi3</em>, <em class="sig-param">chi4</em>, <em class="sig-param">sig1</em>, <em class="sig-param">sig2</em>, <em class="sig-param">sig3</em>, <em class="sig-param">sig4</em><span class="sig-paren">)</span></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>p</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamer</p></li>
+<li><p><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi1 dihedral in range [-pi,pi[</p></li>
+<li><p><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi2 dihedral in range [-pi,pi[</p></li>
+<li><p><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi3 dihedral in range [-pi,pi[</p></li>
+<li><p><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi4 dihedral in range [-pi,pi[</p></li>
+<li><p><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi1 dihedral</p></li>
+<li><p><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi2 dihedral</p></li>
+<li><p><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi3 dihedral</p></li>
+<li><p><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi4 dihedral</p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
<p><strong>Attributes:</strong></p>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.probability">
-<code class="descname">probability</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.probability" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">probability</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.probability" title="Permalink to this definition">¶</a></dt>
<dd><p>probability of rotamer</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi1">
-<code class="descname">chi1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi1" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">chi1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi1" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi1 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi2">
-<code class="descname">chi2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi2" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">chi2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi2" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi2 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi3">
-<code class="descname">chi3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi3" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">chi3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi3" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi3 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi4">
-<code class="descname">chi4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi4" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">chi4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi4" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi4 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig1">
-<code class="descname">sig1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig1" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">sig1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig1" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi1 Dihedral, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig2">
-<code class="descname">sig2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig2" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">sig2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig2" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi2 Dihedral, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig3">
-<code class="descname">sig3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig3" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">sig3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig3" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi3 Dihedral, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig4">
-<code class="descname">sig4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig4" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">sig4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig4" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi4 Dihedral, NaN if not defined</p>
</dd></dl>
-<dl class="staticmethod">
+<dl class="method">
<dt id="promod3.sidechain.RotamerLibEntry.FromResidue">
-<em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
-The function tries to automatically identify the <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> based
+<em class="property">static </em><code class="sig-name descname">FromResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
+The function tries to automatically identify the <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> based
on the residue name. The probability and standard deviations are set to 0.0,
all not required chi angles with their corresponding standard deviations to
NaN.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if residue name cannot be
-translated to <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> or when not all required atoms
-are present in <em>res</em>.</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="staticmethod">
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if residue name cannot be
+translated to <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> or when not all required atoms
+are present in <em>res</em>.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="method">
<dt>
-<em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em>, <em>id</em><span class="sig-paren">)</span></dt>
-<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
+<em class="property">static </em><code class="sig-name descname">FromResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em><span class="sig-paren">)</span></dt>
+<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
The probability gets set to zero and the standard deviations to 0.
All not required chi angles with their corresponding standard deviations
are NaN.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code> if not all required atoms are
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p>
+</dd>
+<dt class="field-odd">Raises</dt>
+<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required atoms are
present in <em>res</em>.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLibEntry.IsSimilar">
-<code class="descname">IsSimilar</code><span class="sig-paren">(</span><em>other</em>, <em>thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.IsSimilar" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">IsSimilar</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.IsSimilar" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares two RotamerLibEntries for their similarity in dihedral angles.
The function goes from chi1 to chi4 and checks one after the other
-for similarity. The function doesn’t know the identity of the entries
+for similarity. The function doesn’t know the identity of the entries
and can therefore not specifically treat symmetric rotamers
(TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
-<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
+<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> Whether the two entries have the same
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether the two entries have the same
amount of defined chi angles (not NaN) and whether
they are within the specified threshold.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">IsSimilar</code><span class="sig-paren">(</span><em>other</em>, <em>thresh</em>, <em>id</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">IsSimilar</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">thresh</em>, <em class="sig-param">id</em><span class="sig-paren">)</span></dt>
<dd><p>Compares two RotamerLibEntries for their similarity in dihedral angles.
The function goes from chi1 to chi4 and checks one after the other
for similarity. Sidechains with ambigous naming that are symmetric
(TYR,PHE,ASP,GLU) get treated specifically. E.g. in case of aspartate,
the chi2 is checked for its actual value, but also for its flipped state.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
-<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
+<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> Whether the two entries have the same
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether the two entries have the same
amount of defined chi angles (not NaN) and whether
they are within the specified threshold.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLibEntry.SimilarDihedral">
-<code class="descname">SimilarDihedral</code><span class="sig-paren">(</span><em>other</em>, <em>dihedral_idx</em>, <em>thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.SimilarDihedral" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">SimilarDihedral</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">dihedral_idx</em>, <em class="sig-param">thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.SimilarDihedral" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares a specific dihedral angle.
-The function doesn’t know the identity of the entries and can therefore
+The function doesn’t know the identity of the entries and can therefore
not specifically treat symmetric rotamers
(TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
-<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
-(0 for chi1, 3 for chi4)</li>
-<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
+<li><p><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
+(0 for chi1, 3 for chi4)</p></li>
+<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
(not NaN) and within the specified threshold</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt>
-<code class="descname">SimilarDihedral</code><span class="sig-paren">(</span><em>other</em>, <em>dihedral_idx</em>, <em>thresh</em>, <em>id</em><span class="sig-paren">)</span></dt>
+<code class="sig-name descname">SimilarDihedral</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">dihedral_idx</em>, <em class="sig-param">thresh</em>, <em class="sig-param">id</em><span class="sig-paren">)</span></dt>
<dd><p>Compares a specific dihedral angle.
Symmetric sidechains with ambigous naming (TYR,PHE,ASP,GLU)
get treated specifically. E.g. in case of aspartate, the chi2 is checked
for its actual value, but also for its flipped state.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
-<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
-(0 for chi1, 3 for chi4)</li>
-<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
+<li><p><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
+(0 for chi1, 3 for chi4)</p></li>
+<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.6/library/functions.html#bool" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
(not NaN) and within the specified threshold</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</dd></dl>
@@ -615,60 +548,54 @@ The non-rotameric ones behave differently. ProMod3 offers some functionality
to estimate those configurations.</p>
<dl class="class">
<dt id="promod3.sidechain.DihedralConfiguration">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">DihedralConfiguration</code><a class="headerlink" href="#promod3.sidechain.DihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">DihedralConfiguration</code><a class="headerlink" href="#promod3.sidechain.DihedralConfiguration" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the possible sidechain dihedral configurations</p>
<table class="hlist"><tr><td><ul class="simple">
-<li>TRANS - Trans configuration (120 < angle < -120)</li>
-<li>GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)</li>
-<li>GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)</li>
-<li>NON_ROTAMERIC - Dihedral without SP3-SP3 bond</li>
-<li>INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist...)</li>
+<li><p>TRANS - Trans configuration (120 < angle < -120)</p></li>
+<li><p>GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)</p></li>
+<li><p>GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)</p></li>
+<li><p>NON_ROTAMERIC - Dihedral without SP3-SP3 bond</p></li>
+<li><p>INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist…)</p></li>
</ul>
</td></tr></table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetRotamericConfiguration">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">GetRotamericConfiguration</code><span class="sig-paren">(</span><em>angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetRotamericConfiguration" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetRotamericConfiguration</code><span class="sig-paren">(</span><em class="sig-param">angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetRotamericConfiguration" title="Permalink to this definition">¶</a></dt>
<dd><p>Evaluates the <em>angle</em> according to the ranges specified for
-<a class="reference internal" href="#promod3.sidechain.DihedralConfiguration" title="promod3.sidechain.DihedralConfiguration"><code class="xref py py-class docutils literal"><span class="pre">DihedralConfiguration</span></code></a>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle to be evaluated</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
-INVALID if <em>angle</em> is NaN.</td>
-</tr>
-</tbody>
-</table>
+<a class="reference internal" href="#promod3.sidechain.DihedralConfiguration" title="promod3.sidechain.DihedralConfiguration"><code class="xref py py-class docutils literal notranslate"><span class="pre">DihedralConfiguration</span></code></a>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle to be evaluated</p>
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
+INVALID if <em>angle</em> is NaN.</p>
+</dd>
+</dl>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetDihedralConfiguration">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">GetDihedralConfiguration</code><span class="sig-paren">(</span><em>entry</em>, <em>id</em>, <em>dihedral_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetDihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetDihedralConfiguration</code><span class="sig-paren">(</span><em class="sig-param">entry</em>, <em class="sig-param">id</em>, <em class="sig-param">dihedral_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetDihedralConfiguration" title="Permalink to this definition">¶</a></dt>
<dd><p>Estimates configuration of a sidechain dihedral angle in a specific
-<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> with the knowledge of its identity. This allows
+<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> with the knowledge of its identity. This allows
to also return NON_ROTAMERIC (e.g. chi2 for ASN).</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>entry</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) – Sidechain dihedral angle comes from here</li>
-<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</li>
-<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies angle (0 => chi1, ..., 3 => chi4)</li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entry</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – Sidechain dihedral angle comes from here</p></li>
+<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</p></li>
+<li><p><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Specifies angle (0 => chi1, …, 3 => chi4)</p></li>
</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Result of <a class="reference internal" href="#promod3.sidechain.GetRotamericConfiguration" title="promod3.sidechain.GetRotamericConfiguration"><code class="xref py py-meth docutils literal"><span class="pre">GetRotamericConfiguration()</span></code></a> if specified
+</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>Result of <a class="reference internal" href="#promod3.sidechain.GetRotamericConfiguration" title="promod3.sidechain.GetRotamericConfiguration"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetRotamericConfiguration()</span></code></a> if specified
angle is Rotameric, NON_ROTAMERIC if specified angle is
valid and non rotameric, INVALID otherwise.</p>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -681,22 +608,45 @@ valid and non rotameric, INVALID otherwise.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="../index.html">Table Of Contents</a></h3>
- <ul>
-<li><a class="reference internal" href="#">Rotamer Library</a><ul>
-<li><a class="reference internal" href="#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
-<li><a class="reference internal" href="#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
-<li><a class="reference internal" href="#the-library-entry-type">The Library Entry Type</a></li>
-<li><a class="reference internal" href="#rotamer-configurations">Rotamer Configurations</a></li>
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="rotamer_constructor.html" title="previous chapter">Rotamer Constructor</a></li>
<li>Next: <a href="graph.html" title="next chapter">Rotamer Graph</a></li>
</ul></li>
@@ -704,23 +654,24 @@ valid and non rotameric, INVALID otherwise.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/rotamer_lib.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -729,11 +680,11 @@ valid and non rotameric, INVALID otherwise.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/rotamer_lib.txt"
+ <a href="../_sources/sidechain/rotamer_lib.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 8c246da7d2a01a1fdde19b112c6f94adf4419c86..4b570a0c38d886bc95da5a261b6f4b0a32f55789 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Subrotamer Optimization — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Subrotamer Optimization — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="../_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="../index.html" />
- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
<link rel="prev" title="Loading Rotamer Libraries" href="loading.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -65,28 +51,24 @@ that you might want to prefer the currently active subrotamers if no
pairwise energies to other rotamers are observed.</p>
<dl class="method">
<dt id="promod3.sidechain.SubrotamerOptimizer">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">SubrotamerOptimizer</code><span class="sig-paren">(</span><em>rotamers, [active_internal_energy=-2.0, inactive_internal_energy=0.0, max_complexity=100000000, initial_epsilon=0.02</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SubrotamerOptimizer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Takes the <strong>rotamers</strong> of type <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>, converts all their
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SubrotamerOptimizer</code><span class="sig-paren">(</span><em class="sig-param">rotamers, [active_internal_energy=-2.0, inactive_internal_energy=0.0, max_complexity=100000000, initial_epsilon=0.02</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SubrotamerOptimizer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Takes the <strong>rotamers</strong> of type <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>, converts all their
subrotamers into rigid rotamers, solves the sidechain reconstruction problem
and assigns the ideal subrotamers as active in the input <strong>rotamers</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – The rotamers to be optimized</li>
-<li><strong>active_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
-currently active subrotamers</li>
-<li><strong>inactive_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
-currently inactive subrotamers</li>
-<li><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#int" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max complexity of the internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal"><span class="pre">RotamerGraph</span></code></a></li>
-<li><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.6/library/functions.html#float" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Epsilon value controlling the pruning of
-internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal"><span class="pre">RotamerGraph</span></code></a></li>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – The rotamers to be optimized</p></li>
+<li><p><strong>active_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
+currently active subrotamers</p></li>
+<li><p><strong>inactive_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
+currently inactive subrotamers</p></li>
+<li><p><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max complexity of the internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a></p></li>
+<li><p><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Epsilon value controlling the pruning of
+internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a></p></li>
</ul>
-</td>
-</tr>
-</tbody>
-</table>
+</dd>
+</dl>
</dd></dl>
</div>
@@ -97,36 +79,71 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="../users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="../gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="loading.html" title="previous chapter">Loading Rotamer Libraries</a></li>
- <li>Next: <a href="../scoring/index.html" title="next chapter"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+ <li>Next: <a href="../scoring/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="../_sources/sidechain/subrotamer_optimizer.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -135,11 +152,11 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="../_sources/sidechain/subrotamer_optimizer.txt"
+ <a href="../_sources/sidechain/subrotamer_optimizer.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index 2a54439d115fa45102c1cc0c688a62f12963b78c..483876a4d0d5c592e330f84c73d5012edb202c10 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -1,33 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Contributing — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Contributing — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="Documentation For Developers" href="developers.html" />
<link rel="prev" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
@@ -36,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -54,7 +40,7 @@ that you believe is worth sharing with other users.
They can review the code and add it to the repository at:
<a class="reference external" href="https://git.scicore.unibas.ch/schwede/ProMod3">https://git.scicore.unibas.ch/schwede/ProMod3</a>. Consider
opening an account for the GitLab instance at sciCORE, University of Basel if
-you directly want to contribute to ProMod3‘s core features. You can find more
+you directly want to contribute to ProMod3’s core features. You can find more
information on that matter in the developer section of the documentation
(<a class="reference internal" href="contributing.html#how-to-contribute"><span class="std std-ref">Contributing</span></a>).</p>
</div>
@@ -65,34 +51,69 @@ information on that matter in the developer section of the documentation
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="users.html">Users</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="users.html">Documentation For Users</a><ul>
- <li>Previous: <a href="core/setcompoundschemlib.html" title="previous chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ <li>Previous: <a href="core/setcompoundschemlib.html" title="previous chapter"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li>Next: <a href="developers.html" title="next chapter">Documentation For Developers</a></li>
</ul></li>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/user_contributions.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -101,11 +122,11 @@ information on that matter in the developer section of the documentation
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/user_contributions.txt"
+ <a href="_sources/user_contributions.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/users.html b/doc/html/users.html
index 42319962320ee59da12c3b76020f4c6543dc9d27..e2705ef0a7a2e9aec0f538a07b6102331cdd230e 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -1,32 +1,20 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>Documentation For Users — ProMod3 3.0.0 documentation</title>
-
+ <meta charset="utf-8" />
+ <title>Documentation For Users — ProMod3 3.1.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: './',
- VERSION: '3.0.0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
+ <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+ <script type="text/javascript" src="_static/language_data.js"></script>
+ <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="top" title="ProMod3 3.0.0 documentation" href="index.html" />
<link rel="next" title="Getting Started" href="gettingstarted.html" />
<link rel="prev" title="ProMod3" href="index.html" />
@@ -35,8 +23,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
- </head>
- <body role="document">
+ </head><body>
<div class="document">
@@ -75,7 +62,7 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="container/singularity.html">Singularity</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="modelling/index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="modelling/pipeline.html">Modelling Pipeline</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/model_checking.html">Model Checking</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/gap_handling.html">Handling Gaps</a></li>
@@ -86,7 +73,7 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="modelling/algorithms.html">Modelling Algorithms</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Representing Sidechains - Rotamers & Co.</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame - The Rigid Part</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_constructor.html">Rotamer Constructor</a></li>
@@ -97,31 +84,31 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="sidechain/subrotamer_optimizer.html">Subrotamer Optimization</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="scoring/index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_score_env.html">Backbone Score Environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_scorers.html">Backbone Scorers</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/all_atom_scorers.html">All Atom Scorers</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/other_scoring_functions.html">Other Scoring Functions</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="loop/index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="loop/backbone.html">Representing Loops</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/torsion_sampler.html">Sampling Dihedral Angles</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/structure_db.html">Structural Data</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/all_atom.html">Handling All Atom Positions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/mm_system_creation.html">Generate <code class="docutils literal"><span class="pre">ost.mol.mm</span></code> systems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/mm_system_creation.html">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/load_loop_objects.html">Loading Precomputed Objects</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="core/index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="core/pm3argparse.html"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="core/pm3argparse.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/geometry.html">Geometry functions</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/runtime_profiling.html">Runtime profiling</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/graph_minimizer.html">Graph Minimizer</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l1"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</div>
@@ -133,7 +120,41 @@ scripts using the functionality of this library.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper"><div class="relations">
+ <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">ProMod3</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Users</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
+<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
+</ul>
+
+<div class="relations">
<h3>Related Topics</h3>
<ul>
<li><a href="index.html">Documentation overview</a><ul>
@@ -142,23 +163,24 @@ scripts using the functionality of this library.</p>
</ul></li>
</ul>
</div>
- <div role="note" aria-label="source link">
- <h3>This Page</h3>
- <ul class="this-page-menu">
- <li><a href="_sources/users.txt"
- rel="nofollow">Show Source</a></li>
- </ul>
- </div>
<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
+ <h3 id="searchlabel">Quick search</h3>
+ <div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <div><input type="text" name="q" /></div>
- <div><input type="submit" value="Go" /></div>
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
+ <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="submit" value="Go" />
</form>
+ </div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
</div>
</div>
<div class="clearer"></div>
@@ -167,11 +189,11 @@ scripts using the functionality of this library.</p>
©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.9</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
|
- <a href="_sources/users.txt"
+ <a href="_sources/users.rst.txt"
rel="nofollow">Page source</a>
</div>
diff --git a/modelling/pymod/_raw_model.py b/modelling/pymod/_raw_model.py
index b08ae45b3c51846a0303069c4646c1e5c64ae2fa..50bb31defea8058bd06acfaa603e6ad653d92d0b 100644
--- a/modelling/pymod/_raw_model.py
+++ b/modelling/pymod/_raw_model.py
@@ -77,8 +77,11 @@ def BuildRawModel(aln, chain_names = None, include_ligands = False,
If *aln* is of type :class:`ost.seq.AlignmentHandle`,
*chain_names* is expected to be a :class:`str`.
If *aln* is of type :class:`ost.seq.AlignmentList`,
- chain_names is expected to be a :class:`list` of
- :class:`str` of same size as *aln*.
+ *chain_names* is expected to be a :class:`list` of
+ :class:`str` of same size as *aln* or a :class:`str`.
+ For the latter case, chains will consecutively named
+ according to characters in *chain_names*.
+
:type chain_names: :class:`str` / :class:`list`
:param spdbv_style: True, if we need a model in the old SPDBV style.
@@ -130,9 +133,15 @@ def BuildRawModel(aln, chain_names = None, include_ligands = False,
raise RuntimeError('Number of alns and chain_names must be '\
'consistent')
name_list = chain_names
+ elif isinstance(chain_names, str):
+ if len(chain_names) < len(aln_list):
+ raise RuntimeError('If you provide a string as chain_names, '\
+ 'it must be at least as long as the '\
+ 'AlignmentList in aln.')
+ name_list = [n for n in chain_names[:len(aln_list)]]
else:
- raise RuntimeError('chain_names must be list if aln is of type '\
- 'ost.seq.AlignmentList')
+ raise RuntimeError('chain_names must be list of str or str if aln '\
+ 'is of type ost.seq.AlignmentList')
else:
raise RuntimeError('aln must be of type ost.seq.AlignmentHandle or '\
'ost.seq.AlignmentList')
diff --git a/modelling/tests/test_modelling.py b/modelling/tests/test_modelling.py
index f8e8b946b4120d24b820c041d12a6a1d7b65ec3d..3e99059ac00f92af1691bc0ed406d306d9fda6a7 100644
--- a/modelling/tests/test_modelling.py
+++ b/modelling/tests/test_modelling.py
@@ -76,24 +76,28 @@ class ModellingTests(unittest.TestCase):
result = modelling.BuildRawModel(aln_lst, ['cheese', 'steak'])
self.assertEqual(result.model.chains[0].GetName(), 'cheese')
self.assertEqual(result.model.chains[1].GetName(), 'steak')
+ result = modelling.BuildRawModel(aln_lst, 'ch')
+ self.assertEqual(result.model.chains[0].GetName(), 'c')
+ self.assertEqual(result.model.chains[1].GetName(), 'h')
+ result = modelling.BuildRawModel(aln_lst, 'cheese')
+ self.assertEqual(result.model.chains[0].GetName(), 'c')
+ self.assertEqual(result.model.chains[1].GetName(), 'h')
# we only accept a string as chain_names if aln is AlignmentHandle
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln, 1)
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln, ['A'])
- # we only accept a list as chain_names if aln is AlignmentList
+ # we only accept a list or str as chain_names if aln is AlignmentList
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst, 1)
- self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst, 'A')
# size also matters...
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst, ['A'])
+ self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst, 'A')
# increase size of aln_list => at some point we should run out of
# default chain_names
aln_lst = 100*[aln]
self.assertRaises(RuntimeError, modelling.BuildRawModel, aln_lst)
-
-
def testModeledSequence(self):
# test if the model has the sequence we want.
tpl = io.LoadPDB('data/gly.pdb')
diff --git a/scripts/bump-version.py b/scripts/bump-version.py
index ec9c0e88c580d3a28dadb17528a318140dd453f9..178dcb723d0fd17b195e6d6ebce673e5aa59c567 100644
--- a/scripts/bump-version.py
+++ b/scripts/bump-version.py
@@ -1,10 +1,12 @@
#!/usr/bin/env python
import sys
-if len(sys.argv) < 3:
- print("USAGE: python scripts/bump-version.py PM3_VERSION OST_VERSION")
+if len(sys.argv) < 4:
+ print("USAGE: python scripts/bump-version.py PM3_VERSION OST_VERSION OST_DOCKER_IMAGE_TAG")
print("-> *_VERSION format is MAJOR.MINOR.PATCH (e.g. 1.9.1)")
print("-> assumption is that git tags will exist for those *_VERSION")
+ print("-> OST_DOCKER_IMAGE_TAG refers to the image in the OpenStructure")
+ print(" Docker registry from which the ProMod3 image will bootstrap")
sys.exit(1)
# split up version number
@@ -12,6 +14,7 @@ version_string = sys.argv[1]
version = version_string.split('.')
major, minor, patch = (int(version[0]), int(version[1]), int(version[2]))
ost_version_string = sys.argv[2]
+ost_docker_image_tag = sys.argv[3]
# fix CMakeLists
lines = open("CMakeLists.txt").readlines()
@@ -36,8 +39,8 @@ open("CHANGELOG", "w").writelines(lines)
# fix Docker recipe
lines = open("container/Dockerfile").readlines()
for i, line in enumerate(lines):
- if line.startswith("ARG OPENSTRUCTURE_VERSION"):
- lines[i] = 'ARG OPENSTRUCTURE_VERSION="%s"\n' % ost_version_string
+ if line.startswith("ARG OPENSTRUCTURE_IMAGE_TAG"):
+ lines[i] = 'ARG OPENSTRUCTURE_IMAGE_TAG="%s"\n' % ost_docker_image_tag
elif line.startswith("ARG PROMOD_VERSION"):
lines[i] = 'ARG PROMOD_VERSION="%s"\n' % version_string
open("container/Dockerfile", "w").writelines(lines)
@@ -48,7 +51,7 @@ lines = open(vfile).readlines()
for i, line in enumerate(lines):
if line.startswith("From: registry.scicore.unibas.ch/schwede/promod3:"):
lines[i] = 'From: registry.scicore.unibas.ch/schwede/promod3:'+\
- '%s' % version_string
+ '%s-OST%s\n' % (version_string, ost_docker_image_tag)
break
open(vfile, "w").writelines(lines)