diff --git a/CHANGELOG b/CHANGELOG
index c001a95b00a6dbd5a337c008af97eb422a0eb186..0e9ceb554298f192f7dea1e1b082a380fff4a766 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,9 +5,11 @@
 Changelog
 ================================================================================
 
-Release 2.x.x
+Release 2.1.0
 --------------------------------------------------------------------------------
 
+* This is expected to be the last release supporting Python 2.
+* This project now requires a C++11 compatible compiler.
 * Introduced VINA scoring function in the sidechain module. A scoring function 
   specific RotamerConstructor is provided that comes with extensive heuristics 
   to parametrize arbitrary compounds. 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0d32d35736f6603ab6777c884c460d5128acb644..696f3592cf5f815f916b28a4e1618c75528f74b2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,7 +24,7 @@ include(PROMOD3)
 
 # versioning info
 set(PROMOD3_VERSION_MAJOR 2)
-set(PROMOD3_VERSION_MINOR 0)
+set(PROMOD3_VERSION_MINOR 1)
 set(PROMOD3_VERSION_PATCH 0)
 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 1.10.0 REQUIRED
+find_package(OPENSTRUCTURE 1.11.0 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 34a7ec04e2b60c8afdd3eb1d8748fc378cc09846..f32022d62ec1c437023115d1a37c0f06aff7843d 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -1,8 +1,9 @@
-FROM registry.scicore.unibas.ch/schwede/openstructure:python3_test
+FROM registry.scicore.unibas.ch/schwede/openstructure:python3_test2
 
 # ARGUMENTS
 ###########
-ARG PROMOD_VERSION=python3_port
+ARG OPENSTRUCTURE_VERSION="python3_test2"
+ARG PROMOD_VERSION="3.0.0"
 ARG SRC_FOLDER="/usr/local/src"
 
 
diff --git a/doc/conf.py.in b/doc/conf.py.in
index cd8b794058aa1d9be11db588ff328f662e3106bf..116d11e729b688038b06a349769f8509fb1af301 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:: 1.10.0
+.. |ost_version| replace:: 1.11.0
 .. |python| replace:: Python
 .. |sphinx| replace:: Sphinx
 .. _sphinx: http://sphinx-doc.org/
diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
index 85b7a525b04c252d4c43059a8d31c9efce17e6ec..8999dcc45b033ce13018725478f17af851462344 100644
--- a/doc/container/singularity.rst
+++ b/doc/container/singularity.rst
@@ -26,7 +26,6 @@ Build the image with:
 
   sudo singularity build promod.img Singularity
 
-
 Available apps
 --------------
 
@@ -57,7 +56,6 @@ To list all available ProMod3 modelling actions:
 
     singularity run --app PM promod.img help
 
-
 The Compound Library
 --------------------
 
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ec26dc0ee6fef295ef194dba1d795681478d920
--- /dev/null
+++ b/doc/html/_sources/buildsystem.txt
@@ -0,0 +1,170 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+.. _building-promod:
+
+Building |project|
+================================================================================
+
+--------------------------------------------------------------------------------
+Dependencies
+--------------------------------------------------------------------------------
+
+|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version 
+|ost_version|. A C++11 compatible compiler is required. |ost_s| must be
+configured and compiled with ``ENABLE_MM=1`` to use |openmm|_. To create the
+build system, |cmake|_ is required. The same versions of |python|_ and |boost|_
+are needed as used in |ost_s|. For |eigen3|_ we need at least version 3.3.0. To
+build the documentation, |sphinx|_ is required.
+
+The currently preferred versions are:
+
+* |ost_s|_ |ost_version|
+* |openmm|_ 7.1.1
+* |cmake|_ 2.8.12
+* |python|_ 2.7.11
+* |boost|_ 1.53.0
+* |eigen3|_ 3.3.1
+* |sphinx|_ 1.4.1
+
+--------------------------------------------------------------------------------
+ Using |cmake|
+--------------------------------------------------------------------------------
+|cmake| is used to configure the build system and in the end produces makefiles
+and certain directories needed for building |project|. Basically it is called
+right from a shell with the directory containing the top-level
+:file:`CMakeLists.txt` as an argument. The preferred approach is to generate a
+build folder and configure and compile in there:
+
+.. code-block:: console
+
+   # execute this in the ProMod3 root folder
+   $ mkdir build
+   $ cd build
+   $ cmake .. -DOST_ROOT=<PATH TO OST> 
+
+For us, at least pointer to the |ost_s| installation directory is needed, 
+handed over to |cmake| by ``-D`` into the variable ``OST_ROOT`` (e.g. |ost_s|
+headers would be located in ``OST_ROOT/include/ost``).
+
+Similarly, one can specify folders for |boost|, |python| and |eigen3| 
+if multiple versions exist and/or they are not installed in a default location.
+These are set with the ``BOOST_ROOT`` (make sure that's the same as for |ost_s|), 
+``PYTHON_ROOT`` and ``EIGEN3_INCLUDE_DIR``.
+
+Here is a list of more options used within |project|:
+
+* ``DISABLE_DOCUMENTATION`` Don't build documentation, don't search for |sphinx|
+* ``DISABLE_DOCTEST`` Don't run example code from documentation on
+  ``make check`` (implicit by ``DISABLE_DOCUMENTATION``)
+* ``DISABLE_LINKCHECK`` Don't test links from documentation on ``make check``
+  (implicit by ``DISABLE_DOCUMENTATION``)
+* ``ENABLE_SSE`` 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_s| has been compiled with single precision.
+  (``OST_DOUBLE_PRECISION`` flag)
+
+Since we use |ost_s| 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 |project| 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 :file:`CMakeCache.txt` of |ost_s|:
+
+* ``OPTIMIZE``
+* ``OST_DOUBLE_PRECISION``
+
+.. doesn't work (yet?)
+  Instead of providing all those options at the command line, you can also use
+  ``ccmake`` instead of ``cmake``, which allows you to set the |cmake| variables
+  interactively. Press 'c' to try to configure the build. If it fails, enter the
+  requested paths and configure again. Advanced settings can be edited by 
+  pressing 't'.
+
+Instead of calling |cmake| by yourself, there is the :file:`conf-scripts`
+directory, providing smallish scripts to invoke |cmake| the right way for
+various systems. Usually those scripts just need the |ost_s| path
+and the location of the top-level :file:`CMakeLists.txt`.
+
+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
+again. No searching for |cmake| cache files or checking if certain files
+really got rebuild and similar things required.
+
+--------------------------------------------------------------------------------
+Running Make
+--------------------------------------------------------------------------------
+After configuring, you want to build |project| by
+
+.. code-block:: console
+
+   $ make
+
+to populate the :file:`stage` directory with a ready-to-go version of the
+latest code.
+
+.. index::
+   single: Make targets
+
+Beside the usual ``make all`` and other default targets, there are a few
+special targets:
+
+* ``check`` :index:`make check` Runs unit tests and if |cmake| was invoked in
+  its standard configuration also documentation examples (``doctest``) and
+  links in the doc. (``linkcheck``) are checked
+* ``html`` :index:`make html` Creates documentation as web page using the
+  |sphinx| ``html`` builder
+* ``man`` :index:`make man` Creates a manual page using the |sphinx| ``man``
+  builder
+* ``doc`` :index:`make doc` Creates documentation using the ``html`` and
+  ``man`` targets
+* ``help`` :index:`make help` Prints a list of targets available
+
+--------------------------------------------------------------------------------
+Installing |project|
+--------------------------------------------------------------------------------
+If you wish to install |project| (note that you can also safely keep it all in
+the :file:`stage` directory), you can use
+
+.. code-block:: console
+
+   $ make install
+
+By default, this will copy the :file:`stage` directory to :file:`/usr/local`. To
+override this, you can add the ``-DCMAKE_INSTALL_PREFIX=<INSTALL PATH>`` flag to
+your ``cmake`` call.
+
+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 :file:`extras/sanity_checks/README` to setup
+and run those tests after moving the source folder. If everything works, you can
+safely delete the whole source folder.
+
+
+.. |qmean| replace:: QMEAN
+.. |eigen3| replace:: Eigen 3
+.. |openmm| replace:: OpenMM
+.. _qmean: https://swissmodel.expasy.org/qmean/
+.. _ost_l: https://www.OpenStructure.org
+.. _cmake: https://cmake.org/
+.. _python: https://www.python.org/
+.. _boost: https://www.boost.org/
+.. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page
+.. _openmm: http://openmm.org
+
+..  LocalWords:  cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html
+..  LocalWords:  doctest linkcheck qmean DQMEAN eigen CMakeCache
+..  LocalWords:  OPTIMIZE
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e9ceb554298f192f7dea1e1b082a380fff4a766
--- /dev/null
+++ b/doc/html/_sources/changelog.txt
@@ -0,0 +1,115 @@
+.. ProMod3 Changelog file. This is actually a reStructuredText formatted file,
+   which will be copied to the right place in the stage directory as
+   'changelog.txt'. This way it is immediately available in the documentation.
+
+Changelog
+================================================================================
+
+Release 2.1.0
+--------------------------------------------------------------------------------
+
+* This is expected to be the last release supporting Python 2.
+* This project now requires a C++11 compatible compiler.
+* Introduced VINA scoring function in the sidechain module. A scoring function 
+  specific RotamerConstructor is provided that comes with extensive heuristics 
+  to parametrize arbitrary compounds. 
+* Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+  The algorithm is based on principles of geometric hashing.
+* Several minor bug fixes, improvements, and speed-ups  
+
+
+Release 2.0.0
+--------------------------------------------------------------------------------
+
+* 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).
+* Enable possibility to use structural fragments in default modelling pipeline
+  and build-model action
+* Enable possibility to enforce full coverage models including termini without
+  template coverage in default modelling pipeline and build-model action
+* Modelling pipeline can track issues in the ModellingHandle object
+* External example scripts can now be found in extras/external_scripts
+* Improved support for recent compilers and libraries.
+* Several minor bug fixes, improvements, and speed-ups  
+
+
+Release 1.3.0
+--------------------------------------------------------------------------------
+
+* Apply Apache Version 2.0 License to the project
+* 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
+* 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
+* SampleMonteCarlo function moved to Python. This makes it possible to provide 
+  sampler/closer/scorer/cooler objects implemented in both, Python and C++
+* Action script for sidechain modelling
+* Allow sequence profiles as input for build-model action script.
+* Recipe for Docker / Singularity container 
+* Check peptide bonds when building a RawModel. Treat as gap if bond is 
+  stereochemically problematic despite being in sequence.
+* Several minor bug fixes, improvements, and speed-ups  
+
+
+Release 1.2.0
+--------------------------------------------------------------------------------
+
+* 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.
+* 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).
+* Most scores based on pairwise interactions are now pairwise decomposable.
+* Disconnected loops at several locations can be scored at once.
+* Avoid the usage of the DSSP executable and use the OpenStructure internal
+  secondary structure assignment instead.
+* 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.
+* The naming of the entries in the StructureDB is not strictly limited to 
+  4 letter codes anymore, arbitrary strings can be used instead.
+* Adding coordinates to the StructureDB does not require external tools anymore
+  (msms, dssp etc.), internal implementations are used instead.
+* The data that is stored in a StructureDB can be controlled at initialization,
+  everything except the sequence and the actual coordinates is optional.
+* Entries in the StructureDB can be removed again.
+* Allow to search positions of arbitrary copies in DynamicSpatialOrganizer 
+  by providing RT operators.
+* Several minor bug fixes, improvements, and speed-ups
+
+
+Release 1.1.0
+--------------------------------------------------------------------------------
+
+* Updated dependencies: need Eigen 3.3.0 and OST 1.7
+* 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
+* Improved build-model action to generate oligomeric models, input multiple
+  files, and allow for residue offsets into structure files
+* Improved computational runtime of relevant operations in pipeline (CCD,
+  scorers, backbone list operations), superpositions and loop candidate
+  clustering
+* High-level functionality moved consistently to modelling module
+* New modelling algorithms: rigid blocks to compare structures and improved
+  fragment sampling for de novo modelling
+* New rotamer graph solvers for sidechains: AStar and Monte Carlo
+* Refactored backbone scoring to simplify extensions
+* Added all atom scoring with possibilities to reconstruct sidechains for
+  selected loops, reconstruct hydrogens and minimize energy with MM
+* Refactored backbone list to speed it up
+* Added runtime profiling for developers
+* Several minor bug fixes, improvements, and speed-ups
+
+
+Release 1.0
+--------------------------------------------------------------------------------
+
+* Initial release of ProMod3 for use in productive instances of SMNG
diff --git a/doc/html/_sources/container/singularity.txt b/doc/html/_sources/container/singularity.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16af7e051382508f764bddb533647d423db67fd7
--- /dev/null
+++ b/doc/html/_sources/container/singularity.txt
@@ -0,0 +1,126 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Singularity
+===========
+
+We do not provide a "standalone" Singularity image, but rather bootstrap from a 
+Docker image.
+
+Build Singularity Image
+-----------------------
+
+
+If you built the Docker image locally you can use it as a starting point. For 
+this we have to fire up a local Docker registry and pull from there. Let's 
+assume you built the Docker image with tag promod.
+
+Fire the local Registry and push the promod image to it:
+
+.. code-block:: bash
+
+  sudo docker run -d -p 5000:5000 --restart=always --name registry registry:2
+  sudo docker tag promod localhost:5000/promod
+  sudo docker push localhost:5000/promod
+
+If port 5000 is already taken on your machine, use a different ``<PORT>`` by
+using the flag ``-p <PORT>:5000`` and ``localhost:<PORT>`` in these commands.
+Make sure, that on top of your Singularity recipe you have something like:
+
+.. code-block:: bash
+
+  BootStrap: docker
+  Registry: http://localhost:5000
+  Namespace:
+  From: promod:latest
+
+and build the image with:
+
+.. code-block:: bash
+
+  sudo SINGULARITY_NOHTTPS=1 singularity build promod.img Singularity
+
+
+Run scripts and actions with OST/PM
+-----------------------------------
+
+The created container can run the ost, pm or chemdict_tool executables. 
+For convenience, a jupyter notebook playground with OST, ProMod3 and nglview is 
+available.
+
+To run ost, pm or chemdict_tool executables, use the exec command.
+E.g. to run scripts with pm:
+
+.. code-block:: bash
+
+  singularity exec <IMAGE> pm my_script.py [options]
+
+The jupyter notebook is setup as an app in the container. 
+To get help on how to run it:
+
+.. code-block:: bash
+
+  singularity help --app Notebook <IMAGE>
+
+Within the notebook you can test OST, ProMod3 and nglview as follows:
+
+.. 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
+--------------------
+
+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: :ref:`docker_compound_lib`. 
+
+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.
+
+Build a new library:
+
+.. code-block:: bash
+
+  singularity exec <IMAGE_NAME> chemdict_tool create components.cif.gz \
+              compounds.chemlib
+
+Run some script with an updated compound library from localhost:
+
+.. code-block:: bash
+
+  singularity exec -B <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> \
+              pm my_script.py 
+
+Same as for the Docker, if you didn't meddle with the original Dockerfile, 
+<COMPLIB_DIR_CONTAINER> should be /usr/local/share/ost_complib. 
+<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
+as expected by executing the exact same lines of Python code as described 
+in the Docker documentation: :ref:`docker_compound_lib`. 
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5e2d9964cfb6cd7cce133bd1cd5869c3bd19d19
--- /dev/null
+++ b/doc/html/_sources/loop/backbone.txt
@@ -0,0 +1,552 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Representing Loops
+================================================================================
+
+.. currentmodule:: promod3.loop
+
+
+The most simple representation of structural information in |project| is the
+:class:`BackboneList`. 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 :class:`ost.mol.EntityHandle`.
+
+.. literalinclude:: ../../../tests/doc/scripts/loop_backbone.py
+
+
+The BackboneList class
+--------------------------------------------------------------------------------
+
+.. class:: BackboneList()
+  
+  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 (**indexing to access each
+  residue starts at 0**). 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
+  allow amino acid types belonging to the 20 default amino acids. Note that the
+  omega torsion angle defined here for residue *i* is the dihedral between CA-C
+  of residue *i* and N-CA of residue *i+1* (this is shifted by 1 residue
+  compared to OST's :meth:`~ost.mol.ResidueHandle.GetOmegaTorsion`).
+
+  .. method:: BackboneList()
+
+    Creates empty BackboneList
+
+  .. method:: BackboneList(sequence)
+
+    Creates a helical BackboneList from given sequence
+
+    :param sequence:    Sequence of created BackboneList
+
+    :type sequence:     :class:`str`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *sequence* contains a one letter
+             code which is not one of the 20 default amino acids.
+
+  .. method:: BackboneList(sequence, dihedral_angles)
+
+    Creates a BackboneList from given *sequence* and *dihedral_angles*
+
+    :param sequence:    Sequence of created BackboneList
+    :param dihedral_angles: List of :class:`tuple` objects defining the backbone
+                            dihedral angles of created BackboneList. Every
+                            :class:`tuple` 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.
+
+    :type sequence:     :class:`str`
+    :type dihedral_angles: :class:`list`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *sequence* contains a one letter
+             code which is not one of the 20 default amino acids or if
+             *sequence* and *dihedral_angles* are inconsistent in size.
+
+  .. method:: BackboneList(residues)
+
+    Creates a BackboneList with positions and sequence extracted from
+    *residues*.
+
+    :param residues:    List of :class:`ost.mol.ResidueHandle` objects from
+                        which the backbone positions and one letter codes
+                        are extracted.
+
+    :type residues:     :class:`list`
+
+    :raises: :exc:`~exceptions.RuntimeError` if a residue in *residues*
+              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.
+
+  .. method:: BackboneList(sequence, residues)
+
+    Creates a BackboneList from given *sequence* and positions extracted from
+    *residues*.
+
+    :param sequence:    Sequence of created BackboneList
+    :param residues:    List of :class:`ost.mol.ResidueHandle` objects from
+                        which the backbone positions are extracted.
+
+    :type sequence:     :class:`str`
+    :type residues:     :class:`list`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *sequence* contains a one letter
+             code which is not one of the 20 default amino acids or if
+             *sequence* and *residues* are inconsistent in size or when there is
+             a residue not providing all necessary positions. 
+
+
+  .. method:: ToDensity(padding=10.0, sampling=Vec3(1.0,1.0,1.0), \
+                        resolution=3.0, high_resolution=false)
+    
+    :return: The whole backbone list converted to a density map.
+    :rtype:  :class:`ost.img.ImageHandle`
+
+    .. note that ImageHandle and MapHandle are the same, but former is mentioned
+       in OST doc, so we use that for documentation purposes
+
+    :param padding:
+    :type padding:  :class:`float`
+    :param sampling:
+    :type sampling:  :class:`~ost.geom.Vec3`
+    :param resolution:
+    :type resolution:  :class:`float`
+    :param high_resolution:
+    :type high_resolution:  :class:`bool`
+
+  .. method:: ToEntity()
+
+    :return: The whole backbone list converted to an OST entity.
+    :rtype:  :class:`ost.mol.EntityHandle`
+
+  .. method:: InsertInto(chain, start_resnum)
+
+    Inserts the backbone list into the *chain*. If the residues corresponding
+    to the :class:`BackboneList` are already present in the entity, they will
+    be replaced, otherwise they will be added to the entity.
+
+    :param chain:        The chain
+    :type chain:         :class:`ost.mol.ChainHandle`
+    :param start_resnum: Residue number defining the start location of insertion
+    :type start_resnum:  :class:`int` / :class:`ost.mol.ResNum`
+
+  .. method:: InsertInto(map, resolution=3.0, high_resolution=false)
+
+    :param map: 
+    :type map:  :class:`ost.img.ImageHandle`
+    :param resolution:
+    :type resolution:  :class:`float`
+    :param high_resolution:
+    :type high_resolution:  :class:`bool`
+
+  .. method:: GetBounds(all_atom=True)
+
+    :returns:
+    :rtype:   :class:`ost.geom.AlignedCuboid`
+    :param all_atom: 
+    :type all_atom:  :class:`bool`
+
+
+  .. method:: GetSequence()
+
+    :return: The amino acid sequence.
+    :rtype:  :class:`str`
+
+  .. method:: SetSequence(sequence)
+
+    :param sequence: Set amino acid sequence to this.
+    :type sequence:  :class:`str`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *sequence* contains a one letter
+             code which is not one of the 20 default amino acids or size of 
+             *sequence* does not match.
+
+
+  .. method:: Extract(from, to)
+
+    :returns: Items with indices *from*, ..., *to*-1 of this list.
+    :rtype:   :class:`BackboneList`
+
+  .. method:: ReplaceFragment(sub_fragment, index, superpose_stems)
+
+    Replaces a fragment of the :class:`BackboneList` starting at position
+    *index* by the *sub_fragment*.
+
+    :param sub_fragment:          The fragment to be inserted
+    :param index:                 The position at which the fragment 
+                                  replacement will begin
+    :param superpose_stems:       If set to false, the function will simply
+                                  replace the according 
+                                  :class:`Backbone` objects. If set to True,
+                                  the n-terminal and c-terminal tails are superposed onto the *sub_fragment* 
+                                  stems using the positions at *index* and 
+                                  *index* + len( *sub_fragment* )-1.
+    :type sub_fragment:           :class:`BackboneList`
+    :type index:                  :class:`int`
+    :type superpose_stems:        :class:`bool`
+
+    :raises:                      :exc:`~exceptions.RuntimeError` if
+                                  *sub_fragment* does not fully fit into
+                                  actual fragment at specified *index*
+
+
+  .. method:: GetN(index)
+              GetCA(index)
+              GetCB(index)
+              GetC(index)
+              GetO(index)
+
+    :return: Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
+             atom for residue at given index.
+    :rtype:  :class:`~ost.geom.Vec3`
+    :param index: Residue index.
+    :type index:  :class:`int`
+
+  .. method:: SetN(index, pos)
+              SetCA(index, pos)
+              SetCB(index, pos)
+              SetC(index, pos)
+              SetO(index, pos)
+
+    :param index: Residue index.
+    :type index:  :class:`int`
+    :param pos: Set position of nitrogen / alpha carbon / beta carbon / carbon
+                / oxygen atom to this.
+    :type pos:  :class:`~ost.geom.Vec3`
+
+  .. method:: GetOLC(index)
+
+    :return: One letter code of the residue at given index.
+    :rtype:  :class:`char`
+    :param index: Residue index.
+    :type index:  :class:`int`
+
+  .. method:: SetOLC(index, olc)
+
+    :param index: Residue index.
+    :type index:  :class:`int`
+    :param olc: Set one letter code of the residue to this.
+    :type olc:  :class:`char`
+
+  .. method:: GetAA(index)
+
+    :return: Amino acid type of the residue at given index.
+    :rtype:  :class:`ost.conop.AminoAcid`
+    :param index: Residue index.
+    :type index:  :class:`int`
+
+  .. method:: SetAA(index, aa)
+
+    :param index: Residue index.
+    :type index:  :class:`int`
+    :param aa: Set amino acid type of the residue to this.
+    :type aa:  :class:`ost.conop.AminoAcid`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *aa* == ost.conop.XXX.
+
+
+  .. method:: Set(index, n_pos, ca_pos, cb_pos, c_pos, o_pos, olc)
+              Set(index, n_pos, ca_pos, c_pos, o_pos, olc)
+              Set(index, res, olc)
+
+    Set all backbone informations. This will reconstruct CB positions if needed
+    and set the amino acid type according to the given one letter code.
+
+    :param index: Residue index.
+    :type index:  :class:`int`
+    :param res: Residue from which to extract backbone atom positions
+    :type res:  :class:`~ost.mol.ResidueHandle`
+    :param n_pos: Set position of nitrogen atom to this.
+    :type n_pos:  :class:`~ost.geom.Vec3`
+    :param ca_pos: Set position of alpha carbon atom to this.
+    :type ca_pos:  :class:`~ost.geom.Vec3`
+    :param cb_pos: Set position of beta carbon atom to this.
+    :type cb_pos:  :class:`~ost.geom.Vec3`
+    :param c_pos: Set position of carbon atom to this.
+    :type c_pos:  :class:`~ost.geom.Vec3`
+    :param o_pos: Set position of oxygen atom to this.
+    :type o_pos:  :class:`~ost.geom.Vec3`
+    :param olc: Set one letter code of the residue to this.
+    :type olc:  :class:`char`
+
+
+  .. method:: __len__()
+
+    :returns: Number of residues in this backbone list.
+    :rtype:   :class:`int`
+
+  .. method:: resize(new_size)
+
+    :param new_size: 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).
+    :type new_size:  :class:`int`
+
+  .. method:: empty()
+
+    :returns: True if the list is empty (i.e. size 0).
+    :rtype:   :class:`bool`
+
+  .. method:: append(n_pos, ca_pos, cb_pos, c_pos, o_pos, olc)
+              append(n_pos, ca_pos, c_pos, o_pos, olc)
+              append(res, olc)
+
+    Appends a new residue at the end of the :class:`BackboneList`. This will
+    reconstruct CB positions if needed and set the amino acid type according
+    to the given one letter code.
+
+    :param res: Residue from which to extract backbone atom positions
+    :type res:  :class:`~ost.mol.ResidueHandle`
+    :param n_pos: Set position of nitrogen atom to this.
+    :type n_pos:  :class:`~ost.geom.Vec3`
+    :param ca_pos: Set position of alpha carbon atom to this.
+    :type ca_pos:  :class:`~ost.geom.Vec3`
+    :param cb_pos: Set position of beta carbon atom to this.
+    :type cb_pos:  :class:`~ost.geom.Vec3`
+    :param c_pos: Set position of carbon atom to this.
+    :type c_pos:  :class:`~ost.geom.Vec3`
+    :param o_pos: Set position of oxygen atom to this.
+    :type o_pos:  :class:`~ost.geom.Vec3`
+    :param olc: Set one letter code of the residue to this.
+    :type olc:  :class:`char`
+
+  .. method:: clear()
+
+    Remove all residues from this list.
+
+  .. method:: Copy()
+    
+    Creates and returns a deep copy of this :class:`BackboneList`. This can be
+    useful, since Python uses reference assignments.
+
+    :rtype:  :class:`BackboneList`
+
+  .. method:: ReconstructCBetaPositions()
+
+    Does a simple reconstruction of all CB positions based on the current
+    N, CA and C positions.
+
+  .. method:: ReconstructOxygenPositions(last_psi=-0.78540)
+
+    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.
+
+    :param last_psi:    Psi angle of the last BackboneList residue,
+                        the default value corresponds to a typical alpha-helix.
+    :type last_psi:     :class:`float`
+
+  .. method:: ReconstructCStemOxygen(after_c_stem)
+
+    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.
+
+    :param after_c_stem: Residue following the C stem (C stem residue is last
+                         element of this backbone list)
+    :type after_c_stem:  :class:`ost.mol.ResidueHandle`
+
+
+  .. method:: ApplyTransform(index, transform)
+
+    Applies a transformation to the positions of a single residue.
+
+    :param index: Residue index.
+    :type index:  :class:`int`
+    :param transform:  The transformation
+    :type transform:   :class:`ost.geom.Mat4`
+
+  .. method:: ApplyTransform(from, to, transform)
+
+    Applies a transformation to the positions of the residues with indices
+    *from*, ..., *to*-1 of this list.
+
+    :param from: Start index.
+    :type from:  :class:`int`
+    :param to: End index (one past last residue to transform).
+    :type to:  :class:`int`
+    :param transform:  The transformation
+    :type transform:   :class:`ost.geom.Mat4`
+
+  .. method:: ApplyTransform(transform)
+
+    Applies a transformation to all positions of this list.
+
+    :param transform:  The transformation
+    :type transform:   :class:`ost.geom.Transform` / :class:`ost.geom.Mat4`
+
+  .. method:: GetTransform(index, res)
+              GetTransform(index, other, other_index)
+
+    :returns: Minimum RMSD transformation of residue *index* onto *res* or
+              residue *other_index* of *other* backbone list considering the
+              positions of the N, CA and C atoms.
+    :rtype:   :class:`ost.geom.Mat4`
+
+    :param index: Residue index.
+    :type index:  :class:`int`
+    :param res:   The other residue.
+    :type res:    :class:`ost.mol.ResidueHandle`
+    :param other: The other backbone list.
+    :type other:  :class:`BackboneList`
+    :param other_index: Residue index in *other* backbone list.
+    :type other_index:  :class:`int`
+
+  .. method:: GetTransform(other)
+
+    :returns: Get minimum RMSD transformation of CA positions of this backbone
+              list onto CA positions of *other* backbone list.
+    :rtype:   :class:`ost.geom.Mat4`
+
+    :param other: The other backbone list.
+    :type other:  :class:`BackboneList`
+
+  .. method:: SuperposeOnto(other)
+
+    Superposes this backbone list onto another one using CA positions.
+
+    :param other: The other backbone list.
+    :type other:  :class:`BackboneList`
+
+
+  .. method:: RotateAroundPhiTorsion(index, phi, sequential=False)
+              RotateAroundPsiTorsion(index, psi, sequential=False)
+              RotateAroundOmegaTorsion(index, omega, sequential=False)
+              RotateAroundPhiPsiTorsion(index, phi, psi, sequential=False)
+              SetAroundPhiTorsion(index, phi, sequential=False)
+              SetAroundPsiTorsion(index, psi, sequential=False)
+              SetAroundOmegaTorsion(index, omega, sequential=False)
+              SetAroundPhiPsiTorsion(index, phi, psi, sequential=False)
+
+    Rotates/sets the phi/psi/omega torsion angle of the backbone at position
+    *index* in the backbone list by/to the given angle(s).
+
+    :param index: Residue index.
+    :type index:  :class:`int`
+    :param phi: Angle by which to rotate phi torsion.
+    :type phi:  :class:`float`
+    :param psi: Angle by which to rotate psi torsion.
+    :type psi:  :class:`float`
+    :param omega: Angle by which to rotate omega torsion.
+    :type omega:  :class:`float`
+    :param sequential: If *True*, the rotation will be propagated to all
+                       residues after the one with *index*. Otherwise, it will
+                       be propagated in the direction where it will affect the
+                       least number of residues.
+    :type sequential:  :class:`bool`
+
+  .. method:: GetPhiTorsion(index)
+              GetPsiTorsion(index)
+              GetOmegaTorsion(index)
+
+    :return: The phi/psi/omega torsion angle for residue at given index.
+    :rtype:  :class:`float`
+    :param index: Residue index.
+    :type index:  :class:`int`
+
+
+  .. method:: TransOmegaTorsions(thresh=20/180*pi, allow_prepro_cis=True)
+
+    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.
+
+    :param thresh: Allowed deviation from ideal trans angle (pi)
+    :type thresh:  :class:`float`
+    :param allow_prepro_cis: Flag, whether cis-omega torsions should be
+                             allowed in case of a subsequent proline.
+    :type allow_prepro_cis:  :class:`bool`
+
+    :returns: whether *bb_list* only contains trans-omega torsions.
+    :rtype:   :class:`bool`
+
+    :raises: :exc:`~exceptions.RuntimeError` if size of this backbone list is
+             smaller than 3.
+
+  .. method:: SetBackrub(index, primary_rot_angle, flanking_rot_angle_one, flanking_rot_angle_two)
+
+    Applies a backrub motion [davis2006]_ at residue defined by **index**. 
+    The first rotation axis is defined by the CA positions from residues at
+    **index** -1 and **index** +1. All atoms in between get rotated around this
+    axis by **primary_rot_angle**. To restore the the hydrogen bond network
+    of the two transformed oxygens, the backrub motion gets completed by
+    two compensatory rotations. The first rotation is around the axis defined by 
+    the CA position from residue **index**-1 and the transformed central CA
+    position with an angle of **flanking_rot_angle_one**. The second rotation is 
+    around the axis from the transformed central CA position to the CA position 
+    from residue at position **index** +1 with an angle of 
+    **flanking_rot_angle_two**.
+
+    :param index:       Position of central residue of the backrub motion
+    :param primary_rot_angle: Angle of the first rotation in radians
+    :param flanking_rot_angle_one: Angle of the first compensatory rotation 
+                                   in radians
+    :param flanking_rot_angle_two: Angle of the second compensatory rotation 
+                                   in radians
+
+    :type index:        :class:`int`
+    :type primary_rot_angle: :class:`float`
+    :type flanking_rot_angle_one: :class:`float`
+    :type flanking_rot_angle_two: :class:`float`
+
+    :raises: :exc:`~exceptions.RuntimeError` if **index** is smaller 1 or
+                                             larger size of BackboneList - 2
+
+  .. method:: SetBackrub(index, primary_rot_angle, [scaling=1.0])
+
+    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 **scaling** to make them less extreme.
+
+    :param index:       Position of central residue of the backrub motion
+    :param primary_rot_angle: Angle of the first rotation in radians
+    :param scaling:     The ideal angles for the compensatory rotations will
+                        be scaled by this value. 
+
+    :type index:        :class:`int`
+    :type primary_rot_angle: :class:`float`
+    :type scaling:      :class:`float`
+
+    :raises: :exc:`~exceptions.RuntimeError` if **index** is smaller 1 or
+                                             larger size of BackboneList - 2
+
+
+
+  .. method:: MinCADistance(other)
+
+    :returns: Minimal pairwise CA-distance between this and the *other*
+              backbone list.
+    :rtype:   :class:`float`
+
+    :param other: The other backbone list.
+    :type other:  :class:`BackboneList`
+
+  .. method:: RMSD(other, superposed_rmsd=False)
+              CARMSD(other, superposed_rmsd=False)
+
+    :returns: RMSD / C-alpha RMSD between this and the *other* backbone list.
+    :rtype:   :class:`float`
+
+    :param other: The other backbone list.
+    :type other:  :class:`BackboneList`
+    :param superposed_rmsd: Whether to superpose before calculating the RMSD.
+    :type superposed_rmsd:  :class:`bool`
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.txt
new file mode 100644
index 0000000000000000000000000000000000000000..756afe78cd46954025953926e787eb618c2f5f58
--- /dev/null
+++ b/doc/html/_sources/loop/structure_db.txt
@@ -0,0 +1,1045 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Structural Data
+================================================================================
+
+.. currentmodule:: promod3.loop
+
+The :class:`StructureDB` 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: :class:`FragDB`) or sequence
+features (see: :class:`Fragger`). 
+Besides backbone and sequence data, derived features can  
+optionally be stored. E.g. sequence profiles or secondary structure information.
+Optional data includes:
+
+  * The phi/psi dihedral angles
+  * The secondary structure state as defined by dssp
+  * The solvent accessibility in square Angstrom 
+  * The amino acid frequencies as given by an input sequence profile
+  * 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:
+    relative solvent accessibility > 25% and at least one atom being exposed
+    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 [chakravarty1999]_ and gets 
+    directly calculated when structural information is added to the StructureDB.
+  * The amino acid frequency derived from structural alignments as described
+    in [zhou2005]_ - 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).
+
+Defining Chains and Fragments
+--------------------------------------------------------------------------------
+
+.. class:: CoordInfo()
+
+  The CoordInfo gets automatically generated when new chains are added to
+  a :class:`StructureDB`. It contains internal information of how a 
+  connected stretch of residues is stored in the database.
+
+  .. attribute:: id
+
+    An id string specified when adding the corresponding stretch to the 
+    structure db
+
+  .. attribute:: chain_name
+
+    A chain name string specified when adding the corresponding stretch to the
+    structure db
+
+  .. attribute:: offset
+
+    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. (:class:`int`)
+
+  .. attribute:: size
+
+    The number of residues in that stretch (:class:`int`)
+
+  .. attribute:: start_resnum
+
+    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. (:class:`int`)
+
+  .. attribute:: shift
+
+    Translation from original coordinates that has been applied before storing
+    structural information in db. (:class:`ost.geom.Vec3`)
+
+
+.. class:: FragmentInfo(chain_index, offset, length)
+
+  The FragmentInfo defines any fragment in the :class:`StructureDB`. If you 
+  implement your own accessor object, thats the information you want to store.
+
+  :param chain_index:   Fills :attr:`chain_index`
+
+  :param offset:        Fills :attr:`offset`
+
+  :param length:        Fills :attr:`length`
+
+  .. attribute:: chain_index
+    
+    The index of the chain (defined by :class:`CoordInfo`) in the 
+    :class:`StructureDB` this particle belongs to. (:class:`int`)
+
+  .. attribute:: offset
+
+    Index of residue in **chain** the fragment starts. (0-based, :class:`int`)
+
+  .. attribute:: length
+
+    Length of the fragment (:class:`int`)
+
+
+
+The Structure Database
+--------------------------------------------------------------------------------
+
+The following code example demonstrates how to create a structural database
+and fill it with content.
+
+.. literalinclude:: ../../../tests/doc/scripts/loop_structure_db.py
+
+Calculating the structural profiles is expensive and heavily depends on
+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:
+
+1. Use a database of limited size to generate the actual profiles (something
+   in between 5000 and 10000 nonredundant chains is enough)
+2. Use the :class:`ost.seq.ProfileDB` to gather profiles produced from jobs
+   running in parallel
+
+
+.. class:: StructureDBDataType
+
+  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 :class:`StructureDB`). 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...).
+
+  Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP, 
+  AAFrequencies, AAFrequenciesStruct
+  
+
+.. class:: StructureDB(data_to_store)
+
+  Generates an empty :class:`StructureDB` that can be filled with content 
+  through :func:`AddCoordinates`. The information extracted there is defined by
+  *data_to_store*. Have a look at the :class:`StructureDBDataType` 
+  documentation and at the example script...
+
+  :param data_to_store: Specifies what data to store in the database, several
+                        flags can be combined with a bitwise or operator.
+  :type data_to_store:  :class:`StructureDBDataType` 
+
+
+
+  .. staticmethod:: Load(filename)
+                    LoadPortable(filename)
+
+    Loads raw binary file generated with :meth:`Save` (optimized for fast
+    reading) / portable file generated with :meth:`SavePortable` (slower but
+    less machine-dependent).
+    
+    :param filename: Path to the file from which to load the database.
+    :type filename:  :class:`str`
+
+    :returns: The loaded data base
+    :rtype:   :class:`StructureDB`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened or if
+              file cannot be parsed (see :ref:`here <portableIO>` for details).
+
+
+  .. method:: Save(filename)
+              SavePortable(filename)
+
+    Saves a raw / portable binary representation. Use portable files for
+    distribution and convert locally to raw files. See :ref:`here <portableIO>`
+    for details.
+
+    :param filename: Path to the file where the database will be saved
+    :type filename:  :class:`str`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened 
+
+
+  .. method:: HasData(data_type)
+
+    Checks, whether requested data type is available in the current database.
+
+    :param data_type:   Data type to check
+    :type data_type:    :class:`StructureDBDataType`
+
+    :returns:           Whether the requested datatype is available
+    :rtype:             :class:`bool`
+
+
+  .. method:: AddCoordinates(id, chain_name, ent, seqres, prof=None, \
+                             only_longest_stretch=True)
+
+    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
+    fully automatically by considering the full *ent* (e.g. when 
+    calculating solvent accessibilities etc.).
+    The only exception is AAFrequencies, where a valid sequence profile 
+    is expected in *prof* that has matching sequence with *seqres*
+    All residues in chain with name *chain_name* must have residue numbers 
+    that directly relate them to the *seqres* with an indexing scheme 
+    starting from one.
+    If this is not the case, an error gets thrown. You might want to
+    consider to use :meth:`ost.seq.Renumber` 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 
+    :class:`CoordInfo` as a descriptor. 
+    To avoid cluttering the database with many small fragments, the flag:
+    *only_longest_stretch* can be used. Set it to False if all
+    connected stretches of chain with name *chain_name* should be added.
+    There is one final catch you have to consider: Due to the internal
+    lossy data compression for the positions, the extent in x, y and
+    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 *shift* attribute
+    in the according :class:`CoordInfo` object.
+
+    :param id:          identifier of the added structure (e.g. pdb id)
+    :param chain_name:  Name of the chain in *ent* you want to add
+    :param ent:         The full entity that must contain a chain named
+                        as specified by *chain_name*.
+    :param seqres:      The reference sequence of chain with name *chain_name*
+    :param prof:        Profile information for the chain with name 
+                        *chain_name*. The profile sequence must match *seqres*.
+    :param only_longest_stretch: Flag whether you want to add only the longest
+                                 connected stretch of residues are all connected
+                                 stretches of residues
+
+    :type id:           :class:`str`
+    :type chain_name:   :class:`str`
+    :type ent:          :class:`ost.mol.EntityHandle` / 
+                        :class:`ost.mol.EntityView`
+    :type seqres:       :class:`ost.seq.SequenceHandle`
+    :type prof:         :class:`ost.seq.ProfileHandle`
+    :type only_longest_strech: :class:`bool`
+
+    :returns: indices of added stretches in db
+    :rtype:   :class:`list` of `int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if the residues in chain with
+              name *chain_name* do not match *seqres* given the 
+              residue numbers, when AAFrequencies have to to be extracted and
+              the sequence in *prof* does not match the *seqres* or *prof* is 
+              invalid. 
+
+
+  .. method:: RemoveCoordinates(coord_idx) 
+
+    Removes coordinates at specified location and all its associated data. This
+    has an impact on the offset values of all :class:`CoordInfo` 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! 
+
+    :param coord_idx:   Specifies coordinates to be removed
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if *coord_idx* is invalid
+
+  .. method:: GetCoordIdx(id, chain_name)
+
+    :returns: The :class:`StructureDB` indices (in [0, :meth:`GetNumCoords`-1]) 
+              of all coords (connected stretches) with matching 
+              *id* / *chain_name*.
+    :rtype:   :class:`list` of :class:`int`
+
+    :param id:          Identifier given when calling :meth:`AddCoordinates`
+    :param chain_name:  Name of chain given when calling :meth:`AddCoordinates`
+
+    :type pdb_id:       :class:`str`
+    :type chain_name:   :class:`str`
+
+
+  .. method:: GetCoordInfo(idx)
+
+    :returns: Object describing the stretch of connected residues with 
+              index *idx*.
+    :rtype:   :class:`CoordInfo`
+
+    :param idx: The :class:`StructureDB` index (in [0, :meth:`GetNumCoords`-1])
+    :type idx:  :class:`int`
+
+
+  .. method:: GetNumCoords()
+
+    :returns: Number of connected stretches of residues that have been added to 
+              the database.
+    :rtype:   :class:`int`
+
+
+  .. method:: PrintStatistics()
+
+    Prints out some information about the db.
+
+
+  .. method:: GetBackboneList(fragment, sequence)
+              GetBackboneList(n_stem, c_stem, fragment, sequence="")
+              GetBackboneList(coord_idx, sequence="")
+              GetBackboneList(n_stem, c_stem, coord_idx, sequence="")
+
+
+    :returns: Backbone list with positions extracted from *fragment* or
+              full entry at *coord_idx*
+    :rtype:   :class:`BackboneList`
+
+    :param fragment: Fragment definition from which to extract positions.
+    :type fragment:  :class:`FragmentInfo`
+    :param coord_idx:   Idx of entry from which to extract positions.
+    :type coord_idx:    :class:`int`
+    :param sequence: Sequence of the returned backbone list. If not
+                     set, the original sequence at specified location in the 
+                     database is used.
+    :type sequence:  :class:`str`
+    :param n_stem: Positions on which the backbone list's N-terminus should be
+                   superposed onto.
+    :type n_stem:  :class:`ost.mol.ResidueHandle`
+    :param c_stem: Positions on which the backbone list's C-terminus should be
+                   superposed onto.
+    :type c_stem:  :class:`ost.mol.ResidueHandle`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if the length of *sequence* does
+              not match with the desired backbone list, if *sequence* contains 
+              a character which does not belong to the 20 proteinogenic amino 
+              acids or 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. 
+
+  .. method:: GetSequence(fragment)
+              GetSequence(coord_idx)
+
+    :returns: The sequence of *fragment* or full entry at *coord_idx*
+    :rtype:   :class:`str`
+
+    :param fragment:    Fragment definition from which to extract the sequence.
+    :type fragment:     :class:`FragmentInfo`
+
+    :param coord_idx:   Idx of entry from which to extract the sequence
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` 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.
+
+
+  .. method:: GetDSSPStates(fragment)
+              GetDSSPStates(coord_idx)
+
+    :returns: The dssp states of *fragment* or full entry at *coord_idx*
+    :rtype:   :class:`str`
+
+    :param fragment: Fragment definition from which to extract the states.
+    :type fragment:  :class:`FragmentInfo`
+
+    :param coord_idx:   Idx of entry from which to extract the dssp states
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` 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.
+
+
+  .. method:: GetDihedralAngles(fragment)
+              GetDihedralAngles(coord_idx)
+
+    :returns: The phi and psi dihedral angles of every residue of *fragment*
+              or full entry at *coord_idx*
+    :rtype:   :class:`list` of pairs (:class:`tuple`)
+
+    :param fragment: Fragment definition from which to extract the dihedrals.
+    :type fragment:  :class:`FragmentInfo`
+
+    :param coord_idx:   Idx of entry from which to extract the dihedral angles
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` 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.
+
+
+  .. method:: GetResidueDepths(fragment)
+              GetResidueDepths(coord_idx)
+
+    :returns: Residue depth for each residue of *fragment* or full entry 
+              at *coord_idx*
+    :rtype:   :class:`list` of :class:`float`
+
+    :param fragment: Fragment definition from which to extract the residue
+                     depths
+    :type fragment:  :class:`FragmentInfo`
+
+    :param coord_idx:   Idx of entry from which to extract the residue depths
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` 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.
+
+
+  .. method:: GetSolventAccessibilitites(fragment)
+              GetSolventAccessibilitites(coord_idx)
+
+    :returns: Solvent accessibility for each residue of *fragment* or full entry
+              at *coord_idx* in square A as calculated by 
+              :meth:`~ost.mol.alg.Accessibility` when adding the structure to 
+              the database.
+    :rtype:   :class:`list` of :class:`float`
+
+    :param fragment: Fragment definition from which to extract the solvent
+                     accessibilities
+    :type fragment:  :class:`FragmentInfo`
+
+    :param coord_idx:   Idx of entry from which to extract the solvent 
+                        accessibilities
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` 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.
+
+
+  .. method:: GetSequenceProfile(fragment)
+              GetSequenceProfile(coord_idx)
+
+    :returns: The sequence profile for the residues defined by *fragment* or 
+              full entry at *coord_idx* with the BLOSUM62 probabilities as NULL 
+              model.
+    :rtype:   :class:`ost.seq.ProfileHandle`
+
+    :param fragment:    Fragment definition from which to extract the sequence
+                        profile
+
+    :type fragment:     :class:`FragmentInfo`
+
+    :param coord_idx:   Idx of entry from which to extract the sequence profile
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` 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.
+                    
+
+  .. method:: GetStructureProfile(fragment)
+              GetStructureProfile(coord_idx)
+
+    :returns: The structure profile for the residues defined by *fragment* or
+              full entry at *coord_idx* with the BLOSUM62 probabilities as NULL 
+              model.
+    :rtype:   :class:`ost.seq.ProfileHandle`
+
+    :param fragment:    Fragment definition from which to extract the structure
+                        profile
+
+    :type fragment:     :class:`FragmentInfo`
+
+    :param coord_idx:   Idx of entry from which to extract the structure profile
+    :type coord_idx:    :class:`int`
+
+    :raises:  :exc:`~exceptions.RuntimeError` 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.
+
+
+  .. method:: GenerateStructureProfile(bb_list, residue_depths)
+
+    Calculates a structure profile for *bb_list* with given *residue_depths*
+    using the full internal data of this StructureDB.
+
+    :param bb_list:  Positions for which to calculate the structural profile
+    :type bb_list:   :class:`BackboneList`
+    :param residue_depths: The residue depth for each residue in *bb_list* 
+                           as you would extract it from any StructureDB 
+                           containing that data. 
+    :type residue_depths:  :class:`list` of :class:`float`
+
+    :returns: The structure profile for the input with the BLOSUM62
+              probabilities as NULL model.
+    :rtype:   :class:`ost.seq.ProfileHandle`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if *bb_list* and 
+              *residue_depths* differ in size, when their size is 0
+              or when database does not contain residue depth data.
+
+
+  .. method:: SetStructureProfile(coord_idx, prof)
+
+    Takes the *prof* and sets the corresponding StructureProfile
+    frequencies in entry with *coord_idx*
+
+    :param prof:      Source of profile frequencies
+    :param coord_idx: StructureDB index of entry for which to set frequencies
+                      (in [0, :meth:`GetNumCoords`-1])
+
+    :type prof:       :class:`ost.seq.ProfileHandle`
+    :type coord_idx:  :class:`int`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *coord_idx* does not match
+             any entry in the db, when the size of the *prof* does not
+             exactly match the size of entry at *coord_idx* or when database
+             does not contain aa frequency struct data.
+
+
+  .. method:: GetSubDB(indices)
+
+    :return: 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.
+    :rtype:  :class:`StructureDB`
+
+    :param indices: Indices of chains to be added to the sub database (in [0,
+                    :meth:`GetNumCoords`-1])
+    :type indices:  :class:`list`
+
+    :raises: :exc:`~exceptions.RuntimeError` if you provide an invalid index
+
+
+
+Finding Fragments based on Geometric Features
+--------------------------------------------------------------------------------
+
+The fragment database allows to organize, search and access the information
+stored in a structural database (:class:`StructureDB`). 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.
+
+This example illustrates how to create a custom FragDB based on a StructureDB:
+
+.. literalinclude:: ../../../tests/doc/scripts/loop_frag_db.py
+
+.. class:: FragDB(dist_bin_size, angle_bin_size)
+
+  :param dist_bin_size: Size of the distance parameter binning in A
+  :param angle_bin_size: Size of the angle parameter binning in degree
+  :type dist_bin_size:  :class:`float`
+  :type angle_bin_size: :class:`int`
+
+  .. staticmethod:: Load(filename)
+                    LoadPortable(filename)
+
+    Loads raw binary file generated with :meth:`Save` (optimized for fast
+    reading) / portable file generated with :meth:`SavePortable` (slower but
+    less machine-dependent).
+
+    :param filename: Path to the file from which to load the database.
+    :type filename:  :class:`str`
+
+    :returns: The loaded database
+    :rtype:   :class:`FragDB`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened or if
+              file cannot be parsed (see :ref:`here <portableIO>` for details).
+
+  .. method:: Save(filename)
+              SavePortable(filename)
+
+    Saves a raw / portable binary representation. Use portable files for
+    distribution and convert locally to raw files. See :ref:`here <portableIO>`
+    for details.
+
+    :param filename: path to the file where the database will be saved
+    :type filename:  :class:`str`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened.
+
+  .. method:: GetAngularBinSize()
+
+    The size of the bins for the 4 angles describing the stem geometry and used 
+    to organize the fragments in the database.
+
+    :return:    The bin size in degrees
+    :rtype:     :class:`int`
+
+  .. method:: GetDistBinSize()
+
+    The size of the bins for the distance describing the stem geometry and used 
+    to organize the fragments in the database.
+
+    :return:    The bin size
+    :rtype:     :class:`float`
+
+
+  .. method:: AddFragments(fragment_length, rmsd_cutoff, structure_db)
+
+    Iterates over all fragments of length **fragment_length** in 
+    **structure_db** and adds them to the fragment database. 
+    Fragments will be skipped if there is already a fragment in the database 
+    that has an RMSD smaller than **rmsd_cutoff**, where RMSD is calculated 
+    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.
+
+    :param fragment_length:    The length of the fragments that should be added to the databse
+    :param rmsd_cutoff:        The minimal RMSD between two fragments in the fragment database
+    :param structure_db:       Database delivering the structural info
+    :type fragment_length:     :class:`int`
+    :type rmsd_cutoff:         :class:`float`
+    :type structure_db:        :class:`StructureDB`
+
+
+  .. method:: PrintStatistics()
+
+    Prints statistics about the fragment database, notably:
+
+    1. the number of different stem groups (number of bins used to group the
+       fragments according to the geometry of their stem residues)
+    2. The total number of fragments in the database
+    3. The minimal and maximal number of fragments found in a stem group.
+
+
+  .. method:: GetNumStemPairs()
+              GetNumStemPairs(loop_length)
+    
+    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.
+    
+    :param loop_length:   The length of the fragments
+    :type loop_length:    :class:`int`
+
+    :returns:   The number of groups
+    :rtype:     :class:`int`
+
+  .. method:: GetNumFragments()
+              GetNumFragments(loop_length)
+
+    Returns the number of fragments in the database in total or for fragments of
+    a given length.
+
+    :param loop_length:   The length of the fragments
+    :type loop_length:    :class:`int`
+
+    :returns: Number of fragments
+    :rtype:   :class:`int`
+
+  .. method:: HasFragLength(loop_length)
+
+    :param loop_length:   The length of the fragments
+    :type loop_length:    :class:`int`
+
+    :returns: True if fragments of given length exist.
+    :rtype:   :class:`bool`
+
+  .. method:: MaxFragLength()
+
+    :returns: Maximal fragment length contained in db.
+    :rtype:   :class:`int`
+
+  .. method:: SearchDB(n_stem, c_stem, frag_size, extra_bins=0)
+
+    Search the database for fragments matching the geometry of the **n_stem**
+    and **c_stem** and of the same length as the **frag_size**.
+
+    :param n_stem: The N-stem
+    :type n_stem:  :class:`ost.mol.ResidueHandle`
+    :param c_stem: The C-stem
+    :type c_stem:  :class:`ost.mol.ResidueHandle`
+    :param frag_size: Number of residues of the fragment
+    :type frag_size:  :class:`int`
+    :param extra_bins: Whether to extend the search to include fragments from
+                       *extra_bins* additional bins surrounding the bin given by
+                       the *n_stem* and *c_stem* geometry. If odd, we extend to
+                       the closer bin, otherwise symmetrically.
+    :type extra_bins:  :class:`int`
+
+    :returns: A list of :class:`FragmentInfo` objects. These objects are related
+              to the structural database with which you called the AddFragments
+              function.
+
+
+Finding Fragments based on Sequence Features
+--------------------------------------------------------------------------------
+
+In some cases you might want to use the :class:`StructureDB` to search 
+for fragments that possibly represent the structural conformation of interest.
+The :class:`Fragger` searches a :class:`StructureDB` 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 :class:`Fragger`
+wrapped in a full fletched pipeline implemented in 
+:class:`~promod3.modelling.FraggerHandle` or search for fragments from scratch 
+using an arbitrary linear combination of scores:
+
+* **SeqID**:
+  Calculates the fraction of amino acids being identical when comparing
+  a potential fragment from the :class:`StructureDB` and the target sequence
+
+* **SeqSim**:
+  Calculates the avg. substitution matrix based sequence similarity of amino acids 
+  when comparing a potential fragment from the :class:`StructureDB` and the target 
+  sequence
+
+* **SSAgree**:
+  Calculates the avg. agreement of the predicted secondary structure by PSIPRED [Jones1999]_
+  and the dssp [kabsch1983]_ assignment stored in the :class:`StructureDB`.
+  The Agreement term is based on a probabilistic approach also used in HHSearch [soding2005]_.
+
+* **TorsionProbability**:
+  Calculates the avg. probability of observing the phi/psi dihedral angles of a potential
+  fragment from the :class:`StructureDB` given the target sequence. The probabilities are
+  extracted from the :class:`TorsionSampler` class.
+
+* **SequenceProfile**:
+  Calculates the avg. profile score between the amino acid frequencies of a potential
+  fragment from the :class:`StructureDB` and a target profile assuming a gapfree alignment
+  in between them. The scores are calculated as L1 distances between the profile columns.
+
+* **StructureProfile**:
+  Calculates the avg. profile score between the amino acid frequencies of a potential
+  fragment from the :class:`StructureDB` 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.
+
+.. literalinclude:: ../../../tests/doc/scripts/loop_fragger.py
+
+.. class:: Fragger(seq)
+
+  A Fragger object to search a :class:`StructureDB` for fragments with **seq**
+  as target sequence. You need to add some score components before you can
+  finally call the Fill function.
+
+  :param seq:         Sequence of fragments to be searched
+  :type seq:          :class:`str`
+
+  .. method:: Fill(db, rmsd_thresh, num_fragments)
+
+    Searches **db** for **num_fragments** fragments with maximal 
+    score based on the defined score components. 
+    There will be no pair of fragments with RMSD below **rmsd_thresh**.
+
+    :param db:          Source of structural data
+    :param rmsd_thresh: To guarantee structural diversity
+    :param num_fragments: Number of fragments to be extracted
+
+    :type db:           :class:`StructureDB`
+    :type rmsd_thresh:  :class:`float`
+    :type num_fragments: :class:`int`
+
+  .. method:: AddSeqIDParameters(w)
+
+    Add SeqID score component with linear weight **w**
+
+    :param w:           linear weight
+
+    :type w:            :class:`float`
+
+  .. method:: AddSeqSimParameters(w, subst)
+
+    Add SeqSim score component with linear weight **w**
+
+    :param w:           linear weight
+    :param subst:       Substitution matrix to calculate sequence similarity
+
+    :type w:            :class:`float`
+    :type subst:        :class:`ost.seq.SubstWeightMatrix`
+
+  .. method:: AddSSAgreeParameters(w, psipred_prediction)
+
+    Add SSAgree score component with linear weight **w**
+
+    :param w:           linear weight
+    :param psipred_prediction:  Psipred prediction for fraggers target_sequence
+
+    :type w:            :class:`str`
+    :type psipred_prediction: :class:`PsipredPrediction`
+
+
+  .. method:: AddTorsionProbabilityParameters(w, torsion_sampler, \
+                                              aa_before, aa_after)
+              AddTorsionProbabilityParameters(w, torsion_sampler_list, \
+                                              aa_before, aa_after)
+
+    Add TorsionProbability component of linear weight **w**
+
+    :param w:           linear weight
+    :type w:            :class:`float`
+    :param torsion_sampler: Torsion sampler to be used for all residues.
+    :type torsion_sampler:  :class:`TorsionSampler`
+    :param torsion_sampler_list: One torsion sampler for each residue.
+    :type torsion_sampler_list:  :class:`list` of :class:`TorsionSampler`
+    :param aa_before:   Name (3 letter code) of the residue before the sequence
+                        linked to this object.
+    :type aa_before:    :class:`str`
+    :param aa_after:    Name (3 letter code) of the residue after the sequence
+                        linked to this object.
+    :type aa_after:     :class:`str`
+
+  .. method:: AddSequenceProfileParameters(w, prof)
+
+    Add SequenceProfile component of linear weight **w**
+
+    :param w:           linear weight
+    :param prof:        Profile for the fraggers target_sequence
+
+    :type w:            :class:`float`
+    :type prof:         :class:`ost.seq.ProfileHandle`
+
+  .. method:: AddStructureProfileParameters(w, prof)
+
+    Add StructureProfile component of linear weight **w**
+
+    :param w:           linear weight
+    :param prof:        Profile for the fraggers target_sequence
+
+    :type w:            :class:`float`
+    :type prof:         :class:`ost.seq.ProfileHandle`
+
+  .. method:: __len__()
+
+    :returns:           Number of fragments stored in fragger.
+
+  .. method:: __getitem__(index)
+
+    :param index:       Item to extract
+
+    :returns:           Fragment at given position
+    :rtype:             :class:`BackboneList`
+
+  .. method:: GetFragmentInfo(index)
+
+    :param index:       Index of fragment
+
+    :type index:        :class:`int`
+
+    :returns:           :class:`FragmentInfo` of fragment at position **index**
+
+  .. method:: GetScore(index)
+
+    Returns the final score of fragment defined by **index**
+
+    :param index:       Index of fragment
+
+    :type index:        :class:`int`
+
+    :returns:           Score of fragment at position **index**
+
+  .. method:: GetScore(parameter_index, index)
+
+    Returns the  single feature score defined by **parameter_index** of
+    fragment defined by **index** with parameter indexing based on the order
+    you added them to the :class:`Fragger`
+
+    :param parameter_index: Index of score (0-indexed in order of score
+                            components that were added)
+    :param index:           Index of fragment
+
+    :type parameter_index: :class:`int`
+    :type index:           :class:`int`
+
+.. class:: FraggerMap
+
+  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.
+
+  You can use :meth:`Contains` to check if an item with a given key
+  (:class:`int`) already exists and access items with the [] operator (see
+  :meth:`__getitem__` and :meth:`__setitem__`).
+
+  Serialization is meant to be temporary and is not guaranteed to be portable.
+
+  .. method:: Load(filename, db)
+
+    Loads raw binary file generated with :meth:`Save`.
+    
+    :param filename: Path to the file.
+    :type filename:  :class:`str`
+    :param db:       Source of structural data used when filling the fragments.
+    :type db:        :class:`StructureDB`
+
+    :returns:        The loaded map.
+    :rtype:          :class:`FraggerMap`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened.
+
+  .. method:: Save(filename)
+
+    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.
+
+    :param filename: Path to the file.
+    :type filename:  :class:`str`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened.
+
+  .. method:: LoadBB(filename)
+
+    Loads raw binary file generated with :meth:`SaveBB`.
+    
+    :param filename: Path to the file.
+    :type filename:  :class:`str`
+
+    :returns:        The loaded map.
+    :rtype:          :class:`FraggerMap`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened.
+
+  .. method:: SaveBB(filename)
+
+    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
+    :meth:`Save`.
+
+    :param filename: Path to the file.
+    :type filename:  :class:`str`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if file cannot be opened.
+
+  .. method:: Contains(id)
+
+    :return: True, iff a fragger object for this id is already in the map.
+    :rtype:  :class:`bool`
+
+  .. method:: __getitem__(id)
+              __setitem__(id)
+
+    Allow read/write access (with [*id*]) to fragger object with given ID.
+
+
+The PsipredPrediction class
+--------------------------------------------------------------------------------
+
+.. class:: PsipredPrediction
+
+  A container for the secondary structure prediction by PSIPRED [Jones1999]_.
+
+  .. method:: PsipredPrediction()
+    
+    Constructs empty container
+
+  .. method:: PsipredPrediction(prediction, confidence)
+
+    Constructs container with given content
+
+    :param prediction:  Secondary structure prediction as element in ['H','E','C']
+    :param confidence:  Confidence of prediction as element in [0,9]
+
+    :type prediction:   :class:`list`
+    :type confidence:   :class:`list`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if size of **prediction** and
+              **confidence** are inconsistent or if they contain an invalid
+              element
+
+  .. method:: FromHHM(filename)
+
+    Static function to Load a :class:`PsipredPrediction` object from hhm file, 
+    as they are provided by the hhsearch suite
+
+    :param filename:    Name of file
+    :type filename:     :class:`str`
+
+  .. method:: FromHoriz(filename)
+
+    Static function to Load a :class:`PsipredPrediction` object from horiz file, 
+    as they are produced by the psipred executable
+
+    :param filename:    Name of file
+    :type filename:     :class:`str` 
+
+  .. method:: Add(prediction, confidence)
+
+    Adds and appends a single residue psipred prediction at the end
+
+    :param prediction:  Prediction, must be one in ['H','E','C']
+    :param confidence:  Confidence of prediction, must be in [0,9]
+
+    :type prediction:   :class:`str`
+    :type confidence:   :class:`int`
+
+    :raises: :exc:`~exceptions.RuntimeError` if input contains invalid elements
+
+  .. method:: Extract(from, to)
+
+    Extracts content and returns a sub-:class:`PsipredPrediction` with range **from**
+    to **to**, not including **to** itself
+
+    :param from:        Idx to start
+    :param to:          Idx to end
+
+    :type from:         :class:`int`
+    :type to:           :class:`int`
+
+    :returns:           :class:`PsipredPrediction` with the specified range
+
+    :raises: :exc:`~exceptions.RuntimeError` if **from** or **to** are invalid
+
+  .. method:: GetPrediction(idx)
+
+    :param idx:         Index to get prediction from
+    :type idx:          :class:`int`
+    :returns:           Psipred prediction at pos **idx**
+    :raises:  :exc:`~exceptions.RuntimeError` if **idx** is invalid
+
+  .. method:: GetConfidence(idx)
+
+    :param idx:         Index to get confidence from
+    :type idx:          :class:`int`
+    :returns:           Psipred confidence at pos **idx**
+    :raises: :exc:`~exceptions.RuntimeError` if **idx** is invalid  
+
+  .. method:: GetPredictions()
+
+    Get all the predictions in the container
+
+    :returns:           :class:`list` containing all the predictions in the container
+
+  .. method:: GetConfidences()
+
+    Get all the confidences in the container
+
+    :returns:           :class:`list` containing all the confidences in the container
+
+  .. method:: __len__()
+
+    :returns:           Number of elements in container
diff --git a/doc/html/_sources/modelling/algorithms.txt b/doc/html/_sources/modelling/algorithms.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c775b0a1ba537244c4f7e22bdff9a38cb5ef582
--- /dev/null
+++ b/doc/html/_sources/modelling/algorithms.txt
@@ -0,0 +1,328 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Modelling Algorithms
+================================================================================
+
+.. currentmodule:: promod3.modelling
+
+A collection of algorithms that can be useful in modelling
+
+
+Rigid Blocks
+--------------------------------------------------------------------------------
+
+RMSD is a typical measure for similarity of two structures. Given an atom atom
+mapping between two structures, the minimum RMSD and the according superposition
+can efficiently be calculated using an approach based on singular value 
+decomposition. This approach is problematic if there are very dissimilar regions
+or when domain movement events occur. We can therefore implement an iterative
+superposition. The two structures undergo an initial superposition. For every
+iteration we then select a subset of atoms that are within a certain distance
+threshold that serve as input for the next superposition. This iterative
+superpostion typically converges to the largest common subpart but is
+non-deterministic since it depends on the initial superposition.
+The RigidBlocks algorithm is based on only the CA positions and performs this 
+iterative superposition multiple times by using a sliding window to select the 
+initial subset and gathers all unique results. These results can be very 
+similar and only differ by single positions. The algorithm therefore reduces
+the amount of solutions by merging them based on a threshold of similarity.
+The similarity is defined by the fraction of positions in solution A that are
+also present in solution B. As a final result, the algorithm therefore detects 
+common rigid subsets of positions.
+
+.. method:: RigidBlocks(bb_list_one, bb_list_two, [window_length = 12, max_iterations=20, distance_thresh=3.0, cluster_thresh=0.9])
+
+  Performs the RigidBlock algorithm on given input
+
+  :param bb_list_one:   First piece structural information from which CA
+                        positions will be extracted
+  :param bb_list_two:   Second piece of structural information from which CA
+                        positions will be extracted
+  :param window_length: Length of sliding window to generate initial subsets
+  :param max_iterations: Maximal numbers of iterations for every single
+                         iterative superposition
+  :param distance_thresh: 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
+  :param cluster_thresh: Threshold of similarity to perform the final merging
+                         of the solutions
+
+  :type bb_list_one:    :class:`promod3.loop.BackboneList`
+  :type bb_list_two:    :class:`promod3.loop.BackboneList`
+  :type window_length:  :class:`int`
+  :type max_iterations: :class:`int`
+  :type distance_thresh: :class:`float`
+  :type cluster_thresh: :class:`float`
+
+  :returns:             :class:`tuple` with the first element being a 
+                        :class:`list` of :class:`list` defining the
+                        indices of the common subsets (rigid blocks) relative
+                        to the input :class:`promod3.loop.BackboneList` objects 
+                        and the second element being a :class:`list` of 
+                        :class:`ost.geom.Mat4` defining the transformations to 
+                        superpose the according positions in **bb_list_one** 
+                        onto **bb_list_two**
+
+
+.. method:: RigidBlocks(aln, [seq_one_idx=0, seq_two_idx=1,window_length = 12, max_iterations=20, distance_thresh=3.0, cluster_thresh=0.9])
+
+  Performs the RigidBlock algorithm on given input
+
+  :param aln:           An alignment with attached :class:`ost.mol.EntityView`
+                        objects from which the positions are extracted
+  :param seq_idx_one:   The idx of the first sequence from which the CA 
+                        positions will be extracted
+  :param seq_idx_two:   The idx of the second sequence from which the CA
+                        positions will be extracted
+  :param window_length: Length of sliding window to generate initial subsets
+  :param max_iterations: Maximal numbers of iterations for every single
+                         iterative superposition
+  :param distance_thresh: 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
+  :param cluster_thresh: Threshold of similarity to perform the final merging
+                         of the solutions
+
+  :type aln:            :class:`ost.seq.AlignmentHandle`
+  :type seq_idx_one:    :class:`int`
+  :type seq_idx_two:    :class:`int`
+  :type window_length:  :class:`int`
+  :type max_iterations: :class:`int`
+  :type distance_thresh: :class:`float`
+  :type cluster_thresh: :class:`float`
+
+  :returns:             :class:`tuple` with the first element being a 
+                        :class:`list` of :class:`list` defining the
+                        column indices of the common subsets (rigid blocks) 
+                        relative to the input :class:`ost.seq.AlignmentHandle` 
+                        and the second element being a :class:`list` of 
+                        :class:`ost.geom.Mat4` defining the transformations to 
+                        superpose the according positions from the first
+                        sequence onto the second sequence.
+
+.. method:: RigidBlocks(pos_one, pos_two, [window_length = 12, max_iterations=20, distance_thresh=3.0, cluster_thresh=0.9])
+
+  Performs the RigidBlock algorithm on given input
+
+  :param pos_one:       First piece position information 
+  :param pos_two:       Second piece of position information
+  :param window_length: Length of sliding window to generate initial subsets
+  :param max_iterations: Maximal numbers of iterations for every single
+                         iterative superposition
+  :param distance_thresh: 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
+  :param cluster_thresh: Threshold of similarity to perform the final merging
+                         of the solutions
+
+  :type pos_one:        :class:`ost.geom.Vec3List`
+  :type pos_two:        :class:`ost.geom.Vec3List`
+  :type window_length:  :class:`int`
+  :type max_iterations: :class:`int`
+  :type distance_thresh: :class:`float`
+  :type cluster_thresh: :class:`float`
+
+  :returns:             :class:`tuple` with the first element being a 
+                        :class:`list` of :class:`list` defining the
+                        indices of the common subsets (rigid blocks) relative
+                        to the input :class:`ost.geom.Vec3List` objects 
+                        and the second element being a :class:`list` of 
+                        :class:`ost.geom.Mat4` defining the transformations to 
+                        superpose the according positions in **pos_one** 
+                        onto **pos_two**
+
+
+De Novo Modelling
+--------------------------------------------------------------------------------
+
+ProMod3 provides algorithms for sampling and fragment detection. 
+Here we provide an object, that facilitates fragment detection and caching,
+as well as a convenient function to combine the functionalities into an
+example pipeline.
+
+.. autoclass:: FraggerHandle
+  :members:
+
+
+.. autofunction:: GenerateDeNovoTrajectories
+
+
+Motif Finder
+--------------------------------------------------------------------------------
+
+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 
+[nussinov1991]_. The algorithm consists of a learning stage, a detection stage 
+and a refinement stage.
+
+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 
+triangle one can define an orthogonal vector basis 
+(in our case v1 = norm(p2-p1), v3 = norm(cross(v1,p3-p1), 
+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.
+
+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 
+in the input query. We then iterate over each possible triangle with vertices 
+p1, p2 and p3 in the target coordinates. At the beginning of each iteration, 
+all counters in the accumulator are set to zero. Again, we build a vector basis 
+given that triangle and transform all coordinates not in [p1,p2,p3] into that 
+vector space. For each transformed coordinate we obtain a key for the query hash 
+map. If there is one or several values at that location in the hash map, 
+we increment the corresponding locations in the accumulator. 
+Once all coordinates are processed, we search for high counts in the 
+accumulator. Given *N* query coordinates, we keep a solution for further 
+refinement if count/(*N*-3) >= *hash_tresh*. This is repeated until all 
+triangles in the target are processed. One key problem with this approach is 
+the discretization of floating point numbers that give raise to the hash map 
+keys. Two extremely close values might end up in different bins just because
+they are close to the bin boundaries. For each of the 6 relevant numbers
+we estimate the actual bin as well as the closest neighbouring bin. Processing
+all possible combinations results in 64 hash map lookups instead of only one.
+
+Refinement Stage: Every potential solution identified in the detection stage is
+further refined based on the *distance_thresh* and *refine_thresh* parameters.
+A potential solution found in the detection stage is a pair of triangles, one
+in the query and one in the target, for which we find many matching coordinates 
+in their respective vector space. We start with a coordinate mapping based on 
+the triangle vertices from the query and the target (3 pairs). 
+This coordinate mapping is iteratively updated by estimating the minimum RMSD 
+superposition of the mapped query coordinates onto the target, apply that 
+superposition on the query, find the closest target coordinate for each 
+coordinate in the query and redo the mapping by including all pairs with 
+minimum distance < *distance_thresh*. Iteration stops if nothing changes 
+anymore. The solution is returned to the user if the final fraction of mapped 
+query coordinates is larger or equal *refine_thresh*.
+The larger the mapping, the more accurate the superposition. As we start with 
+only the three triangle vertices, *distance_thresh* is doubled for the initial 
+iteration.
+
+.. literalinclude:: ../../../tests/doc/scripts/modelling_motif_finder.py
+
+.. class:: MotifQuery(positions, identifier, min_triangle_edge_length, \
+                      max_triangle_edge_length, bin_size)
+           MotifQuery(positions, identifier, min_triangle_edge_length, \
+                      max_triangle_edge_length, bin_size, flags)
+           MotifQuery(query_list)
+
+  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. 
+
+  :param positions:     Coordinates of the query
+  :param identifier:    Descriptor of the query
+  :param min_triangle_edge_length: To avoid the full O(n^3) hell, triangles
+                        with any edge length below *min_triangle_edge_length*
+                        are skipped
+  :param max_triangle_edge_length: Same as *min_triangle_edge_length* but 
+                        upper bound
+  :param bin_size:      Bin size in A, relevant to generate hash map keys
+  :param flags:         Flag in range [0,63] for every coordinate in *positions*.
+                        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.
+  :param query_list:    E pluribus unum
+
+  :type positions:      :class:`ost.geom.Vec3List`
+  :type identifier:     :class:`str`
+  :type min_triangle_edge_length: :class:`float`
+  :type max_triangle_edge_length: :class:`float`
+  :type bin_size:       :class:`float`
+  :type flags:          :class:`list` of :class:`int`
+  :type query_list:     :class:`list` of :class:`MotifQuery`
+
+
+  .. method:: Save(filename)
+
+    Saves the query down to disk 
+
+    :param filename:    filename
+    :type filename:     :class:`str`
+
+  .. staticmethod:: Load(filename)
+
+    Load query from disk
+
+    :param filename:    filename
+    :type filename:     :class:`str`
+
+  .. method:: GetPositions(query_idx)
+
+    Returns coordinates of specified query
+
+    :param query_idx:   Query from which you want the positions
+    :type query_idx:    :class:`int`
+
+  .. method:: GetIdentifiers()
+
+    Returns a list of all query identifiers.
+
+  .. method:: GetN()
+
+    Returns the number of queries
+
+
+
+.. class:: MotifMatch
+
+  Object that holds information about a match found in :meth:`FindMotifs`
+
+  .. attribute:: query_idx 
+
+    Index of matching query
+
+  .. attribute:: mat 
+
+    Transformation matrix to superpose matching query onto target
+
+  .. attribute:: alignment 
+
+    List of tuples which define matching pairs of query/target coordinates
+
+
+.. method:: FindMotifs(query, target_positions, hash_tresh=0.4, \
+                       distance_thresh=1.0, refine_thresh=0.7, \
+                       flags=list())
+
+  Performs the detection and refinement stages of the geometric hashing 
+  algorithm. 
+
+  :param query:         Query to be searched
+  :param target_positions: Coordinates of the target
+  :param hash_thresh:   Parameter relevant for detection stage
+  :param distance_thresh: Parameter relevant for refinement stage
+  :param refine_thresh: Parameter relevant for refinement stage
+  :param flags:         Equivalent to *flags* in :class:`MotifQuery`
+                        constructor. If you didn't provide anything there,
+                        this can be ignored. Only the actual coordinates
+                        matter in this case.
+
+  :returns:             All found matches
+
+  :rtype:               :class:`list` of :class:`MotifMatch`
diff --git a/doc/html/_sources/references.txt b/doc/html/_sources/references.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18a5a3b25ba4779ccd336b9bbfdae278f04735ab
--- /dev/null
+++ b/doc/html/_sources/references.txt
@@ -0,0 +1,90 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+References
+==========
+
+.. [biasini2013] 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.
+
+.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). 
+                   Cyclic coordinate descent: A robotics algorithm for protein 
+                   loop closure. Protein Sci.
+
+.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). 
+                    A graph-theory algorithm for rapid protein side-chain 
+                    prediction. Protein Sci.
+
+.. [coutsias2005] Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+                  Resultants and loop closure. International Journal of Quantum 
+                  Chemistry. 
+
+.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). 
+                     Residue depth: a novel parameter for the analysis of 
+                     protein structure and stability. Structure.
+
+.. [davis2006] Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+               The backrub motion: how protein backbone shrugs when a sidechain 
+               dances. Structure.
+
+.. [goldstein1994] Goldstein RF (1994). 
+                   Efficient rotamer elimination applied to protein side-chains 
+                   and related spin glasses. Biophys J.
+
+.. [Jones1999] Jones DT (1999). 
+               Protein secondary structure prediction based on position-specific 
+               scoring matrices. J. Mol. Biol. 
+
+.. [kabsch1983] Kabsch W, Sander C (1983). 
+                Dictionary of protein secondary structure: pattern recognition of 
+                hydrogen-bonded and geometrical features. Biopolymers.
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). 
+                Improved prediction of protein side-chain conformations with 
+                SCWRL4. Proteins.
+
+.. [leach1998] Leach AR, Lemon AP (1998). 
+               Exploring the conformational space of protein side chains using 
+               dead-end elimination and the A* algorithm. Proteins.
+
+.. [nussinov1991] Nussinov R and Wolfson HJ (1991).
+                  Efficient detection of three-dimensional structural motifs in
+                  biological macromolecules by computer vision techniques. PNAS.
+
+.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). 
+                    A smoothed backbone-dependent rotamer library for proteins 
+                    derived from adaptive kernel density estimates and 
+                    regressions. Structure.
+
+.. [soding2005] Söding J (2005). 
+                Protein homology detection by HMM-HMM comparison. 
+                Bioinformatics.
+
+.. [solis2006] Solis AD, Rackovsky S (2006). Improvement of statistical 
+               potentials and threading score functions using information 
+               maximization. Proteins. 
+
+.. [trott2010] 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
+
+.. [zhou2005] Zhou H, Zhou Y (2005). 
+              Fold Recognition by Combining Sequence Profiles Derived From 
+              Evolution and From Depth-Dependent Structural Alignment of 
+              Fragments. Proteins.
+
diff --git a/doc/html/_sources/sidechain/frame.txt b/doc/html/_sources/sidechain/frame.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94a3150d0361fa6fe2b468b35752f0f19d57cebb
--- /dev/null
+++ b/doc/html/_sources/sidechain/frame.txt
@@ -0,0 +1,68 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Frame - The Rigid Part
+================================================================================
+
+.. currentmodule:: promod3.sidechain
+
+In contrast to the rotamers, the frame is a rigid object. It either
+represents the protein backbone or sidechains kept rigid during the 
+sidechain modelling process. Regions, that should not be occupied by
+any sidechain atoms can also be blocked by adding particles to the frame.
+The frame is built using single frame residues, all of them associated to
+a residues index. If a rotamer associated to the same residue index
+enters the frame energy calculation, all interaction with particles 
+belonging to the frame residue with the same residue index are neglected.
+
+
+The Frame Objects
+--------------------------------------------------------------------------------
+
+.. class:: FrameResidue(particles, residue_index)
+
+  :param particles:     particles building frame residue
+  :param residue_index: Interaction energies between the constructed frame
+                        residue and any rotamer associated to the same 
+                        residue index are neglected
+                        
+  :type particles:      :class:`list` of :class:`Particle`
+  :type residue_index:  :class:`int`
+
+  .. method:: __len__()   
+
+    :returns:           Number of particles in :class:`FrameResidue`
+
+
+  .. method:: __getitem__(index)
+
+    :param index:       :class:`Particle` index
+    :type index:        :class:`int`
+
+    :returns:           :class:`Particle` at position **index**
+
+    :raises:   :exc:`~exceptions.RuntimeError` if index is invalid
+
+
+ 
+.. class:: Frame(frame_residues)
+
+  The :class:`Frame` object is used as a container for rigid particles, that
+  can be passed to rotamer groups for calculating frame energies.
+
+  :param frame_residues:  residues building the frame.
+  :type frame_residues:   :class:`list` of :class:`FrameResidue`
+
diff --git a/doc/html/_sources/sidechain/index.txt b/doc/html/_sources/sidechain/index.txt
new file mode 100644
index 0000000000000000000000000000000000000000..192257b499d3826c3ed5891cadb39ede1f7a7291
--- /dev/null
+++ b/doc/html/_sources/sidechain/index.txt
@@ -0,0 +1,54 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+:mod:`~promod3.sidechain` - Sidechain Modelling
+================================================================================
+
+.. module:: promod3.sidechain
+  :synopsis: Sidechain Modelling
+
+.. currentmodule:: promod3.sidechain
+
+Tools and algorithms to model sidechains given backbone coordinates. The full
+module is heavily based on SCWRL4 [krivov2009]_ . 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.
+
+The following code fragment shows an example of a basic sidechain reconstruction
+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. 
+
+
+.. literalinclude:: ../../../tests/doc/scripts/sidechain_steps.py
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   rotamer
+   frame
+   rotamer_constructor
+   rotamer_lib
+   graph
+   disulfid
+   loading
+   subrotamer_optimizer
+
+
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56b95301448e5a955ef38ee0105c9d60b9de291f
--- /dev/null
+++ b/doc/html/_sources/sidechain/rotamer.txt
@@ -0,0 +1,861 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Representing Sidechains - Rotamers & Co. 
+================================================================================
+
+.. currentmodule:: promod3.sidechain
+
+A rotamer represents an amino acid sidechain identified by a :class:`RotamerID` 
+and is a set of :class:`Particle` objects. 
+Two types of rotamers exist. The :class:`RRMRotamer` and :class:`FRMRotamer`. 
+To gather all possible rotamers for one location,
+ProMod3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
+All parts of the structure that are kept rigid can be represented by
+a :class:`Frame` object.
+
+
+RotamerID
+--------------------------------------------------------------------------------
+
+The sidechain module has its own definition of amino acids to satisfy custom 
+requirements for the implemented sidechain construction algorithms. 
+As an example there are histidine in two possible protonation states, 
+that affect the hbond term or different versions of proline/cysteine. 
+
+.. class:: RotamerID
+
+  Enumerates the amino acids. Possible values:
+
+  .. hlist::
+    :columns: 2
+  
+    * ARG - Arginine
+    * ASN - Asparagine
+    * ASP - Aspartate
+    * GLN - Glutamine
+    * GLU - Glutamate
+    * LYS - Lysine
+    * SER - Serine
+    * CYS - Cystein
+    * CYH - "free" Cystein
+    * CYD - disulfid bonded Cystein
+    * MET - Methionine
+    * TRP - Tryptophane
+    * TYR - Tyrosine
+    * THR - Threonine
+    * VAL - Valine
+    * ILE - Isoleucine
+    * LEU - Leucine
+    * PRO - Proline
+    * CPR - cis-Proline
+    * TPR - trans-Proline
+    * HIS - Histidine
+    * HSD - d-protonated Histidine
+    * HSE - e-protonated Histidine
+    * PHE - Phenylalanine
+    * GLY - Glycine
+    * ALA - Alanine
+    * XXX - Invalid
+  
+  The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
+  or as ``promod3.sidechain.RotamerID.ARG``.
+
+  
+How can I get an ID?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The RotamerID enum can directly be accessed from Python. Two convenient
+functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
+or from amino acid three letter codes.
+
+.. method:: TLCToRotID(tlc)
+
+  Directly translates the three letter code into a RotamerID. Following
+  exactly the naming convention defined above.  
+
+  :param tlc:           Three letter code of amino acid
+  :type tlc:            :class:`str`
+
+  :returns:             :class:`RotamerID`, XXX if **tlc** cannot be recoginzed.
+
+
+.. method:: AAToRotID(aa)
+
+  Directly translates **aa** 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 :class:`ost.conop.AminoAcid` 
+
+  :param aa:            AA enum of amino acid
+  :type  aa:            :class:`ost.conop.AminoAcid`
+
+  :returns:             :class:`RotamerID`, XXX if **aa** is invalid.
+
+
+The Smallest Building Block - The Particle
+--------------------------------------------------------------------------------
+
+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
+function.
+
+.. class:: PScoringFunction
+
+  The available scoring functions between :class:`Particle` objects
+
+  * SCWRL4 - :ref:`scwrl4-scoring-function`
+  * SCWRL3 - :ref:`scwrl3-scoring-function`
+  * VINA - :ref:`vina-scoring-function`
+
+.. class:: Particle
+
+  The particle class. There's no constructor. You can either use the
+  :class:`RotamerConstructor` to create full :class:`RotamerGroup` objects
+  with all underlying particles or the energy function specific creation 
+  functions.
+
+  .. method:: PairwiseScore(other_particle)
+
+    Calculates score between the two particles
+
+    :param other_particle:  The interacting particle
+    :type other_particle:  :class:`Particle`
+
+    :returns:           The score
+    :rtype:             :class:`float`
+
+    :raises:  :exc:`~exceptions.RuntimeError` if the scoring function 
+              parametrization of the two particles is inconsistent         
+
+  .. method:: GetName()
+
+    :returns:           The name of the particle, which corresponds to the
+                        atom name
+    :rtype:             :class:`str`
+
+  .. method:: GetCollisionDistance()
+
+    :returns:           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.
+
+    :rtype:             :class:`float`
+
+  .. method:: GetPos()
+
+    :returns:           The position of the particle
+    :rtype:             :class:`ost.geom.Vec3`
+
+  .. method:: GetScoringFunction()
+
+    :returns:           The underlying scoring function
+    :rtype:             :class:`PScoringFunction`
+
+
+
+.. _scwrl4-scoring-function:
+
+The SCWRL4 scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The SCWRL4 scoring function combines a Lennard-Jones style term with 
+a hydrogen bond term. Details can be found in the relevant publication
+[krivov2009]_.
+
+.. class:: SCWRL4ParticleType
+
+  The SCWRL4 energy function differentiates between following particle types
+  that define the behaviour of the Lennard-Jones style term:
+
+  * HParticle   - represents hydrogen
+  * CParticle   - default representation of a carbon
+  * CH1Particle - represents carbon bound to 1 hydrogen
+  * CH2Particle - represents carbon bound to 2 hydrogen
+  * CH3Particle - represents carbon bound to 3 hydrogen
+  * NParticle   - represents nitrogen
+  * OParticle   - default representation of oxygen
+  * OCParticle  - represents carbonyl-oxygen for ASP/GLU
+  * SParticle   - represents sulfur
+
+.. method:: CreateSCWRL4Particle(name, particle_type, pos, [charge, \
+                                 lone_pairs=None, polar_direction=None])
+
+  Creates and returns a :class:`Particle` that can evaluate the SCWRL4 scoring 
+  function
+
+  :param name:          The name of the particle
+  :param particle_type: The type of the particle
+  :param pos:           The position of the particle
+  :param charge:        The charge of the particle, relevant for the hydrogen 
+                        bond term
+  :param lone_pairs:    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.
+  :param polar_direction: 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 
+                          *polar_direction* would be a vector 
+                          estimated as follows: hg_pos-og_pos.
+
+  :type name:           :class:`str`
+  :type particle_type:  :class:`SCWRL4ParticleType`
+  :type pos:            :class:`ost.geom.Vec3`
+  :type charge:         :class:`float`
+  :type lone_pairs:     :class:`ost.geom.Vec3List`
+  :type polar_direction: :class:`ost.geom.Vec3`
+
+
+.. _scwrl3-scoring-function:
+
+The SCWRL3 scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+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 [canutescu2003]_.
+
+.. method:: CreateSCWRL3Particle(name, radius, pos)
+
+  Creates and returns a :class:`Particle` that can evaluate the SCWRL3 scoring
+  function
+
+  :param name:          The name of the particle
+  :param radius:        The hard-sphere radius of the particle, relevant for the
+                        repulsion term.
+  :param pos:           The position of the particle
+
+  :type name:           :class:`str`
+  :type radius:         :class:`float`
+  :type pos:            :class:`ost.geom.Vec3`
+
+
+.. _vina-scoring-function:
+
+The VINA scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The VINA scoring function is a combination of scores that are named 
+gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
+software [trott2010]_. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+and repulsion are evaluated for all pairs of particles. Hydrophobic is only
+evaluated between C_VINAParticle :class:`VINAParticleType` 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.
+
+The VINA scoring function differentiates between the following particle types:
+
+.. class:: VINAParticleType
+
+    * O_D_VINAParticle - Oxygen that can be a hydrogen bond donor 
+    * N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor
+    * O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor
+    * N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor
+    * O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor
+    * N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor
+    * O_VINAParticle - Oxygen
+    * N_VINAParticle - Nitrogen    
+    * S_VINAParticle - Sulfur    
+    * P_VINAParticle - Phosphorus    
+    * C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom  
+    * C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens
+    * F_VINAParticle - Fluorine
+    * Cl_VINAParticle - Chlorine   
+    * Br_VINAParticle - Bromine
+    * I_VINAParticle - Iodine    
+    * M_VINAParticle - Metals    
+    * INVALID_VINAParticle - Invalid particle... 
+
+
+.. method:: CreateVINAParticle(name, particle_type, pos)
+
+  Creates and returns a :class:`Particle` that can evaluate the VINA scoring
+  function
+
+  :param name:          The name of the particle
+  :param radius:        The type of the particle
+  :param pos:           The position of the particle
+
+  :type name:           :class:`str`
+  :type radius:         :class:`VINAParticleType`
+  :type pos:            :class:`ost.geom.Vec3`
+
+
+Rotamers
+--------------------------------------------------------------------------------
+
+
+.. class:: RRMRotamer(particles, probability, internal_e_prefactor)
+
+  The RRMRotamer represents a rotamer of the so called rigid rotamer model.
+ 
+  :param particles:     List of :class:`Particle` objects
+  :param probability:   Probability of rotamers. In case of the SCWRL4
+                        energy calculation, this directly controls the 
+                        internal energy of that rotamer. 
+  :param internal_e_prefactor: Factor applied to the internal energy calculated 
+                               as -log(**probability**/max_probability),
+                               where max_probability is the maximum
+                               rotamer probability of any rotamer in a
+                               particular :class:`RRMRotamerGroup`.
+
+  :type particles:      :class:`list`
+  :type probability:    :class:`float`
+  :type internal_e_prefactor: :class:`float`
+
+
+  .. method:: __getitem__(index)
+
+    Access particle at specified index
+
+    :param index:       Index of particle of interest
+
+    :type index:        :class:`int`
+
+    :returns:           :class:`Particle` at specified index
+
+    :raises:  :exc:`~exceptions.RuntimeError` if index is invalid
+
+
+  .. method:: __len__()
+
+    :returns:           Number of particles the rotamer contains
+
+  .. method:: ApplyOnResidue(res, consider_hydrogens=False, new_res_name="")
+
+    Iterates over every particle and searches for the according atom in
+    **res**. If it's present, the position gets reset to the particle position.
+    If not, a new atom gets added to **res**. No atoms are removed from **res**
+    in this process. 
+
+    :param res:         Residue to be reconstructed
+    :param consider_hydrogens: Flag, whether polar hydrogens should be added to 
+                               **res**
+    :param new_res_name: New name of **res**. Nothing happens in case of the 
+                         default value ("")
+
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type consider_hydrogens: :class:`bool`
+    :type new_res_name: :class:`str`
+
+    :raises: :exc:`~exceptions.RuntimeError` if not all required backbone atoms
+             are present in *res*
+
+  .. method:: ApplyOnResidue(all_atom, res_idx)
+
+    Set all sidechain atom positions for given residue to the positions of the
+    particles in the rotamer.
+    
+    :param all_atom:    Container to which to apply rotamer
+    :param res_idx:     Residue index into *all_atom*
+
+    :type all_atom:     :class:`~promod3.loop.AllAtomPositions`
+    :type res_idx:      :class:`int`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *res_idx* is invalid
+
+  .. method:: ToFrameResidue(res_idx)
+
+    Generates and returns a :class:`FrameResidue` based on the internal
+    particles.
+
+    :param res_idx:     Idx passed over to :class:`FrameResidue` constructor
+    :type res_idx:      :class:`int`
+
+    :returns:           The constructed :class:`FrameResidue` 
+
+  .. method:: GetInternalEnergyPrefactor()
+
+    :returns:           Prefactor used in internal energy calculation
+
+
+  .. method:: GetInternalEnergy()
+
+    :returns:           Internal Energy if calculated, 0.0 otherwise 
+
+
+  .. method:: GetFrameEnergy()
+
+    Returns frame energy. This energy can either be manually set or calculated
+    using a :class:`Frame` and the :class:`RRMRotamerGroup` this rotamer 
+    belongs to.
+
+    :returns: Frame energy if calculated, 0.0 otherwise 
+
+
+  .. method:: GetSelfEnergy()
+
+    :returns:           Self energy consisting of internal plus frame energy
+
+
+  .. method:: GetProbability()
+
+    :returns:           probability of this rotamer
+
+
+  .. method:: SetInternalEnergyPrefactor(prefactor)
+
+    :param energy:      Internal energy prefactor to be set
+
+    :type energy:       :class:`float`
+
+
+  .. method:: SetInternalEnergy(energy)
+
+    :param energy:      Internal energy to be set
+
+    :type energy:       :class:`float`
+
+
+  .. method:: SetFrameEnergy(energy)
+
+    :param energy:      Frame energy to be set
+
+    :type energy:       :class:`float`
+
+
+  .. method:: AddFrameEnergy(energy)
+
+    :param energy:      Frame energy to be added
+
+    :type energy:       :class:`float`
+
+
+  .. method:: SetProbability(probability)
+
+    :param energy:      Internal probability to be set
+
+    :type energy:       :class:`float`
+
+
+
+.. class:: FRMRotamer(particles, T, probability, internal_e_prefactor)
+
+  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.
+
+  :param particles:     List of :class:`Particle` objects
+  :param probability:   Probability of rotamers. In case of the SCWRL4
+                        energy calculation, this directly controls the 
+                        internal energy of that rotamer. 
+  :param T:             Temperature factor, that is used to generate a final
+                        energy given the subrotamers according to the formalism
+                        described in the SCWRL4 paper.
+  :param internal_e_prefactor: Factor applied to the internal energy calculated 
+                               as -log(**probability**/max_probability),
+                               where max_probability is the maximum
+                               rotamer probability of any rotamer in a
+                               particular :class:`FRMRotamerGroup`.
+
+  :type particles:      :class:`list`
+  :type probability:    :class:`float`
+  :type T:              :class:`float`
+  :type internal_e_prefactor: :class:`float`
+
+
+  .. method:: __getitem__(index)
+
+    Access particle at specified index
+
+    :param index:       Index of particle of interest
+
+    :type index:        :class:`int`
+
+    :returns:           :class:`Particle` at specified index
+
+    :raises:  :exc:`~exceptions.RuntimeError` if index is invalid
+
+
+  .. method:: __len__()
+
+    :returns:           Number of particles the rotamer contains
+
+
+  .. method:: GetNumSubrotamers()
+
+    :returns:           Number of subrotamers
+
+  .. method:: ApplyOnResidue(res, consider_hydrogens=False, new_res_name="")
+
+    Iterates over every particle of the active subrotamer and searches for the 
+    according atom in **res**. If it's present, the position gets reset to the 
+    particle position. If not, a new atom gets added to **res**. 
+    No atoms are removed from **res** in this process. 
+
+    :param res:         Residue to be reconstructed
+    :param consider_hydrogens: Flag, whether polar hydrogens should be added to 
+                               the sidechain
+    :param new_res_name: New name of residue. Nothing happens in case of the 
+                         default value ("")
+
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type consider_hydrogens: :class:`bool`
+    :type new_res_name: :class:`str`
+
+    :raises: :exc:`~exceptions.RuntimeError` if not all required backbone atoms
+             are present in *res*
+
+  .. method:: ApplyOnResidue(all_atom, res_idx)
+
+    Set all sidechain atom positions for given residue to the positions of the
+    particles in the active surotamer.
+    
+    :param all_atom:    Container to which to apply rotamer
+    :param res_idx:     Residue index into *all_atom*
+
+    :type all_atom:     :class:`~promod3.loop.AllAtomPositions`
+    :type res_idx:      :class:`int`
+
+    :raises: :exc:`~exceptions.RuntimeError` if *res_idx* is invalid
+
+  .. method:: ToFrameResidue(res_idx)
+
+    Generates and returns a :class:`FrameResidue` based on the internal
+    particles of the active subrotamer.
+
+    :param res_idx:     Idx passed over to :class:`FrameResidue` constructor
+    :type res_idx:      :class:`int`
+
+    :returns:           The constructed :class:`FrameResidue`
+
+  .. method:: ToRRMRotamer()
+
+    Generates and returns a :class:`RRMRotamer` 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),
+    frame_energy (The frame energy of that particular subrotamer if already 
+    calculated), internal_energy (the internal energy of the whole FRMRotamer)
+
+  .. method:: GetSubrotamerDefinition(index)
+
+    :param index:       Index of subrotamer
+
+    :type index:        :class:`int`
+
+    :returns:           :class:`list` of particle indices belonging to this
+                        particular subrotamer
+
+    :raises:  :exc:`~exceptions.RuntimeError` if index is invalid
+
+
+  .. method:: GetInternalEnergyPrefactor()
+
+    :returns:           Prefactor used in internal energy calculation
+
+  .. method:: GetInternalEnergy()
+
+    :returns:           Internal Energy if calculated, 0.0 otherwise 
+
+  .. method:: GetFrameEnergy()
+
+    Returns frame energy. This energy can either be manually set or calculated
+    using a :class:`Frame` and the :class:`FRMRotamerGroup` this rotamer 
+    belongs to.
+
+    :returns: Frame energy if calculated, 0.0 otherwise 
+
+  .. method:: GetFrameEnergy(index)
+
+    Returns frame energy of specified **index**.
+
+    :param index:       Index of subrotamer you want the frame energy from
+
+    :type index:        :class:`int`
+
+    :returns: Frame energy if calculated, 0.0 otherwise 
+
+    :raises:  :exc:`~exceptions.RuntimeError` if index is invalid
+
+
+  .. method:: GetSelfEnergy()
+
+    :returns:           Self energy consisting of internal plus frame energy
+
+
+  .. method:: GetTemperature()
+
+    :returns:           The temperature factor for this rotamer
+
+
+  .. method:: GetProbability()
+
+    :returns:           Probability of this rotamer
+
+
+  .. method:: SetInternalEnergyPrefactor(prefactor)
+
+    :param energy:      Internal energy prefactor to be set
+
+    :type energy:       :class:`float`
+
+
+  .. method:: SetInternalEnergy(energy)
+
+    :param energy:      Internal energy to be set
+
+    :type energy:       :class:`float`
+
+
+  .. method:: SetFrameEnergy(energy)
+
+    :param energy:      Frame energy for full rotamer to be set
+
+    :type energy:       :class:`float`
+
+
+  .. method:: SetFrameEnergy(energy, index)
+
+    :param energy:      Frame energy for single  subrotamer to be set
+    :param index:       Index of subrotamer
+
+    :type energy:       :class:`float`
+    :type index:        :class:
+
+  .. method:: AddFrameEnergy(energy)
+
+    :param energy:      Frame energy for full rotamer to be added
+
+    :type energy:       :class:`float`
+
+
+  .. method:: AddFrameEnergy(energy, index)
+
+    :param energy:      Frame energy for single  subrotamer to be added
+    :param index:       Index of subrotamer
+
+    :type energy:       :class:`float`
+    :type index:        :class:
+
+  .. method:: AddSubrotamerDefinition(indices)
+
+    :param indices:     List of indices defining a subrotamer
+
+    :type indices:      :class:`list`
+
+  .. method:: SetActiveSubrotamer(idx)
+
+    The provided **idx** relates to the subrotamer definitions added at the
+    rotamer buildup. This idx controls which subrotamer is used when
+    :func:`ApplyOnResidue`, :func:`ToFrameResidue` or :func:`ToRRMRotamer` 
+    gets called. By default, the value is 0 => first added subrotamer 
+    definition gets used.
+
+    :param idx:         Index of subrotamer definition applied on residues
+
+    :type idx:          :class:`int`
+
+  .. method:: GetActiveSubrotamer()
+
+    Get the index of the active subrotamer
+
+  .. method:: SetTemperature(temperature)
+
+    :param temperature: Temperature factor for this rotamer
+
+    :type temperature:  :class:`float`
+
+  .. method:: SetProbability(probability)
+
+    :param energy:      Internal probability to be set
+
+    :type energy:       :class:`float`
+
+
+
+Rotamer Groups
+--------------------------------------------------------------------------------
+
+
+.. class:: RRMRotamerGroup(rotamers, residue_index)
+
+  The RRMRotamerGroup groups several :class:`RRMRotamer` objects for the same
+  residue position. 
+
+  :param rotamers: A list of :class:`RRMRotamer` objects
+  :param residue_index: Location of residue this :class:`FRMRotamerGroup`
+                        represents. This index is important when calculating
+                        frame energies to neglect the interactions to frame 
+                        particles of the same residue.
+
+  :type rotamers:       :class:`list`
+  :type residue_index:  :class:`int`
+
+  :raises:  :exc:`~exceptions.RuntimeError` if provided *rotamers* is empty
+
+
+  .. method:: __len__()
+
+    :returns:           Number of rotamers in group
+
+
+  .. method:: __getitem__(index)
+
+    :returns:           :class:`RRMRotamer` at given *index*
+
+    :raises:  :exc:`~exceptions.RuntimeError` if *index* is invalid
+
+
+  .. method:: ApplyOnResidue(index, res, consider_hydrogens=False,\
+                             new_res_name="")
+              ApplyOnResidue(index, all_atom, res_idx)
+
+    Calls ApplyOnResidue function on rotamer at position *index*
+
+    :param index:       Rotamer index
+    :param res:         Residue to be reconstructed
+    :param consider_hydrogens: Flag, whether polar hydrogens should be added to 
+                               the sidechain
+    :param new_res_name: New name of residue. Nothing happens in case of the 
+                         default value ("")
+    :param all_atom:    Container to which to apply rotamer
+    :param res_idx:     Residue index into *all_atom*
+
+    :type index:        :class:`int`
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type consider_hydrogens: :class:`bool`
+    :type new_res_name: :class:`str`
+    :type all_atom:     :class:`~promod3.loop.AllAtomPositions`
+    :type res_idx:      :class:`int`
+
+    :raises: :exc:`~exceptions.RuntimeError` if not all required backbone atoms
+             are present in *res* or when *index* or *res_idx* are invalid
+
+
+  .. method:: Merge(other)
+
+    Adds all rotamers in *other* to current :class:`RRMRotamerGroup`
+
+    :param other:       RotamerGroup to be merged in
+
+    :type other:        :class:`RRMRotamerGroup`
+
+  .. method:: SetFrameEnergy(frame)
+
+    Calculates sets the energy of all rotamers in the group towards the 
+    given **frame**.
+
+    :param frame:       Frame containing rigid particles
+    :type frame:        :class:`Frame`
+
+  .. method:: AddFrameEnergy(frame)
+
+    Calculates adds the energy of all rotamers in the group towards the 
+    given **frame**.
+
+    :param frame:       Frame containing rigid particles
+    :type frame:        :class:`Frame`
+
+  .. method:: ApplySelfEnergyThresh(thresh=30)
+
+    Searches rotamer with lowest self energy *l_e* and deletes all
+    rotamers with *self_energy* > *l_e* + *thresh*
+
+
+.. class:: FRMRotamerGroup(rotamers, residue_index)
+
+  The FRMRotamerGroup groups several :class:`FRMRotamer` objects for the same
+  residue position. 
+
+  :param rotamers: A list of :class:`FRMRotamer` objects
+  :param residue_index: Location of residue this :class:`FRMRotamerGroup`
+                        represents. This index is important when calculating
+                        frame energies to neglect the interactions to frame 
+                        particles of the same residue.
+
+  :type rotamers:       :class:`list`
+  :type residue_index:  :class:`int`
+
+  :raises:  :exc:`~exceptions.RuntimeError` if provided *rotamers* is empty
+
+
+  .. method:: __len__()
+
+    :returns:           Number of rotamers in group
+
+
+  .. method:: __getitem__(index)
+
+    :returns:           :class:`FRMRotamer` at given *index*
+
+    :raises:  :exc:`~exceptions.RuntimeError` if *index* is invalid
+
+
+  .. method:: ApplyOnResidue(index, res, consider_hydrogens=False,\
+                             new_res_name="")
+              ApplyOnResidue(index, all_atom, res_idx)
+
+    Calls ApplyOnResidue function on rotamer at position *index*
+
+    :param index:       Rotamer index
+    :param res:         Residue to be reconstructed
+    :param consider_hydrogens: Flag, whether polar hydrogens should be added to 
+                               the sidechain
+    :param new_res_name: New name of residue. Nothing happens in case of the 
+                         default value ("")
+    :param all_atom:    Container to which to apply rotamer
+    :param res_idx:     Residue index into *all_atom*
+
+    :type index:        :class:`int`
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type consider_hydrogens: :class:`bool`
+    :type new_res_name: :class:`str`
+    :type all_atom:     :class:`~promod3.loop.AllAtomPositions`
+    :type res_idx:      :class:`int`
+
+    :raises: :exc:`~exceptions.RuntimeError` if not all required backbone atoms
+             are present in *res* or when *index* or *res_idx* are invalid
+
+
+  .. method:: Merge(other)
+
+    Adds all rotamers in *other* to current :class:`FRMRotamerGroup`
+
+    :param other:       RotamerGroup to be merged in
+
+    :type other:        :class:`FRMRotamerGroup`
+
+  .. method:: SetFrameEnergy(frame)
+
+    Calculates sets the energy of all rotamers in the group towards the 
+    given **frame**.
+
+    :param frame:       Frame containing rigid particles
+    :type frame:        :class:`Frame`
+
+  .. method:: AddFrameEnergy(frame)
+
+    Calculates adds the energy of all rotamers in the group towards the 
+    given **frame**.
+
+    :param frame:       Frame containing rigid particles
+    :type frame:        :class:`Frame`
+
+  .. method:: ApplySelfEnergyThresh(thresh=30)
+
+    Searches rotamer with lowest self energy *l_e* and deletes all
+    rotamers with *self_energy* > *l_e* + *thresh*
+
diff --git a/doc/html/_sources/sidechain/rotamer_constructor.txt b/doc/html/_sources/sidechain/rotamer_constructor.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8cca8deb12f3b56c889c32e9c9bcc954d38599f
--- /dev/null
+++ b/doc/html/_sources/sidechain/rotamer_constructor.txt
@@ -0,0 +1,489 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Rotamer Constructor
+================================================================================
+
+.. currentmodule:: promod3.sidechain
+
+Instead of creating rotamers or frame residues by yourself, you can use the 
+convenient functionality provided by ProMod3.
+
+
+The RotamerConstructor Baseclass
+--------------------------------------------------------------------------------
+
+
+.. class:: RotamerConstructor
+
+  Abstract base class that cannot be initialized from Python. It builds 
+  an interface implemented by scoring function specific constructors 
+  (e.g. :class:`SCWRL4RotamerConstructor`). 
+
+  .. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
+                                       [phi = -1.0472, psi = -0.7854, \
+                                        n_ter = False, c_ter = False, \
+                                        probability_cutoff = 0.98])
+  .. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
+                                       residue_index, rot_lib,\
+                                       [phi = -1.0472, psi = -0.7854, \
+                                        n_ter = False, c_ter = False, \
+                                        probability_cutoff = 0.98])
+  .. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib_entries,\
+                                       [phi = -1.0472, psi = -0.7854, \
+                                        n_ter = False, c_ter = False, \
+                                        probability_cutoff = 0.98])
+  .. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
+                                       residue_index, rot_lib_entries,\
+                                       [phi = -1.0472, psi = -0.7854, \
+                                        n_ter = False, c_ter = False, \
+                                        probability_cutoff = 0.98])
+
+    All functions are also avaible for their flexible rotamer model counterpart.
+    =>ConstructFRMRotamerGroup(...) with the same parameters. 
+
+    :param res:         To extract the required backbone atoms
+    :param all_atom_pos: To extract the required backbone atoms
+    :param aa_res_idx:  Index of residue in **all_atom_pos** from which to
+                        extract the required backbone atoms
+    :param id:          Identifies the sidechain.
+    :param residue_index: Important for the energy calculations towards the 
+                          :class:`Frame` you don't want to calculate a pairwise
+                          energy of the sidechain particles towards particles
+                          representing the own backbone...
+    :param rot_lib:     To search for rotamers
+    :param rot_lib_entries: :class:`RotamerLibEntry` objects to circumvent the 
+                            direct use of a rotamer library
+    :param phi:         Phi dihedral angle 
+    :param psi:         Psi dihedral angle 
+    :param n_ter:       Whether the residue is n-terminal
+    :param c_ter:       Whether the residue is c-terminal
+    :param probability_cutoff: 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 **probability_cutoff**.
+
+    :returns:           The rotamer group containing all constructed rotamers 
+                        with internal energies assigned. 
+
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
+    :type aa_res_idx:   :class:`int`
+    :type id:           :class:`RotamerID`
+    :type residue_index: :class:`int`
+    :type rot_lib:      :class:`RotamerLib` / :class:`BBDepRotamerLib`
+    :type rot_lib_entries: :class:`list`
+    :type phi:          :class:`float`
+    :type psi:          :class:`float`
+    :type n_ter:        :class:`bool`
+    :type c_ter:        :class:`bool`
+    :type probability_cutoff: :class:`float`
+    :rtype:             :class:`RRMRotamerGroup`
+
+    :raises:  :exc:`~exceptions.RuntimeError` when not all required backbone
+              atoms are present in **residue** or not all required atom
+              positions are set in **all_atom_pos**
+
+
+  .. method:: ConstructBackboneFrameResidue(res, id, residue_index, \
+                                            [phi = -1.0472, psi = -0.7854, \
+                                             n_ter = False, c_ter = False])
+
+  .. method:: ConstructBackboneFrameResidue(all_atom_pos, aa_res_idx, id,\
+                                            residue_index, \
+                                            [phi = -1.0472, psi = -0.7854\
+                                             n_ter = False, c_ter = False])
+
+    Constructs frame residues only containing backbone atoms (the ones that 
+    don't show up in a rotamer).
+
+    :param res:         Residue from which to extract the backbone positions
+    :param all_atom_pos: To extract the backbone positions
+    :param aa_res_idx:  Index of residue in **all_atom_pos** from which to 
+                        extract the backbone positions
+    :param id:          Identifies the sidechain
+    :param residue_index: Important for the energy calculations towards the 
+                          :class:`Frame` you don't want to calculate a pairwise
+                          energy of the sidechain particles towards particles
+                          representing the own backbone...
+    :param phi:         The dihedral angle of the current residue
+    :param psi:         The dihedral angle of the current residue
+    :param n_ter:       Whether the residue is n-terminal
+    :param c_ter:       Whether the residue is c-terminal
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
+    :type aa_res_idx:   :class:`int`
+    :type id:           :class:`RotamerID`
+    :type residue_index: :class:`int`
+    :type phi:          :class:`float`
+    :type psi:          :class:`float`
+    :type n_ter:        :class:`bool`
+    :type c_ter:        :class:`bool`
+
+    :rtype:             :class:`FrameResidue`
+
+
+    :raises:  :exc:`~exceptions.RuntimeError` when not all required backbone
+              atoms are present in **residue** or not all required atom
+              positions are set in **all_atom_pos**.
+
+
+  .. method:: ConstructSidechainFrameResidue(res, id, residue_index, \
+                                             [phi = -1.0472, psi = -0.7854, \
+                                              n_ter = False, c_ter = False])
+
+  .. method:: ConstructSidechainFrameResidue(all_atom_pos, aa_res_idx, id,\
+                                             residue_index, \
+                                             [phi = -1.0472, psi = -0.7854\
+                                             n_ter = False, c_ter = False])
+
+    Constructs frame residues only containing sidechain atoms (the ones that
+    you observe in a rotamer).
+
+    :param res:         Residue from which to extract the backbone positions
+    :param all_atom_pos: To extract the backbone positions
+    :param aa_res_idx:  Index of residue in **all_atom_pos** from which to 
+                        extract the backbone positions
+    :param id:          Identifies the sidechain
+    :param residue_index: Important for the energy calculations towards the 
+                          :class:`Frame` you don't want to calculate a pairwise
+                          energy of the sidechain particles towards particles
+                          representing the own backbone...
+    :param phi:         The dihedral angle of the current residue
+    :param psi:         The dihedral angle of the current residue
+    :param n_ter:       Whether the residue is n-terminal
+    :param c_ter:       Whether the residue is c-terminal
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
+    :type aa_res_idx:   :class:`int`
+    :type id:           :class:`RotamerID`
+    :type residue_index: :class:`int`
+    :type phi:          :class:`float`
+    :type psi:          :class:`float`
+    :type n_ter:        :class:`bool`
+    :type c_ter:        :class:`bool`
+
+    :rtype:             :class:`FrameResidue`
+
+
+    :raises:  :exc:`~exceptions.RuntimeError` when not all required sidechain
+              atoms are present in **residue** or not all required sidechain 
+              atom positions are set in **all_atom_pos**.
+
+  .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+                                     [phi = -1.0472, psi = -0.7854, \
+                                      n_ter = False, c_ter = False])
+
+    Assigns an internal energy to every rotamer in *rot_group*, 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
+    to the energy function specific constructors to override that behaviour.
+
+    :param rot_group:   containing all rotamers for which internal energies have
+                        to be assigned
+    :param id:          Identifies the sidechain
+    :param residue_index: The index of the residue which is represented by 
+                          *rot_group*    
+    :param phi:         The dihedral angle of the current residue
+    :param psi:         The dihedral angle of the current residue
+    :param n_ter:       Whether the residue is n-terminal
+    :param c_ter:       Whether the residue is c-terminal
+
+    :type rot_group:    :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+    :type id:           :class:`RotamerID`
+    :type residue_index: :class:`int`
+    :type phi:          :class:`float`
+    :type psi:          :class:`float`
+    :type n_ter:        :class:`bool`
+    :type c_ter:        :class:`bool`
+
+
+
+Scoring Function Specific RotamerConstructors 
+--------------------------------------------------------------------------------
+
+
+.. class:: SCWRL4RotamerConstructor(cb_in_sidechain)
+
+  This object implements the full interface defined in 
+  :class:`RotamerConstructor` and constructs rotamers and frame residues that 
+  are parametrized according to the SCWRL4 method. They contain all heavy atoms, 
+  but also the polar hydrogens. 
+
+  :param cb_in_sidechain: 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 
+                          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.
+
+  :type cb_in_sidechain: :class:`bool`
+
+  .. method:: ConstructFrameResidue(residue, residue_index)
+  
+    Constructs a :class:`FrameResidue` from a :class:`ost.mol.ResidueHandle`.
+    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 
+    atoms of the residue will be represented as carbons and hydrogens are 
+    skipped.
+
+    :param residue:       Residue from which all atoms will be taken to
+                        construct a :class:`FrameResidue`.
+    :param residue_index: Index this :class:`FrameResidue` belongs to.
+
+    :type residue:        :class:`ost.mol.ResidueHandle`
+    :type residue_index:  :class:`int`
+
+    :returns:             :class:`FrameResidue`
+
+  .. method:: ConstructFrameResidueHeuristic(residue, residue_index, comp_lib)
+
+    Constructs a :class:`FrameResidue` from a :class:`ost.mol.ResidueHandle` using
+    a heuristic treatment of the atoms based on the passed compounds library.
+    This is meant to be used as an alternative to :func:`ConstructFrameResidue`,
+    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:
+  
+    - carbons, nitrogens, oxygens and sulfur particles use an appropriate type
+      as in the :class:`SidechainParticle` enumeration
+    - carbonyls are added as charged oxygen particles as hbond acceptors
+  
+    :param residue:       Residue from which all atoms will be taken to
+                          construct a :class:`FrameResidue`.
+    :param residue_index: Index this :class:`FrameResidue` belongs to.
+    :param comp_lib:      OST compound library to use 
+  
+    :type residue:        :class:`ost.mol.ResidueHandle`
+    :type residue_index:  :class:`int`
+    :type comp_lib:       :class:`ost.conop.CompoundLib`
+  
+    :returns:             :class:`FrameResidue`
+
+  .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+                                     [phi = -1.0472, psi = -0.7854, \
+                                      n_ter = False, c_ter = False])
+
+    Overrides the method defined in :class:`RotamerConstructor`.
+    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
+    rotamer specific and max_p is the maximum probablity of any of the rotamers
+    in **rot_group**. If you construct a rotamer group by the
+    ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function 
+    is already called at construction and the energies are properly assigned.
+
+    :param rot_group:   containing all rotamers for which internal energies have
+                        to be assigned
+    :param id:          Identifies the sidechain
+    :param residue_index: The index of the residue which is represented by 
+                          *rot_group*    
+    :param phi:         The dihedral angle of the current residue
+    :param psi:         The dihedral angle of the current residue
+    :param n_ter:       Whether the residue is n-terminal
+    :param c_ter:       Whether the residue is c-terminal
+
+    :type rot_group:    :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+    :type id:           :class:`RotamerID`
+    :type residue_index: :class:`int`
+    :type phi:          :class:`float`
+    :type psi:          :class:`float`
+    :type n_ter:        :class:`bool`
+    :type c_ter:        :class:`bool`
+
+
+
+
+.. class:: SCWRL3RotamerConstructor(cb_in_sidechain)
+
+  This object implements the full interface defined in 
+  :class:`RotamerConstructor` and constructs rotamers and frame residues that 
+  are parametrized according to the SCWRL3 method. They contain only heavy atoms. 
+
+  :param cb_in_sidechain: 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 
+                          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.
+
+  :type cb_in_sidechain: :class:`bool`
+
+
+  .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+                                     [phi = -1.0472, psi = -0.7854, \
+                                      n_ter = False, c_ter = False])
+
+    Overrides the method defined in :class:`RotamerConstructor`.
+    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
+    rotamer specific and max_p is the maximum probablity of any of the rotamers
+    in **rot_group**. If you construct a rotamer group by the
+    ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function 
+    is already called at construction and the energies are properly assigned.
+
+    :param rot_group:   containing all rotamers for which internal energies have
+                        to be assigned
+    :param id:          Identifies the sidechain
+    :param residue_index: The index of the residue which is represented by 
+                          *rot_group*    
+    :param phi:         The dihedral angle of the current residue
+    :param psi:         The dihedral angle of the current residue
+    :param n_ter:       Whether the residue is n-terminal
+    :param c_ter:       Whether the residue is c-terminal
+
+    :type rot_group:    :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+    :type id:           :class:`RotamerID`
+    :type residue_index: :class:`int`
+    :type phi:          :class:`float`
+    :type psi:          :class:`float`
+    :type n_ter:        :class:`bool`
+    :type c_ter:        :class:`bool`
+
+
+.. class:: VINARotamerConstructor(cb_in_sidechain)
+
+  This object implements the full interface defined in 
+  :class:`RotamerConstructor` and constructs rotamers and frame residues that 
+  are parametrized according to the VINA method. They contain only heavy atoms. 
+
+  :param cb_in_sidechain: 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 
+                          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.
+
+  :type cb_in_sidechain: :class:`bool`
+
+
+  .. method:: AssignInternalEnergies(rot_group, id, residue_index, \
+                                     [phi = -1.0472, psi = -0.7854, \
+                                      n_ter = False, c_ter = False])
+
+    Overrides the method defined in :class:`RotamerConstructor`.
+    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
+    rotamer specific and max_p is the maximum probablity of any of the rotamers
+    in **rot_group**. If you construct a rotamer group by the
+    ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function 
+    is already called at construction and the energies are properly assigned.
+
+    :param rot_group:   containing all rotamers for which internal energies have
+                        to be assigned
+    :param id:          Identifies the sidechain
+    :param residue_index: The index of the residue which is represented by 
+                          *rot_group*    
+    :param phi:         The dihedral angle of the current residue
+    :param psi:         The dihedral angle of the current residue
+    :param n_ter:       Whether the residue is n-terminal
+    :param c_ter:       Whether the residue is c-terminal
+
+    :type rot_group:    :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+    :type id:           :class:`RotamerID`
+    :type residue_index: :class:`int`
+    :type phi:          :class:`float`
+    :type psi:          :class:`float`
+    :type n_ter:        :class:`bool`
+    :type c_ter:        :class:`bool`
+
+
+  .. method:: ConstructFrameResidueHeuristic(res, res_idx)
+
+    Constructs a :class:`FrameResidue` from a :class:`ost.mol.ResidueHandle` 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
+    atom type for oxygens and nitrogens (hydrogen bond donor/acceptor). 
+    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.
+
+    * Carbon is assigned C_VINAParticle :class:`VINAParticleType` if its only 
+      bound to other carbons or hydrogens (and deuterium). All other carbons are
+      assigned C_P_VINAParticle :class:`VINAParticleType`.
+    * 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 :class:`VINAParticleType`. 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 :class:`ost.mol.AtomHandle` 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 :class:`VINAParticleType`.
+    * 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 :class:`VINAParticleType`. 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).
+    * Atoms of elements ["MG", "MN", "ZN", "CA", "FE"] are assigned 
+      M_VINAParticle :class:`VINAParticleType`.
+    * Atoms of elements ["S", "P", "F", "CL", "BR", "I"] are assigned their
+      corresponding :class:`VINAParticleType`.
+    * All other atoms are neglected and not added to the returned
+      :class:`FrameResidue`.
+
+    :param res:         Residue from which to create the 
+                        :class:`FrameResidue`
+    :param res_idx:     Index that is set in :class:`FrameResidue`
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :type res_idx:      :class:`int`
+    :rtype:             :class:`FrameResidue`
+
+
+  .. method:: ConstructRRMRotamerHeuristic(res)
+
+    Construct a :class:`RRMRotamer` with the atom typing heuristic
+    as in the :meth:`ConstructFrameResidueHeuristic` method.
+
+    :param res:         Residue from which to create the 
+                        :class:`RRMRotamer`
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :rtype:             :class:`RRMRotamer`
+
+
+  .. method:: ConstructFRMRotamerHeuristic(res)
+
+    Construct a :class:`FRMRotamer` with the atom typing heuristic
+    as in the :meth:`ConstructFrameResidueHeuristic` method. The
+    constructed :class:`FRMRotamer` only contains one subrotamer that
+    contains the atoms from *residue*.
+
+    :param res:         Residue from which to create the 
+                        :class:`FRMRotamer`
+    :type res:          :class:`ost.mol.ResidueHandle`
+    :rtype:             :class:`FRMRotamer`
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 2da8c84623da727c5cf42bc68c15037238ab0652..69750957944772b6b4066158ccdeef61dd11cc4f 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>ProMod3 Actions &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>ProMod3 Actions &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="Building ProMod3" href="../buildsystem.html" />
     <link rel="prev" title="Getting Started" href="../gettingstarted.html" />
    
@@ -103,10 +127,17 @@ Example:</p>
 </div>
 </li>
 </ul>
+<<<<<<< HEAD
 <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/1.11/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.10.0)"><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
+>>>>>>> develop
 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
@@ -131,7 +162,11 @@ 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.
+<<<<<<< HEAD
 Consider to use <a class="reference external" href="https://www.openstructure.org/docs/1.11/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+=======
+Consider to use <a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+>>>>>>> develop
 file in a3m format at hand.</p>
 <ul class="simple">
 <li>The profiles are mapped based on exact matches towards the gapless
@@ -183,12 +218,21 @@ won’t be modelled.</p>
 </div>
 <p>This reads a structure stored in in.pdb, strips all sidechains,
 detects and models disulfid bonds and reconstructs all sidechains with the
+<<<<<<< HEAD
 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/1.11/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.11.0)"><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>
+=======
+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/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.10.0)"><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>
+>>>>>>> develop
 <p>Several flags control the modelling behaviour:</p>
 <dl class="option">
 <dt id="cmdoption-k">
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 0d37c30c4506339ee5b581dd0adbfaea656dd2e9..51aa0136c2567818f132cdcc57ee1ca48874285a 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>test_actions - Testing Actions &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -17,6 +18,30 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="ProMod3’s Share Of CMake" href="../cmake/index.html" />
+=======
+    
+    <title>test_actions - Testing Actions &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 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" />
+>>>>>>> develop
     <link rel="prev" title="Contributing" href="../contributing.html" />
    
   <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -186,8 +211,13 @@ 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>
+<<<<<<< HEAD
 <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/1.11/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.11.0)"><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/3.6/library/unittest.html#unittest.TestCase" title="(in Python v3.6)"><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
+=======
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>&#8216;s <a class="reference external" href="https://www.openstructure.org/docs/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python&#8216;s
+<a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><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
+>>>>>>> develop
 as a script:</p>
 <div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
 14
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 42555151700097854accc758406e8aee40a650ce..0739d7010be02caaad2e2a469f3f5bd2ea861a3b 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Building ProMod3 &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Building ProMod3 &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+    <link rel="up" title="Documentation For Users" href="users.html" />
+>>>>>>> develop
     <link rel="next" title="ProMod3 and Containers" href="container/index.html" />
     <link rel="prev" title="ProMod3 Actions" href="actions/index.html" />
    
@@ -39,6 +63,7 @@
 <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
+<<<<<<< HEAD
 1.10.0. 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>
@@ -46,15 +71,30 @@ we need at least version 3.3.0. To build the documentation, <a class="reference
 required. We do not provide backwards compatibility to Python 2.7. The last
 release supporting Python 2.7 is 2.1.0 which also requires OST to be
 compiled with Python 2.7.</p>
+=======
+1.11.0. A C++11 compatible compiler is required. OST must be
+configured and compiled with <code class="docutils literal"><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 required.</p>
+>>>>>>> develop
 <p>The currently preferred versions are:</p>
 <ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.10.0</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.11.0</li>
 <li><a class="reference external" href="http://openmm.org">OpenMM</a> 7.1.1</li>
+<<<<<<< HEAD
 <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><a class="reference external" href="https://cmake.org/">CMake</a> 2.8.12</li>
+<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7.11</li>
+<li><a class="reference external" href="https://www.boost.org/">Boost</a> 1.53.0</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> 1.4.1</li>
+>>>>>>> develop
 </ul>
 </div>
 <div class="section" id="using-cmake">
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 2f64e794bc088dd4a9541ad050d3d605eaee8488..0e61d869b775f14c9d2cfc20e0fe7d9b41298f4c 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Changelog &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,28 @@
     <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" />
+=======
+    
+    <title>Changelog &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
     <link rel="prev" title="References" href="references.html" />
    
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -35,9 +58,17 @@
             
   <div class="section" id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<<<<<<< HEAD
 <div class="section" id="release-2-x-x">
 <h2>Release 2.x.x<a class="headerlink" href="#release-2-x-x" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
+=======
+<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>
+>>>>>>> develop
 <li>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>
@@ -152,6 +183,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
+<<<<<<< HEAD
 <h1 class="logo"><a href="index.html">ProMod3</a></h1>
 
 
@@ -164,6 +196,17 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
 <h3>Navigation</h3>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
+=======
+  <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-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>
+>>>>>>> develop
 </ul>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index fb3b599f00514679810c82b81c71b30ca3836338..44d7189adf15d8d5a7c9f0a2380a1de38c5b3d35 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>ProMod3’s Share Of CMake &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>ProMod3‘s Share Of CMake &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Developers" href="../developers.html" />
+>>>>>>> develop
     <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" />
    
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index 0a511e9fc9201580616ce428afc91ecf8599f1bf..a5688a90c466932c40bab5c5e58ef24b49614056 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Docker &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Docker &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="ProMod3 and Containers" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Singularity" href="singularity.html" />
     <link rel="prev" title="ProMod3 and Containers" href="index.html" />
    
@@ -68,7 +92,11 @@ provide the (relative) path to the script and (relative) path to the file eg:</p
 </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>
+<<<<<<< HEAD
 <p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
+>>>>>>> develop
 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
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index b4cfa56d8d01a8bd7850444eba27cfdb98fdaa32..62d6a65b04a57ea72ba591e7b4d4fefad755fec3 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>ProMod3 and Containers &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>ProMod3 and Containers &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="Docker" href="docker.html" />
     <link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
    
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index 3ab0c93c9a297888403159878ec349ae8d362c8b..20141888ef215867c430c62db3a8cdac3b49ebed 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Singularity &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Singularity &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="ProMod3 and Containers" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
     <link rel="prev" title="Docker" href="docker.html" />
    
@@ -38,8 +62,29 @@
 <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
 Docker image.</p>
+<<<<<<< HEAD
 <p>Build the image with:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo singularity build promod.img Singularity
+=======
+<div class="section" id="build-singularity-image">
+<h2>Build Singularity Image<a class="headerlink" href="#build-singularity-image" title="Permalink to this headline">¶</a></h2>
+<p>If you built the Docker image locally you can use it as a starting point. For
+this we have to fire up a local Docker registry and pull from there. Let&#8217;s
+assume you built the Docker image with tag promod.</p>
+<p>Fire the local Registry and push the promod image to it:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>sudo docker run -d -p 5000:5000 --restart<span class="o">=</span>always --name registry registry:2
+sudo docker tag promod localhost:5000/promod
+sudo docker push localhost:5000/promod
+</pre></div>
+</div>
+<p>If port 5000 is already taken on your machine, use a different <code class="docutils literal"><span class="pre">&lt;PORT&gt;</span></code> by
+using the flag <code class="docutils literal"><span class="pre">-p</span> <span class="pre">&lt;PORT&gt;:5000</span></code> and <code class="docutils literal"><span class="pre">localhost:&lt;PORT&gt;</span></code> in these commands.
+Make sure, that on top of your Singularity recipe you have something like:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>BootStrap: docker
+Registry: http://localhost:5000
+Namespace:
+From: promod:latest
+>>>>>>> develop
 </pre></div>
 </div>
 <div class="section" id="available-apps">
@@ -65,8 +110,29 @@ Docker image.</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity <span class="nb">help</span> --app PM promod.img
 </pre></div>
 </div>
+<<<<<<< HEAD
 <p>To list all available ProMod3 modelling actions:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>singularity run --app PM promod.img <span class="nb">help</span>
+=======
+<p>The jupyter notebook is setup as an app in the container.
+To get help on how to run it:</p>
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity <span class="nb">help</span> --app Notebook &lt;IMAGE&gt;
+</pre></div>
+</div>
+<p>Within the notebook you can test OST, ProMod3 and nglview as follows:</p>
+<div class="highlight-python"><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">&quot;HELLYEAH&quot;</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">&quot;test.pdb&quot;</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">&quot;test.pdb&quot;</span><span class="p">)</span>
+<span class="n">view</span>
+>>>>>>> develop
 </pre></div>
 </div>
 </div>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 48f904cc2e1026c0ce6944ea4220bc328923343c..4872a17bbcae0638556788550d43e260d18d86a5 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Contributing &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Contributing &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+    <link rel="up" title="Documentation For Developers" href="developers.html" />
+>>>>>>> develop
     <link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
     <link rel="prev" title="ProMod3 Setup" href="dev_setup.html" />
    
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index ff5e72d54ec806dffbd7420b748b799b29449d87..9be32bac6e0da09a49268fbcead10a6892bee54a 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Geometry functions &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Geometry functions &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
     <link rel="prev" title="helper - Shared Functionality For the Everything" href="helper.html" />
    
@@ -46,16 +70,26 @@
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
+=======
+<li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Gromacs rule</li>
+<li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Desired number of positions (max. 3)</li>
+<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Anchor positions (max. 4)</li>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+=======
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -71,16 +105,26 @@
 <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">
+<<<<<<< HEAD
 <li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C-alpha atom</li>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+=======
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -97,19 +141,32 @@ dihedral (A-B-C-D).</p>
 <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">
+<<<<<<< HEAD
 <li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</li>
+=======
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom C</li>
+<li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Bond length (C-D)</li>
+<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Angle (B-C-D)</li>
+<li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Dihedral (A-B-C-D)</li>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+=======
+<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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -126,16 +183,26 @@ C-alpha and C atoms.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C atom</li>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+=======
+<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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -152,16 +219,26 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
+=======
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Anchor for rotation</li>
+<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Angle (in radians in range [-pi,pi]) of rotation</li>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
+=======
+<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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -178,15 +255,24 @@ going through the origin.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
+=======
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Axis of rotation</li>
+<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Angle (in radians in range [-pi,pi]) of rotation</li>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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/1.11/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
+=======
+<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/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -203,7 +289,11 @@ going through the origin.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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.</td>
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue handle from which to extract N, CA and C coordinates.</td>
+>>>>>>> develop
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><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.</td>
@@ -222,7 +312,11 @@ atoms.</td>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
+=======
+<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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index 3f2d86e49e37e20a43a2df3fda8b05e0649394b5..5564a1be439e2f42ffb8e39c473efb585e297376 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Graph Minimizer &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Graph Minimizer &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
     <link rel="prev" title="Runtime profiling" href="runtime_profiling.html" />
    
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index ed40cb82d8d307f15cbc1a0889d281d6237cdb4e..3be5e7d4f1fee2e3c1ddd8dca38cbec871725e21 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>helper - Shared Functionality For the Everything &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>helper - Shared Functionality For the Everything &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Geometry functions" href="geometry.html" />
     <link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
    
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 176d071d442fda06151b0ebad6a6ee646df693f4..da3a666ab5ea2660b68c4eaf4d887950d0e8512c 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>core - ProMod3 Core Functionality &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>core - ProMod3 Core Functionality &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
     <link rel="prev" title="Loading Precomputed Objects" href="../loop/load_loop_objects.html" />
    
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 0fadf47e9295ca9d6570a2e456747415632344c8..fdb4147a99598db35a6134cf2166aaa10684d192 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>pm3argparse - Parsing Command Lines &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>pm3argparse - Parsing Command Lines &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
     <link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
    
@@ -244,7 +268,11 @@ input is post processed and checked in <a class="reference internal" href="#prom
 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 
+<<<<<<< HEAD
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.11.0)"><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 
+=======
+<a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file 
+>>>>>>> develop
 in a3m format at hand.</li>
 </ul>
 <p>Notes:</p>
@@ -258,7 +286,11 @@ target sequences</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 notranslate"><span class="pre">Parse()</span></code></a>:</p>
 <ul class="simple">
+<<<<<<< HEAD
 <li><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><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/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>, 
+=======
+<li><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code> - <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>, 
+>>>>>>> develop
 ordered to match the target sequences.</li>
 </ul>
 <p>Exit codes related to profile input:</p>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index c1b170393233eed4e80dc7b225a8c18ee7d931b6..12845f5ae91e3ab3dc92625e0ae0927e86fadec9 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Runtime profiling &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Runtime profiling &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
     <link rel="prev" title="Geometry functions" href="geometry.html" />
    
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 426b1bda50288aa485fac2bb5612da8d75d442ef..07370ed8f78b7c23dbde899f1485b79953a408c7 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>SetCompoundsChemlib() &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>SetCompoundsChemlib() &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="Contributing" href="../user_contributions.html" />
     <link rel="prev" title="Graph Minimizer" href="graph_minimizer.html" />
    
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 84fdbc76a5b26241efa946fef9e290ba85909c4b..f3e5901a825af869736d45d50eaf0e1fc1ae087c 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>ProMod3 Setup &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>ProMod3 Setup &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+    <link rel="up" title="Documentation For Developers" href="developers.html" />
+>>>>>>> develop
     <link rel="next" title="Contributing" href="contributing.html" />
     <link rel="prev" title="Documentation For Developers" href="developers.html" />
    
diff --git a/doc/html/developers.html b/doc/html/developers.html
index ce1a805a00216d513751b432bb6438fd0c45a932..00a80535f4b3c8a18a1e36c4c9a3560e1fdc9d49 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Documentation For Developers &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,28 @@
     <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" />
+=======
+    
+    <title>Documentation For Developers &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
     <link rel="prev" title="Contributing" href="user_contributions.html" />
    
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index e34ac7c39b74d6b3020ca9f3a5723ab65ef4327e..3566dce3af5a1e8c77a9d875f86131996e197255 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -7,6 +7,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Index &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -17,6 +18,28 @@
     <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" />
+=======
+    
+    <title>Index &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
    
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
@@ -170,6 +193,7 @@
 
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+<<<<<<< HEAD
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="sidechain/rotamer.html#promod3.sidechain.AAToRotID">AAToRotID() (in module promod3.sidechain)</a>
 </li>
@@ -184,6 +208,33 @@
 </li>
       </ul></li>
       <li>
+=======
+  <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>
+>>>>>>> develop
     add_doc_dependency
 
       <ul>
@@ -193,6 +244,7 @@
       <li>
     add_doc_source
 
+<<<<<<< HEAD
       <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>
@@ -377,6 +429,73 @@
       </ul></li>
   </ul></td>
 </tr></table>
+=======
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+
+      
+  <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>
+>>>>>>> develop
 
 <h2 id="B">B</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
@@ -2244,7 +2363,27 @@
 
 
 
+<<<<<<< HEAD
+
+=======
+      <dd><dl>
+        
+  <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL3RotamerConstructor method)</a>
+  </dt>
+
+        
+  <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>
+>>>>>>> develop
 
 
 
@@ -2284,8 +2423,3413 @@
 
 
 
+<<<<<<< HEAD
+=======
+      
+  <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>
+>>>>>>> develop
+
+
+<<<<<<< HEAD
+=======
+      
+  <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>
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+      
+  <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>
+
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+      
+  <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>
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+
+      
+  <dt><a href="modelling/loop_closing.html#promod3.modelling.KIC.KIC">KIC() (promod3.modelling.KIC method)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+
+      
+  <dt><a href="modelling/pipeline.html#promod3.modelling.MergeMHandle">MergeMHandle() (in module promod3.modelling)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+
+      
+  <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.NaiveSolve">NaiveSolve() (promod3.core.GraphMinimizer method)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.probability">probability (promod3.sidechain.RotamerLibEntry attribute)</a>
+  </dt>
+
+      
+  <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>
+
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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>
+      
+  <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>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <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">
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
+      <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>
+>>>>>>> develop
         </div>
       </div>
       <div class="clearer"></div>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index faf34fe3fb77057e376c24838e75813db94492bb..9743c497ab00421c6d8bf7a1a2eabe0913d74f17 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Getting Started &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Getting Started &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+    <link rel="up" title="Documentation For Users" href="users.html" />
+>>>>>>> develop
     <link rel="next" title="ProMod3 Actions" href="actions/index.html" />
     <link rel="prev" title="Documentation For Users" href="users.html" />
    
@@ -90,7 +114,11 @@ 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 notranslate"><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 notranslate"><span class="pre">sidechain</span></code></a> module)</li>
 <li>Minimize energy of final model using molecular mechanics
+<<<<<<< HEAD
 (using <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.11.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+=======
+(using <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+>>>>>>> develop
 </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
diff --git a/doc/html/index.html b/doc/html/index.html
index 765fa4292fe54ae580387a4f2acf4a4296c957c6..0588f724d39cfcbbb93d775a1c39e57f0a0a193c 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>ProMod3 &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,28 @@
     <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" />
+=======
+    
+    <title>ProMod3 &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="#" />
+>>>>>>> develop
     <link rel="next" title="Documentation For Users" href="users.html" />
    
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
diff --git a/doc/html/license.html b/doc/html/license.html
index cf2102e753e0153e9e1c45e3d520678f0f759d5d..7a0930f24e588fc2795b82d5e94f68192024cca7 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>License &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,28 @@
     <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" />
+=======
+    
+    <title>License &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="References" href="references.html" />
     <link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
    
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index aba8fb069bc15bcac749cb95b94c9b8c02334533..7dbb189008c6ca00fdd18f5afa391446f0970a60 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Handling All Atom Positions &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Handling All Atom Positions &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="loop - Loop Handling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
     <link rel="prev" title="Structural Data" href="structure_db.html" />
    
@@ -83,8 +107,13 @@ new loop is being added.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><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/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><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/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><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/1.11/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) &#8211; Internal SEQRES to be set (single chain or list with one per
+>>>>>>> develop
 chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
 </tr>
 </tbody>
@@ -106,7 +135,11 @@ concatenated one after each other (indexing starts at 0)</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structral data to be set as environment. The chains
+>>>>>>> develop
 in <em>env_structure</em> are expected to be in the same
 order as the SEQRES items provided in constructor.</td>
 </tr>
@@ -133,11 +166,19 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.11.0)"><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.</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 notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
+=======
+<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>) &#8211; 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>) &#8211; 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>) &#8211; Backbone data to be set as environment.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Res. number defining the start position in the SEQRES.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index of chain the structural data belongs to.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -213,7 +254,11 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
 <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>
+<<<<<<< HEAD
 <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/1.11/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+=======
+<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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -346,8 +391,13 @@ and if found set the corresponding position, otherwise we unset it.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
+=======
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue providing atoms</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -392,8 +442,13 @@ out of bounds or if residues in the two containers are inconsistent
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
+=======
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Set position at that index.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Set position to <em>pos</em>.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -443,7 +498,11 @@ out of bounds or if residues in the two containers are inconsistent
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
+=======
+<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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">int</span></code></a>) – Atom position index.</td>
 </tr>
@@ -547,7 +606,11 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">int</span></code></a>) – Residue index</td>
 </tr>
@@ -826,9 +889,15 @@ atom (N, CA, C, O).</p>
 <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.
+<<<<<<< HEAD
 Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+=======
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -847,9 +916,15 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
 <li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
+=======
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) &#8211; Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Residue number for the inserted residue</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -942,8 +1017,13 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
 <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>
 <dd><p>Collection of static methods to lookup properties of amino acid types
+<<<<<<< HEAD
 (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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>
+=======
+(<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
+>>>>>>> develop
 <dl class="staticmethod">
 <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>
@@ -955,7 +1035,11 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </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 notranslate"><span class="pre">str</span></code></a></td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -977,9 +1061,15 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<<<<<<< HEAD
 <li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
+=======
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Atom index (in [0, GetNumAtoms(aa)-1])</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -1007,9 +1097,15 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<<<<<<< HEAD
 <li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
+=======
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Atom index (in [0, GetNumHydrogens(aa)-1])</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -1036,8 +1132,13 @@ atom.</p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<<<<<<< HEAD
 <li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
+=======
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -1064,8 +1165,13 @@ and atom.</p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<<<<<<< HEAD
 <li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
+=======
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -1088,7 +1194,11 @@ hydrogens of <em>aa</em>.</p>
 </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 notranslate"><span class="pre">int</span></code></a></td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -1120,7 +1230,11 @@ hydrogens of <em>aa</em>.</p>
 </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 notranslate"><span class="pre">int</span></code></a></td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -1153,7 +1267,11 @@ hydrogens of <em>aa</em>.</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
@@ -1247,7 +1365,11 @@ 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 notranslate"><span class="pre">int</span></code></a></td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+>>>>>>> develop
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</td>
 </tr>
@@ -1271,7 +1393,11 @@ 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 notranslate"><span class="pre">int</span></code></a></td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+>>>>>>> develop
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</td>
 </tr>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index c8d6329497842a788bcb6f26dbb475d8961d344d..e3c58cc1a5f48bb51f8ce6525c3cce925a7957e6 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Representing Loops &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Representing Loops &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="loop - Loop Handling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
     <link rel="prev" title="loop - Loop Handling" href="index.html" />
    
@@ -39,8 +63,13 @@
 <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 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
+<<<<<<< HEAD
 converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><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>
+=======
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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="k">import</span> <span class="n">io</span>
+>>>>>>> develop
 <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>
 
@@ -151,11 +180,19 @@ code which is not one of the 20 default amino acids or if
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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 notranslate"><span class="pre">RuntimeError</span></code> if a residue in <em>residues</em>
+=======
+<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">list</span></code>) &#8211; List of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><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"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if a residue in <em>residues</em>
+>>>>>>> develop
 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>
@@ -174,8 +211,13 @@ required positions.</td>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+=======
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Sequence of created BackboneList</li>
+<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; List of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+>>>>>>> develop
 which the backbone positions are extracted.</li>
 </ul>
 </td>
@@ -199,7 +241,11 @@ a residue not providing all necessary positions.</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+=======
+<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/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -208,10 +254,17 @@ a residue not providing all necessary positions.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">float</span></code></a>) – </li>
 <li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">bool</span></code></a>) – </li>
+=======
+<li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; </li>
+<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; </li>
+<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; </li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -228,7 +281,11 @@ a residue not providing all necessary positions.</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -245,8 +302,13 @@ be replaced, otherwise they will be added to the entity.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.11.0)"><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</li>
+=======
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) &#8211; The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Residue number defining the start location of insertion</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -262,9 +324,15 @@ be replaced, otherwise they will be added to the entity.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">bool</span></code></a>) – </li>
+=======
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) &#8211; </li>
+<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; </li>
+<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; </li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -281,7 +349,11 @@ be replaced, otherwise they will be added to the entity.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+=======
+<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/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">bool</span></code></a>) – </td>
 </tr>
@@ -385,7 +457,11 @@ actual fragment at specified <em>index</em></p>
 <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>
+<<<<<<< HEAD
 <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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
+=======
+<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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
 </tr>
@@ -409,8 +485,13 @@ atom for residue at given index.</td>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
 <li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><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
+=======
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen / alpha carbon / beta carbon / carbon
+>>>>>>> develop
 / oxygen atom to this.</li>
 </ul>
 </td>
@@ -462,7 +543,11 @@ atom for residue at given index.</td>
 <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>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
 </tr>
@@ -478,8 +563,13 @@ atom for residue at given index.</td>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
 <li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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.</li>
+=======
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Set amino acid type of the residue to this.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -504,6 +594,7 @@ and set the amino acid type according to the given one letter code.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
 <li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
@@ -512,6 +603,16 @@ and set the amino acid type according to the given one letter code.</p>
 <li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
+=======
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) &#8211; Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; 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>) &#8211; Set one letter code of the residue to this.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -580,6 +681,7 @@ to the given one letter code.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
 <li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
@@ -587,6 +689,15 @@ to the given one letter code.</p>
 <li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) &#8211; Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; 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>) &#8211; Set one letter code of the residue to this.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -649,7 +760,11 @@ reconstructed if the residue handle is valid.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue following the C stem (C stem residue is last
+>>>>>>> develop
 element of this backbone list)</td>
 </tr>
 </tbody>
@@ -665,8 +780,13 @@ element of this backbone list)</td>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
 <li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+=======
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -684,9 +804,15 @@ element of this backbone list)</td>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+=======
+<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Start index.</li>
+<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; End index (one past last residue to transform).</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -702,7 +828,11 @@ element of this backbone list)</td>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
+=======
+<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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -722,6 +852,7 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
 positions of the N, CA and C atoms.</p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
 </td>
 </tr>
@@ -730,6 +861,16 @@ positions of the N, CA and C atoms.</p>
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</li>
+=======
+<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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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>) &#8211; The other backbone list.</li>
+<li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index in <em>other</em> backbone list.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -747,7 +888,11 @@ positions of the N, CA and C atoms.</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></td>
+=======
+<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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
 </tr>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 579aaa82d3708d7ef98a601a98aa6716e3f9429c..da2c34e4d987b29e4a4cc7569fcacf3f46231147 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>loop - Loop Handling &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>loop - Loop Handling &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="Representing Loops" href="backbone.html" />
     <link rel="prev" title="Other Scoring Functions" href="../scoring/other_scoring_functions.html" />
    
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 33562795ac8c02153702a441a5141e61520ed9b0..25fbff4594a65a6dcc3c66cd6b7ebb93e099e267 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Loading Precomputed Objects &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Loading Precomputed Objects &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="loop - Loop Handling" href="index.html" />
+>>>>>>> develop
     <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" />
    
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 769cab17ba22d349f5ec8bb8bc47f8acb9d82039..9791f6df0f2d01dbbd23af592514b0a60e588a18 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Generate ost.mol.mm systems &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Generate ost.mol.mm systems &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="loop - Loop Handling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
     <link rel="prev" title="Handling All Atom Positions" href="all_atom.html" />
    
@@ -35,10 +59,17 @@
           <div class="body" role="main">
             
   <div class="section" id="generate-ost-mol-mm-systems">
+<<<<<<< HEAD
 <h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.11.0)"><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/1.11/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.11.0)"><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>
+=======
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><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/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><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>
+>>>>>>> develop
 <p>The example below showcases the creation and use of an MM system:</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">geom</span>
 <span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -281,7 +312,11 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
 <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 notranslate"><span class="pre">SetupSystem()</span></code></a>. Use this to run
 MM simulations.</td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+=======
+<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/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -428,7 +463,11 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
 <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>
+<<<<<<< HEAD
 <dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+=======
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+>>>>>>> develop
 <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 notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -541,7 +580,11 @@ for details.</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
 </tr>
@@ -657,7 +700,11 @@ for details.</p>
 <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
+<<<<<<< HEAD
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+=======
+<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">float</span></code></a></td>
 </tr>
@@ -673,7 +720,11 @@ for details.</p>
 <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
+<<<<<<< HEAD
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+=======
+<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">float</span></code></a></td>
 </tr>
@@ -688,7 +739,11 @@ for details.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+=======
+<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/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+>>>>>>> develop
 </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 notranslate"><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 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>
@@ -712,7 +767,11 @@ for details.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+=======
+<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/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+>>>>>>> develop
 </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 notranslate"><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 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>
@@ -737,7 +796,11 @@ for details.</p>
 <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
+<<<<<<< HEAD
 (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+=======
+(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+>>>>>>> develop
 </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 notranslate"><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 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>
@@ -762,7 +825,11 @@ for details.</p>
 <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
+<<<<<<< HEAD
 (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+=======
+(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+>>>>>>> develop
 </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 notranslate"><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 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>
@@ -908,7 +975,11 @@ for details.</p>
 <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>
 <dd><p>Enumerates the amino acid types for forcefields. The first 20 values
+<<<<<<< HEAD
 correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+>>>>>>> develop
 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>
@@ -924,8 +995,13 @@ types. The full list of values is:</p>
 <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>
 <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
+<<<<<<< HEAD
 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/1.11/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+=======
+separately). Each type of connectivity has it&#8217;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/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+>>>>>>> develop
 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 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
@@ -1035,7 +1111,11 @@ False, False)</em>.</p>
 <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>
+<<<<<<< HEAD
 <dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+=======
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+>>>>>>> develop
 <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>
@@ -1097,7 +1177,11 @@ False, False)</em>.</p>
 <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>
+<<<<<<< HEAD
 <dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+=======
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+>>>>>>> develop
 <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>
@@ -1174,7 +1258,11 @@ False, False)</em>.</p>
 <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>
 <dd><p>Define Urey-Bradley angle
+<<<<<<< HEAD
 (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+=======
+(see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+>>>>>>> develop
 <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>
@@ -1279,8 +1367,13 @@ False, False)</em>.</p>
 <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>
 <dd><p>Define periodic dihedral or improper (see
+<<<<<<< HEAD
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.11.0)"><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/1.11/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+=======
+<a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.10.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+>>>>>>> develop
 <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>
@@ -1384,7 +1477,11 @@ False, False)</em>.</p>
 <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>
+<<<<<<< HEAD
 <dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+=======
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+>>>>>>> develop
 <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>
@@ -1474,7 +1571,11 @@ False, False)</em>.</p>
 <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>
+<<<<<<< HEAD
 <dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+=======
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+>>>>>>> develop
 <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>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 7c5c0bcbf208972e6aa330297dd5bbf8e4f24d9f..95b97d50249611786bac08a20f599a2b972c6297 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Structural Data &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Structural Data &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="loop - Loop Handling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
     <link rel="prev" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
    
@@ -118,7 +142,11 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
 <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>
 <dd><p>Translation from original coordinates that has been applied before storing
+<<<<<<< HEAD
 structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
+=======
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
+>>>>>>> develop
 </dd></dl>
 
 </dd></dl>
@@ -260,7 +288,11 @@ 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>
+<<<<<<< HEAD
 <li>Use the <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+=======
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+>>>>>>> develop
 running in parallel</li>
 </ol>
 <dl class="class">
@@ -275,7 +307,11 @@ 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 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
+<<<<<<< HEAD
 information must be assigned manually (see example script again…).</p>
+=======
+information must be assigned manually (see example script again...).</p>
+>>>>>>> develop
 <p>Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP,
 AAFrequencies, AAFrequenciesStruct</p>
 </dd></dl>
@@ -393,6 +429,7 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
@@ -400,6 +437,15 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
 as specified by <em>chain_name</em>.</li>
 <li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; identifier of the added structure (e.g. pdb id)</li>
+<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) &#8211; 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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; 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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile information for the chain with name
+>>>>>>> develop
 <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
 connected stretch of residues are all connected
@@ -530,6 +576,7 @@ full entry at <em>coord_idx</em></p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<<<<<<< HEAD
 <li><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.</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 notranslate"><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 notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
@@ -538,11 +585,25 @@ database is used.</li>
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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.</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<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>) &#8211; Fragment definition from which to extract positions.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract positions.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Positions on which the backbone list&#8217;s N-terminus should be
+superposed onto.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Positions on which the backbone list&#8217;s C-terminus should be
+>>>>>>> develop
 superposed onto.</li>
 </ul>
 </td>
 </tr>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">RuntimeError</span></code> if the length of <em>sequence</em> does
+=======
+<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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if the length of <em>sequence</em> does
+>>>>>>> develop
 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
@@ -566,6 +627,7 @@ stretches of residues in the database.</p>
 <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>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">str</span></code></a></p>
 </td>
 </tr>
@@ -576,6 +638,18 @@ stretches of residues in the database.</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 notranslate"><span class="pre">RuntimeError</span></code> if fragment or coord_idx is
+=======
+<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/2.7/library/functions.html#str" title="(in Python v2.7)"><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>) &#8211; Fragment definition from which to extract the sequence.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract the sequence</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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment or coord_idx is
+>>>>>>> develop
 invalid. Fragment can be invalid when it does not fully fit into
 one of the connected stretches of residues in the database.</p>
 </td>
@@ -596,6 +670,7 @@ one of the connected stretches of residues in the database.</p>
 <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>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">str</span></code></a></p>
 </td>
 </tr>
@@ -606,6 +681,18 @@ one of the connected stretches of residues in the database.</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 notranslate"><span class="pre">RuntimeError</span></code> if database does not contain dssp
+=======
+<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/2.7/library/functions.html#str" title="(in Python v2.7)"><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>) &#8211; Fragment definition from which to extract the states.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract the dssp states</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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain dssp
+>>>>>>> develop
 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>
@@ -628,6 +715,7 @@ residues in the database.</p>
 or full entry at <em>coord_idx</em></p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">tuple</span></code></a>)</p>
 </td>
 </tr>
@@ -638,6 +726,18 @@ or full entry at <em>coord_idx</em></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 notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+=======
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of pairs (<code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>)</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>) &#8211; Fragment definition from which to extract the dihedrals.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract the dihedral angles</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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+>>>>>>> develop
 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>
@@ -660,6 +760,7 @@ connected stretches of residues in the database.</p>
 at <em>coord_idx</em></p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">float</span></code></a></p>
 </td>
 </tr>
@@ -671,6 +772,19 @@ depths</li>
 </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 notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+=======
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><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>) &#8211; Fragment definition from which to extract the residue
+depths</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract the residue depths</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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+>>>>>>> develop
 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>
@@ -691,6 +805,7 @@ connected stretches of residues in the database.</p>
 <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
 at <em>coord_idx</em> in square A as calculated by
+<<<<<<< HEAD
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.11.0)"><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>
@@ -702,11 +817,28 @@ the database.</p>
 <li><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</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 notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the solvent
+=======
+<a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><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"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><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>) &#8211; Fragment definition from which to extract the solvent
+accessibilities</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract the solvent
+>>>>>>> develop
 accessibilities</li>
 </ul>
 </td>
 </tr>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+=======
+<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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+>>>>>>> develop
 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>
@@ -730,6 +862,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
 model.</p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
 </td>
 </tr>
@@ -741,6 +874,19 @@ profile</li>
 </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 notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+=======
+<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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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>) &#8211; Fragment definition from which to extract the sequence
+profile</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract the sequence profile</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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+>>>>>>> develop
 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>
@@ -764,6 +910,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
 model.</p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
 </td>
 </tr>
@@ -775,6 +922,19 @@ profile</li>
 </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 notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+=======
+<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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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>) &#8211; Fragment definition from which to extract the structure
+profile</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of entry from which to extract the structure profile</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/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+>>>>>>> develop
 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>
@@ -805,7 +965,11 @@ containing that data.</li>
 probabilities as NULL model.</p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+=======
+<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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+>>>>>>> develop
 </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 notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
@@ -827,9 +991,15 @@ frequencies in entry with <em>coord_idx</em></p>
 <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">
+<<<<<<< HEAD
 <li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 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])</li>
+=======
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Source of profile frequencies</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -1130,10 +1300,17 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The C-stem</li>
+<li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of residues of the fragment</li>
+<li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Whether to extend the search to include fragments from
+>>>>>>> develop
 <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>
@@ -1354,8 +1531,13 @@ linked to this object.</li>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
 <li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+=======
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; linear weight</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile for the fraggers target_sequence</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -1372,8 +1554,13 @@ linked to this object.</li>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
 <li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+=======
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; linear weight</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile for the fraggers target_sequence</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index cfa041c06743d19b51fe1eed53d76084d699bd5d..40a21e9c8cbf51f320b7d64ddf85da94c3cd0daf 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Sampling Dihedral Angles &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Sampling Dihedral Angles &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="loop - Loop Handling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Structural Data" href="structure_db.html" />
     <link rel="prev" title="Representing Loops" href="backbone.html" />
    
@@ -131,7 +155,11 @@ acids not matching any of the group definitions.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.11.0)"><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</td>
+=======
+<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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) &#8211; structure from which parameters will be extracted</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -203,9 +231,15 @@ for details.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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</li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -245,9 +279,15 @@ standard amino acid</td>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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</li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; 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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -283,10 +323,17 @@ standard amino acid</td>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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</li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></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 notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; 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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; <em>psi</em> angle</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -327,10 +374,17 @@ standard amino acid</td>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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</li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></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 notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; 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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; <em>phi</em> angle</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -371,11 +425,19 @@ standard amino acid</td>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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.</li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; 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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; psi angle</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -417,11 +479,19 @@ standard amino acid</td>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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.</li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; 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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; psi angle</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -441,11 +511,19 @@ standard amino acid</td>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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.</li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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></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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; 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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; phi angle</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; psi angle</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index e9c1d2172d91eb42436d16ced6952751ce9b367e..dfdd0610bee8007919959bbcb1aa0934d0159d13 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Modelling Algorithms &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Modelling Algorithms &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
     <link rel="prev" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
    
@@ -85,9 +109,15 @@ of the solutions</li>
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">list</span></code></a> defining the
 indices of the common subsets (rigid blocks) relative
+<<<<<<< HEAD
 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/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
+and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
+<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+>>>>>>> develop
 superpose the according positions in <strong>bb_list_one</strong>
 onto <strong>bb_list_two</strong></p>
 </td>
@@ -105,7 +135,11 @@ onto <strong>bb_list_two</strong></p>
 <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">
+<<<<<<< HEAD
 <li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.11.0)"><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/1.11/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
+=======
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) &#8211; An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
+>>>>>>> develop
 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 notranslate"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
 positions will be extracted</li>
@@ -126,9 +160,15 @@ of the solutions</li>
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">list</span></code></a> defining the
 column indices of the common subsets (rigid blocks)
+<<<<<<< HEAD
 relative to the input <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.11.0)"><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/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
+<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+>>>>>>> develop
 superpose the according positions from the first
 sequence onto the second sequence.</p>
 </td>
@@ -163,9 +203,15 @@ of the solutions</li>
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">list</span></code></a> defining the
 indices of the common subsets (rigid blocks) relative
+<<<<<<< HEAD
 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/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+=======
+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 <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
+<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+>>>>>>> develop
 superpose the according positions in <strong>pos_one</strong>
 onto <strong>pos_two</strong></p>
 </td>
@@ -228,11 +274,19 @@ Weird things are happening otherwise.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
+=======
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; 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>) &#8211; Psipred prediction for this chain.</li>
+<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Length (num. residues) of fragments to be extracted.</li>
+<li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of fragments to be extracted at each
+>>>>>>> develop
 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 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>.</li>
@@ -321,7 +375,11 @@ want to generate</li>
 <li><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>
+<<<<<<< HEAD
 <li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><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 
+=======
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; The sequence profile for <strong>sequence</strong>. This increases the 
+>>>>>>> develop
 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 notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
 increases the fragment search performance</li>
@@ -368,7 +426,11 @@ 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
+<<<<<<< HEAD
 specific orthogonal vector basis. That’s 6 numbers in total.</p>
+=======
+specific orthogonal vector basis. That&#8217;s 6 numbers in total.</p>
+>>>>>>> develop
 <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
@@ -404,7 +466,11 @@ 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>
+<<<<<<< HEAD
 <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>
+=======
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example script that loads protein structures that contain ATP and</span>
+>>>>>>> develop
 <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>
@@ -480,6 +546,7 @@ several queries, so they can be searched at once.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>positions</strong> (<code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – To avoid the full O(n^3) hell, triangles
@@ -490,12 +557,28 @@ 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 notranslate"><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 notranslate"><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 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).
+=======
+<li><strong>positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) &#8211; Coordinates of the query</li>
+<li><strong>identifier</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Descriptor of the query</li>
+<li><strong>min_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; 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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; 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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Bin size in A, relevant to generate hash map keys</li>
+<li><strong>flags</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Flag in range [0,63] for every coordinate in <em>positions</em>.
+They&#8217;re also added to the hash map keys (default: 0).
+>>>>>>> develop
 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>
+<<<<<<< HEAD
 <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 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</li>
+=======
+<li><strong>query_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> 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>) &#8211; E pluribus unum</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -509,7 +592,11 @@ only coordinates matter.</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">str</span></code></a>) – filename</td>
+=======
+<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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; filename</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -523,7 +610,11 @@ only coordinates matter.</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">str</span></code></a>) – filename</td>
+=======
+<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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; filename</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -537,7 +628,11 @@ only coordinates matter.</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Query from which you want the positions</td>
+=======
+<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Query from which you want the positions</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -560,7 +655,11 @@ 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>
+<<<<<<< HEAD
 <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>
+=======
+<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>
+>>>>>>> develop
 <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>
@@ -591,6 +690,7 @@ algorithm.</p>
 <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">
+<<<<<<< HEAD
 <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>
@@ -598,6 +698,15 @@ algorithm.</p>
 <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 notranslate"><span class="pre">MotifQuery</span></code></a>
 constructor. If you didn’t provide anything there,
+=======
+<li><strong>query</strong> &#8211; Query to be searched</li>
+<li><strong>target_positions</strong> &#8211; Coordinates of the target</li>
+<li><strong>hash_thresh</strong> &#8211; Parameter relevant for detection stage</li>
+<li><strong>distance_thresh</strong> &#8211; Parameter relevant for refinement stage</li>
+<li><strong>refine_thresh</strong> &#8211; Parameter relevant for refinement stage</li>
+<li><strong>flags</strong> &#8211; 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&#8217;t provide anything there,
+>>>>>>> develop
 this can be ignored. Only the actual coordinates
 matter in this case.</li>
 </ul>
@@ -606,7 +715,11 @@ matter in this case.</li>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">All found matches</p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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 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>
+=======
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> 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>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -623,6 +736,7 @@ matter in this case.</li>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
+<<<<<<< HEAD
 <h1 class="logo"><a href="../index.html">ProMod3</a></h1>
 
 
@@ -646,6 +760,14 @@ matter in this case.</li>
 <li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="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="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>
+=======
+  <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>
+>>>>>>> develop
 </ul>
 </li>
 </ul>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 2d2ad5a8bc339f3c63647475cbf1de3f021ee835..638d8e6964ead1c33e2be44a4cfe4f500cb9b4f6 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Handling Gaps &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Handling Gaps &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
     <link rel="prev" title="Model Checking" href="model_checking.html" />
    
@@ -53,9 +77,15 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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></li>
 <li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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></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 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></li>
+=======
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -109,7 +139,11 @@ are valid and:</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+=======
+<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/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -260,13 +294,21 @@ extend the gap past another gap.</p>
 <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>
+<<<<<<< HEAD
 <dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+=======
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+=======
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+>>>>>>> develop
 </dd></dl>
 
 <dl class="attribute">
@@ -310,8 +352,13 @@ False if no new extension possible.</p>
 <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">
+<<<<<<< HEAD
 <li><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>.</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 notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><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.</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>) &#8211; 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/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The full sequence of the chain, the gap is associated with.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -351,9 +398,15 @@ valid termini.</td>
 <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">
+<<<<<<< HEAD
 <li><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>.</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 notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><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.</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 notranslate"><span class="pre">int</span></code></a>) – <ul>
+=======
+<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>) &#8211; 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/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; <ul>
+>>>>>>> develop
 <li>If -1, all possible non-terminal gaps are returned.</li>
 <li>If &gt;= 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>.</li>
@@ -402,12 +455,21 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
 <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">
+<<<<<<< HEAD
 <li><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>.</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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><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.</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 notranslate"><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 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>
+=======
+<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>) &#8211; 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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Penalty for length of gap.</li>
+<li><strong>penalties</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Penalty for each residue added to gap.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; <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>
+>>>>>>> develop
 (i.e. it stops at gaps and termini).</li>
 <li>If -1, all possible non-terminal gaps are returned.</li>
 <li>If &gt;= 0, this restricts the max. gap-length (w/o termini)
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index ba2b15b8cf5887d6f50c154b3078046dba5f6e5a..86a0195979534b5289d0f4509833a57f410960ff 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>modelling - Protein Modelling &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>modelling - Protein Modelling &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="Modelling Pipeline" href="pipeline.html" />
     <link rel="prev" title="Singularity" href="../container/singularity.html" />
    
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 52f494fcf8368eca6ea5adaa6f0414f07f8f7fc8..c6e8c2ce3a3d7dd085480d10ca50720180e51037 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Handling Loop Candidates &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Handling Loop Candidates &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
     <link rel="prev" title="Handling Gaps" href="gap_handling.html" />
    
@@ -125,9 +149,15 @@ a fragment database.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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</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 notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the C-terminal end of the loop</li>
+<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; The sequence of residues to be added including the
+>>>>>>> develop
 <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 notranslate"><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 notranslate"><span class="pre">StructureDB</span></code></a>) – The according structural database</li>
@@ -237,12 +267,21 @@ not depending on a metropolis criterium.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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>.</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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>.</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 notranslate"><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 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
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
+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>) &#8211; A torsion sampler (used for all residues) or a list
+>>>>>>> develop
 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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Cutoff in stem residue RMSD used to determine
@@ -281,9 +320,15 @@ candidate. This leads to an increase in number of loops.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c-stem positions every candidate
+>>>>>>> develop
 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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Second pivot residue</li>
@@ -357,7 +402,11 @@ anything is raised when calculating the scores.</p>
 <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>
 <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
+<<<<<<< HEAD
 <em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><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/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+>>>>>>> develop
 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
 combining this to other scores, where it is commonly the other way around.</p>
@@ -370,11 +419,19 @@ with this DB).</p>
 <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">
+<<<<<<< HEAD
 <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 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></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 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></li>
 <li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</li>
+=======
+<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>) &#8211; 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>) &#8211; 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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile information for target.</li>
+<li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Loop starts at index <em>offset</em> in <em>prof</em>.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -403,10 +460,17 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
 <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">
+<<<<<<< HEAD
 <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 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></li>
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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.</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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.</li>
+=======
+<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>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the C-terminal end of the loop.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index d68c457f3f90f4154e6eed05b5258a7c73f2ffad..db9b7c7b40ba26b6174b1bed8e3d3253c6761376 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Fitting Loops Into Gaps &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Fitting Loops Into Gaps &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
     <link rel="prev" title="Handling Loop Candidates" href="loop_candidates.html" />
    
@@ -75,6 +99,7 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
@@ -82,6 +107,15 @@ 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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Sequence of the backbones to be closed</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n_stem.
+If the residue before <em>n_stem</em> doesn&#8217;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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c_stem.
+If the residue after <em>c_stem</em> doesn&#8217;t exist, the
+>>>>>>> develop
 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 notranslate"><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 notranslate"><span class="pre">list</span></code></a>
@@ -117,10 +151,17 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c_stem</li>
+<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Maximal number of iterations</li>
+<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The algorithm stops as soon as the c_stem of the loop to
+>>>>>>> develop
 be  closed has RMSD below the given <em>c_stem</em></li>
 </ul>
 </td>
@@ -318,9 +359,15 @@ size or sequence as the initial one.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+=======
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -340,9 +387,15 @@ size or sequence as the initial one.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+=======
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -363,9 +416,15 @@ doesn’t do anything if specified residue is a glycine</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+=======
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -385,9 +444,15 @@ doesn’t do anything if specified residue is a glycine</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+=======
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -407,9 +472,15 @@ doesn’t do anything if specified residue is a glycine</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
+=======
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 6c8d5d9d0f56e188f19570c023357ae0a9c22cf0..2d5e32283cb25465b38a2fbc8dece8160dd035e2 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Model Checking &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Model Checking &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Handling Gaps" href="gap_handling.html" />
     <link rel="prev" title="Modelling Pipeline" href="pipeline.html" />
    
@@ -50,14 +74,25 @@ three of the atoms exist (center and radii are estimated then).</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><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/1.11/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect rings.</td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
 tuple with:
+<<<<<<< HEAD
 center (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><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/1.11/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.11.0)"><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/3.6/library/functions.html#float" title="(in Python v3.6)"><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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</td>
+=======
+center (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.10.0)"><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/2.7/library/functions.html#float" title="(in Python v2.7)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -72,12 +107,21 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">GetRings()</span></code></a>.</li>
 <li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><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/1.11/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</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 notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
+=======
+<li><strong>rings</strong> &#8211; 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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect punches.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
+>>>>>>> develop
 have a punched ring.</p>
 </td>
 </tr>
@@ -95,8 +139,13 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">GetRings()</span></code></a>.</li>
 <li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><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/1.11/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+=======
+<li><strong>rings</strong> &#8211; 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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect punches.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -121,9 +170,15 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
 <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 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.</li>
+<<<<<<< HEAD
 <li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</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 notranslate"><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 notranslate"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
+=======
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) &#8211; 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>.) &#8211; Gap for which loop is to be filled.</li>
+<li><strong>orig_indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; Mapping to old indexing of candidates. If given, it
+>>>>>>> develop
 must have as many elements as <em>candidates</em>.</li>
 </ul>
 </td>
@@ -186,7 +241,11 @@ with <code class="docutils literal notranslate"><span class="pre">MolProbity</sp
 <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 notranslate"><span class="pre">dict</span></code></a></p>
 </td>
 </tr>
+<<<<<<< HEAD
 <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/1.11/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+=======
+<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/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the &#8220;phenix.molprobity&#8221;
+>>>>>>> develop
 executable is not found.</p>
 </td>
 </tr>
@@ -203,7 +262,11 @@ executable is not found.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) &#8211; OST entity on which to do analysis.</td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 68acc9306cf2b1e21a31de0e8e2d028579d06994..cff5e54de23986e168e68c7e99dfd1ca5dd65595 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Generating Loops De Novo &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Generating Loops De Novo &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
     <link rel="prev" title="Fitting Loops Into Gaps" href="loop_closing.html" />
    
@@ -498,6 +522,7 @@ avoid moving into unfavourable phi/psi ranges.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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>.</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
@@ -505,6 +530,15 @@ should adapt. See <a class="reference internal" href="loop_closing.html#promod3.
 <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 notranslate"><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 notranslate"><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 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
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; 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> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
+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>) &#8211; To enforce valid phi/psi ranges. Alternatively, you
+>>>>>>> develop
 can also pass a list of sampler objects to assign a
 unique torsion sampler to every residue of the
 conformation to be closed.</li>
@@ -548,9 +582,15 @@ dihedral angles as it is the case for the <a class="reference internal" href="#p
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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.</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
+should adapt.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
+>>>>>>> develop
 should adapt.</li>
 </ul>
 </td>
@@ -590,9 +630,15 @@ solutions. The KICCloser simply picks the first one.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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.</li>
 <li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
+adapt.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
+>>>>>>> develop
 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 notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
 </ul>
@@ -631,7 +677,11 @@ superposing the c_stem with the desired positions.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
+>>>>>>> develop
 adapt.</td>
 </tr>
 </tbody>
@@ -669,7 +719,11 @@ superposing the n_stem with the desired positions.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
+>>>>>>> develop
 adapt.</td>
 </tr>
 </tbody>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 2c25e977439e7a9346192d04947ae53cf74bce04..328a3d8fb5a62005d090107c249ab6bf74e7f6b0 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Modelling Pipeline &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Modelling Pipeline &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Model Checking" href="model_checking.html" />
     <link rel="prev" title="modelling - Protein Modelling" href="index.html" />
    
@@ -110,7 +134,11 @@ chain follows afterwards.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></td>
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -136,13 +164,21 @@ Gaps of different chains are appended one after another.</p>
 <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>
+<<<<<<< HEAD
 <dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
+=======
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
+>>>>>>> develop
 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">
+<<<<<<< HEAD
 <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/1.11/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></td>
+=======
+<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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -151,16 +187,26 @@ of the target protein.</p>
 <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>
+<<<<<<< HEAD
 <dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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&#8217;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
+>>>>>>> develop
 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 notranslate"><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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+=======
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -347,7 +393,11 @@ 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
+<<<<<<< HEAD
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
+=======
+<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
+>>>>>>> develop
 <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
@@ -375,7 +425,11 @@ as information about insertions and deletions in the gaps list.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><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>) &#8211; Single alignment handle for raw model with single chain or
+>>>>>>> develop
 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 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
@@ -400,8 +454,13 @@ in SMTL). All ligands are added to a new chain named
 <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
+<<<<<<< HEAD
 alignment sequence (note that you can set an “offset” (see
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+=======
+alignment sequence (note that you can set an &#8220;offset&#8221; (see
+<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+>>>>>>> develop
 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>
@@ -444,6 +503,7 @@ return an incomplete model.</p>
 <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 notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
 alignment.</li>
+<<<<<<< HEAD
 <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 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/1.11/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.11.0)"><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/1.11/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.11.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
@@ -451,6 +511,15 @@ 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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.11.0)"><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 
+=======
+<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; if True, use the AMBER force field instead of the def.
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.10.0)"><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/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-func docutils literal"><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> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) &#8211; Additional list of force fields to use if a 
+>>>>>>> develop
 (ligand) residue cannot be parametrized with the
 default force field. The force fields are tried
 in the order as given and ligands without an
@@ -471,7 +540,11 @@ limited. Termini of length 1 won’t be modelled.</li>
 <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>
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -640,6 +713,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info comes from</li>
@@ -648,6 +722,16 @@ environments get updated in <strong>target_mhandle</strong>.</p>
 <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 notranslate"><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/1.11/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.11.0)"><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</li>
+=======
+<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>) &#8211; 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>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; This is the chain where the info goes to</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; First residue of the copied stretch</li>
+<li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Last residue of the copied stretch</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; Transformation to be applied to all atom positions when
+they&#8217;re copied over</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -676,8 +760,13 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
 <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">
+<<<<<<< HEAD
 <li><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</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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
+=======
+<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>) &#8211; Will have the profiles attached afterwards</li>
+<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; The sequence profiles to attach</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -834,9 +923,15 @@ 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 notranslate"><span class="pre">BuildRawModel()</span></code></a> is
 called (e.g. with 
+<<<<<<< HEAD
 <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.11.0)"><code class="xref py py-meth docutils literal notranslate"><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 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
+=======
+<a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.10.0)"><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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; 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
+>>>>>>> develop
 with <cite>use_scoring_extender</cite>. This allows the gap
 extender to skip neighboring gaps and to correctly
 handle gaps close to termini.</li>
@@ -935,12 +1030,21 @@ This function cannot fill gaps at C- or N-terminal.</p>
 <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">
+<<<<<<< HEAD
 <li><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.</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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
+=======
+<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>) &#8211; 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>) &#8211; 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>) &#8211; 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>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Define how many candidates are &#8216;enough&#8217; to be
+>>>>>>> develop
 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>
@@ -1041,10 +1145,17 @@ is only used if the gap length is &gt;= the length of fragments stored.</p>
 <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">
+<<<<<<< HEAD
 <li><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.</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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
+=======
+<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>) &#8211; 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>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Define how many candidates are &#8216;enough&#8217; to be
+>>>>>>> develop
 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 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>)</li>
@@ -1205,7 +1316,11 @@ one is loaded if None.</li>
 <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>
 <dd><p>Minimize energy of final model using molecular mechanics.</p>
+<<<<<<< HEAD
 <p>Uses <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.11.0)"><code class="xref py py-mod docutils literal notranslate"><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/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+>>>>>>> develop
 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>
@@ -1227,6 +1342,7 @@ minimization is aborted. This issue is logged and added as a major issue to
 <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">
+<<<<<<< HEAD
 <li><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.</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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within SD method</li>
@@ -1235,13 +1351,27 @@ minimization is aborted. This issue is logged and added as a major issue to
 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>).</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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.11.0)"><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>).</li>
+=======
+<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>) &#8211; Modelling handle on which to apply change.</li>
+<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Max. number of iterations for SD+LBFGS</li>
+<li><strong>max_iter_sd</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Max. number of iterations within SD method</li>
+<li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Max. number of iterations within LBFGS method</li>
+<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; 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> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -1329,8 +1459,13 @@ set to True, if the problem affects backbone atoms.</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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/1.11/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></td>
+=======
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueView</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index f0f6410e760767caca5098a947637622a03ad28d..aeb52dafe8310b8308a227a07e9fbbe09dd21c97 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Sidechain Reconstruction &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Sidechain Reconstruction &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="modelling - Protein Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Modelling Algorithms" href="algorithms.html" />
     <link rel="prev" title="Generating Loops De Novo" href="monte_carlo.html" />
    
@@ -38,9 +62,15 @@
 <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">
+<<<<<<< HEAD
 <li>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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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
+>>>>>>> develop
 and used to reconstruct sidechains of single loops</li>
 </ul>
 <p>Example usage:</p>
@@ -94,7 +124,11 @@ and used to reconstruct sidechains of single loops</li>
 <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">
+<<<<<<< HEAD
 <li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structure for sidechain reconstruction. Note, that the sidechain
+>>>>>>> develop
 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 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
@@ -206,12 +240,21 @@ environment before calling this!</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Chains the loops belong to.</li>
+=======
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Start of loop.</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Length of loop.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Chain the loop belongs to.</li>
+<li><strong>start_resnum_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Starts of loops.</li>
+<li><strong>num_residues_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Lengths of loops.</li>
+<li><strong>chain_idx_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Chains the loops belong to.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index eb9645e24f41c2b18aab3aaba2691e647d40ecef..47cf43600c2b0bae3824bed63cda4bdff39bc0a0 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Using Binary Files In ProMod3 &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Using Binary Files In ProMod3 &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+    <link rel="up" title="Documentation For Developers" href="developers.html" />
+>>>>>>> develop
     <link rel="next" title="License" href="license.html" />
     <link rel="prev" title="ProMod3’s Share Of CMake" href="cmake/index.html" />
    
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 81417cb1facf91dad3c7164b166b75fb7c1121c7..1026cd5289d88ef78ee9494e8eaddcbd828da9c0 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Python Module Index &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,28 @@
     <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" />
+=======
+    
+    <title>Python Module Index &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
 
    
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
diff --git a/doc/html/references.html b/doc/html/references.html
index f2981f198c1d01517670d3fb792b26da419d34b1..8f39ae974f8192768d1b7585a488c331303effbb 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>References &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,28 @@
     <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" />
+=======
+    
+    <title>References &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Changelog" href="changelog.html" />
     <link rel="prev" title="License" href="license.html" />
    
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 7895090db606ee4cf64314650b4126345e99f5c0..781c37f012cc868c64e75ae721d8870a62fc32d2 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>All Atom Scorers &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>All Atom Scorers &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="scoring - Loop Scoring" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
     <link rel="prev" title="Backbone Scorers" href="backbone_scorers.html" />
    
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index c1a6b7c27a9ce3d814e11d1a2673144e0a7f4a11..043c78896951c7170cfaf8aad9df355cd597c5e5 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Backbone Score Environment &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Backbone Score Environment &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="scoring - Loop Scoring" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
     <link rel="prev" title="scoring - Loop Scoring" href="index.html" />
    
@@ -61,8 +85,13 @@ task.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><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/3.6/library/stdtypes.html#list" title="(in Python v3.6)"><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/3.6/library/stdtypes.html#str" title="(in Python v3.6)"><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/1.11/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) &#8211; Internal SEQRES to be set (single chain or list with one per
+>>>>>>> develop
 chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
 </tr>
 </tbody>
@@ -99,7 +128,11 @@ structural data was already set, all the existing data gets cleared first.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structral data to be set as environment. The chains
+>>>>>>> develop
 in <em>env_structure</em> are expected to be in the same
 order as the SEQRES items provided in constructor.</td>
 </tr>
@@ -122,9 +155,15 @@ positions.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.11.0)"><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.</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 notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</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>) &#8211; Structural data to be set as environment.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Res. number defining the position in the SEQRES.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index of chain the structural data belongs to.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -272,7 +311,11 @@ providing lists of integers.</p>
 <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>
+<<<<<<< HEAD
 <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/1.11/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+=======
+<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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -379,8 +422,13 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.11.0)"><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</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 notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
+=======
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; 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>) &#8211; Whether you want to assess pairwise distances between CA
+>>>>>>> develop
 or CB atoms</li>
 </ul>
 </td>
@@ -394,7 +442,11 @@ or CB atoms</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.11.0)"><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
+=======
+<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/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) &#8211; Alignment, where first sequence represent the initial
+>>>>>>> develop
 SEQRES and the second sequence the actual structural
 info. The second sequence must have a view attached.</td>
 </tr>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 9c478f517be6e839c85666ab327adf29629e1bb4..a32dbb8456b000e47fc0cfa520be7daa4b975532 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Backbone Scorers &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Backbone Scorers &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="scoring - Loop Scoring" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
     <link rel="prev" title="Backbone Score Environment" href="backbone_score_env.html" />
    
@@ -373,9 +397,15 @@ called for every type of amino acids and for every <em>count</em> &lt;= <em>max_
 <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">
+<<<<<<< HEAD
 <li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><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.</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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+=======
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for which to set energy.</li>
+<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of surrounding CB positions for which to set energy.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Energy to set for those parameters.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -507,10 +537,17 @@ SetEnergy(aa2, aa1, bin, energy).</p>
 <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">
+<<<<<<< HEAD
 <li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
 <li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+=======
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for second interaction partner.</li>
+<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the interaction distance.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Energy to set for those parameters.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -687,6 +724,7 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
 <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">
+<<<<<<< HEAD
 <li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
 <li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</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 notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
@@ -694,6 +732,15 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
+=======
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for second interaction partner.</li>
+<li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the interaction distance.</li>
+<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the alpha angle.</li>
+<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the beta angle.</li>
+<li><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the gamma dihedral.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Energy to set for those parameters.</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index a584105b96798d634174c2424fc7e69c9095fa11..09cdbbb7c3fd0d763304fee599b612ae044471b7 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>scoring - Loop Scoring &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>scoring - Loop Scoring &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
     <link rel="prev" title="Subrotamer Optimization" href="../sidechain/subrotamer_optimizer.html" />
    
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index c9283b23f102844b53afde101c79803dafb2b736..5e81b54f4d1d0aa91310db2df1a79e4c4485479e 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Other Scoring Functions &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Other Scoring Functions &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="scoring - Loop Scoring" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
     <link rel="prev" title="All Atom Scorers" href="all_atom_scorers.html" />
    
diff --git a/doc/html/search.html b/doc/html/search.html
index 25734513301dd89f2ba457880c94dae4c4d4ffd0..b9cbb85db22a479bc286f69865bf0988351e43d8 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -6,18 +6,40 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Search &#8212; ProMod3 2.0.0 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+=======
+    
+    <title>Search &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+>>>>>>> develop
     <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 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>
+<<<<<<< HEAD
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="#" />
+=======
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
   <script type="text/javascript">
     jQuery(function() { Search.loadIndex("searchindex.js"); });
   </script>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index a6e0b0268e804671b07fa45b054e8a75557ecc37..695d1bb37563b6378fdc54258514a3ff03735981 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
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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],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:[0,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,25,26,40,45],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,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],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],changelog:[8,19],chapter:[29,33],charact:[13,20,26],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],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,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],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:[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:[2,16,25,37],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]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_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,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,8,12,13,15,16,17,18,20,25,26,27,28,33,39,41,48,51],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,first:[0,1,8,10,13,16,18,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,20,22,26,30,31,34,54],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:[23,32,35],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:[0,1,2,3,5,8,10,13,14,16,18,19,20,23,24,26,27,28,30,31,32,33,35,36,37,39,40,41,48,49,50,51,54],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,getloopstartindi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Actions","<code class=\"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=\"docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"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=\"docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop 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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],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:[0,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,25,26,40,45],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,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],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],changelog:[8,19],chapter:[29,33],charact:[13,20,26],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],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,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],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:[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:[2,16,25,37],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]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_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,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,8,12,13,15,16,17,18,20,25,26,27,28,33,39,41,48,51],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,first:[0,1,8,10,13,16,18,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,20,22,26,30,31,34,54],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:[23,32,35],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:[0,1,2,3,5,8,10,13,14,16,18,19,20,23,24,26,27,28,30,31,32,33,35,36,37,39,40,41,48,49,50,51,54],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,getloopstartindi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Actions","<code class=\"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=\"docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"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=\"docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop 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Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3&#8216;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 &amp; 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:[0,1,4,5,7,8],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],angl:27,api:1,argument:13,atom:[21,32,39],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:[0,2,5,7,35,49],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,exisit:37,extend: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],imag:[5,7],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:[5,7,25],other:43,output:1,own: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:[0,2,4,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,7,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,7,8],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}})
+>>>>>>> develop
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 3e94c5a8b2d11f080f20f21374be73c0cb11dade..ea239ac102aa329782fa46d7052cfc2c09bdf174 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Disulfid Bond Evaluation &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Disulfid Bond Evaluation &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
     <link rel="prev" title="Rotamer Graph" href="graph.html" />
    
@@ -67,12 +91,21 @@ rotamers to the result of the geometric expression.</p>
 <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">
+<<<<<<< HEAD
 <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 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</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 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</li>
 <li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
+=======
+<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>) &#8211; 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>) &#8211; Second rotamer</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CB position of second rotamer</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -103,11 +136,19 @@ possible, the one with the optimal sum of scores gets estimated.</p>
 <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">
+<<<<<<< HEAD
 <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 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</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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><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</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 notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><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</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 notranslate"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
+=======
+<li><strong>rotamer_groups</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> 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>) &#8211; Every group represents a cysteine</li>
+<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The CB positions of the according rotamers</li>
+<li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The score two rotamers must have to be considered
+>>>>>>> develop
 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 notranslate"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
 rotamer groups, the active subrotamers get
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 84fb5b495f650a5362a45fbcff6d1bbcac748b61..4ed58839870434ab5eb75d292abb7db534b9e57d 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Frame - The Rigid Part &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Frame - The Rigid Part &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
     <link rel="prev" title="Representing Sidechains - Rotamers &amp; Co." href="rotamer.html" />
    
@@ -120,6 +144,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
+<<<<<<< HEAD
 <h1 class="logo"><a href="../index.html">ProMod3</a></h1>
 
 
@@ -143,6 +168,12 @@ can be passed to rotamer groups for calculating frame energies.</p>
 <li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="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="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>
+=======
+  <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>
+>>>>>>> develop
 </ul>
 </li>
 </ul>
@@ -158,7 +189,11 @@ can be passed to rotamer groups for calculating frame energies.</p>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
   <li><a href="../users.html">Documentation For Users</a><ul>
+<<<<<<< HEAD
   <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+=======
+  <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+>>>>>>> develop
       <li>Previous: <a href="rotamer.html" title="previous chapter">Representing Sidechains - Rotamers &amp; Co.</a></li>
       <li>Next: <a href="rotamer_constructor.html" title="next chapter">Rotamer Constructor</a></li>
   </ul></li>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index 34e8c2a7fca1ac088836239452b1ea0d1424468c..1b34c8a51b4be6ba233a88aa7a123663a659ee15 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Rotamer Graph &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Rotamer Graph &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
     <link rel="prev" title="Rotamer Library" href="rotamer_lib.html" />
    
@@ -117,7 +141,11 @@ conformations for every amino acid position.</td>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
   <li><a href="../users.html">Documentation For Users</a><ul>
+<<<<<<< HEAD
   <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+=======
+  <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+>>>>>>> develop
       <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>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 6f100c8963a66f22c88210a871aba7d2e8adfb3e..a68ee21166054a444bfa7413e073e27052874b55 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>sidechain - Sidechain Modelling &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>sidechain - Sidechain Modelling &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+>>>>>>> develop
     <link rel="next" title="Representing Sidechains - Rotamers &amp; Co." href="rotamer.html" />
     <link rel="prev" title="Modelling Algorithms" href="../modelling/algorithms.html" />
    
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index 2405ae6f9b6ae29954973778f3261c024fd6f289..e89c99d6518a6353c015a5a07c3c1e6f73a36e02 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Loading Rotamer Libraries &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Loading Rotamer Libraries &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
     <link rel="prev" title="Disulfid Bond Evaluation" href="disulfid.html" />
    
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index d4ac997d9099f3348560b725d83c3a7a6a579306..09860d3753da9c5a72cc2c37f05422e1dd3010ae 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Representing Sidechains - Rotamers &amp; Co. &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Representing Sidechains - Rotamers &amp; Co. &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Frame - The Rigid Part" href="frame.html" />
     <link rel="prev" title="sidechain - Sidechain Modelling" href="index.html" />
    
@@ -36,6 +60,7 @@
             
   <div class="section" id="representing-sidechains-rotamers-co">
 <h1>Representing Sidechains - Rotamers &amp; Co.<a class="headerlink" href="#representing-sidechains-rotamers-co" title="Permalink to this headline">¶</a></h1>
+<<<<<<< HEAD
 <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>.
@@ -43,6 +68,15 @@ 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 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 notranslate"><span class="pre">Frame</span></code></a> object.</p>
+=======
+<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>.
+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>.
+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>
+>>>>>>> develop
 <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
@@ -62,7 +96,11 @@ that affect the hbond term or different versions of proline/cysteine.</p>
 <li>LYS - Lysine</li>
 <li>SER - Serine</li>
 <li>CYS - Cystein</li>
+<<<<<<< HEAD
 <li>CYH - “free” Cystein</li>
+=======
+<li>CYH - &#8220;free&#8221; Cystein</li>
+>>>>>>> develop
 <li>CYD - disulfid bonded Cystein</li>
 <li>MET - Methionine</li>
 <li>TRP - Tryptophane</li>
@@ -85,14 +123,23 @@ that affect the hbond term or different versions of proline/cysteine.</p>
 <li>XXX - Invalid</li>
 </ul>
 </td></tr></table>
+<<<<<<< HEAD
 <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>
+=======
+<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>
+>>>>>>> develop
 </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
+<<<<<<< HEAD
 functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+>>>>>>> develop
 or from amino acid three letter codes.</p>
 <dl class="method">
 <dt id="promod3.sidechain.TLCToRotID">
@@ -103,9 +150,15 @@ exactly the naming convention defined above.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</td>
+=======
+<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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -116,15 +169,26 @@ exactly the naming convention defined above.</p>
 <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>
 <dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
 to generate special IDs this way
+<<<<<<< HEAD
 (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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+=======
+(e.g. HSD, HSE or the special prolines/cysteins) since they&#8217;re simply not
+defined in <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+>>>>>>> develop
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
+=======
+<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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -220,7 +284,11 @@ evaluated by the underlying scoring function.</td>
 <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>
+<<<<<<< HEAD
 <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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
+=======
+<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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -276,18 +344,31 @@ function</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><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 notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
+=======
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; 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>) &#8211; The type of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The position of the particle</li>
+<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; 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>) &#8211; Direction of all possible lone pairs of the particle,
+>>>>>>> develop
 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>
+<<<<<<< HEAD
 <li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+=======
+<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The polar direction of the particle,
+>>>>>>> develop
 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
@@ -309,17 +390,28 @@ Details can be found in the relevant publication <a class="reference internal" h
 <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>
+<<<<<<< HEAD
 <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
+=======
+<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
+>>>>>>> develop
 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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+=======
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; The name of the particle</li>
+<li><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; 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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The position of the particle</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -334,7 +426,11 @@ repulsion term.</li>
 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
 and repulsion are evaluated for all pairs of particles. Hydrophobic is only
+<<<<<<< HEAD
 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 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
+>>>>>>> develop
 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>
@@ -360,23 +456,37 @@ VINA is mainly targeted at interactions between sidechains and ligands.</p>
 <li>Br_VINAParticle - Bromine</li>
 <li>I_VINAParticle - Iodine</li>
 <li>M_VINAParticle - Metals</li>
+<<<<<<< HEAD
 <li>INVALID_VINAParticle - Invalid particle…</li>
+=======
+<li>INVALID_VINAParticle - Invalid particle...</li>
+>>>>>>> develop
 </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>
+<<<<<<< HEAD
 <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
+=======
+<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
+>>>>>>> develop
 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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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/1.11/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+=======
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; 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>) &#8211; The type of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The position of the particle</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -454,8 +564,13 @@ in this process.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
+>>>>>>> develop
 <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 notranslate"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
 default value (“”)</li>
@@ -730,8 +845,13 @@ No atoms are removed from <strong>res</strong> in this process.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
+>>>>>>> develop
 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 notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
 default value (“”)</li>
@@ -1129,9 +1249,15 @@ particles of the same residue.</li>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Rotamer index</li>
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+=======
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Rotamer index</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
+>>>>>>> develop
 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 notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
 default value (“”)</li>
@@ -1263,9 +1389,15 @@ particles of the same residue.</li>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">int</span></code></a>) – Rotamer index</li>
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+=======
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Rotamer index</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
+>>>>>>> develop
 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 notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
 default value (“”)</li>
@@ -1345,6 +1477,7 @@ rotamers with <em>self_energy</em> &gt; <em>l_e</em> + <em>thresh</em></p>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
+<<<<<<< HEAD
 <h1 class="logo"><a href="../index.html">ProMod3</a></h1>
 
 
@@ -1368,6 +1501,23 @@ rotamers with <em>self_energy</em> &gt; <em>l_e</em> + <em>thresh</em></p>
 <li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="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="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>
+=======
+  <h3><a href="../index.html">Table Of Contents</a></h3>
+  <ul>
+<li><a class="reference internal" href="#">Representing Sidechains - Rotamers &amp; 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>
+</ul>
+</li>
+<li><a class="reference internal" href="#rotamers">Rotamers</a></li>
+<li><a class="reference internal" href="#rotamer-groups">Rotamer Groups</a></li>
+>>>>>>> develop
 </ul>
 </li>
 </ul>
@@ -1383,8 +1533,13 @@ rotamers with <em>self_energy</em> &gt; <em>l_e</em> + <em>thresh</em></p>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
   <li><a href="../users.html">Documentation For Users</a><ul>
+<<<<<<< HEAD
   <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
       <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+=======
+  <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>
+>>>>>>> develop
       <li>Next: <a href="frame.html" title="next chapter">Frame - The Rigid Part</a></li>
   </ul></li>
   </ul></li>
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 3871e91515645d9934f052cee6ec892f37f5bead..8f6344cddaad7f00c3d342832f9869b54a3cc604 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Rotamer Constructor &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Rotamer Constructor &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
     <link rel="prev" title="Frame - The Rigid Part" href="frame.html" />
    
@@ -45,7 +69,11 @@ convenient functionality provided by ProMod3.</p>
 <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>
 <dd><p>Abstract base class that cannot be initialized from Python. It builds
 an interface implemented by scoring function specific constructors
+<<<<<<< HEAD
 (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>
+=======
+(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>
+>>>>>>> develop
 <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>
@@ -71,6 +99,7 @@ an interface implemented by scoring function specific constructors
 <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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
@@ -78,6 +107,15 @@ 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 notranslate"><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 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
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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>) &#8211; To extract the required backbone atoms</li>
+<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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>) &#8211; Identifies the sidechain.</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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&#8217;t want to calculate a pairwise
+>>>>>>> develop
 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 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</li>
@@ -126,6 +164,7 @@ don’t show up in a rotamer).</p>
 <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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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</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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
@@ -133,6 +172,15 @@ 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 notranslate"><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 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
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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>) &#8211; To extract the backbone positions</li>
+<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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>) &#8211; Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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&#8217;t want to calculate a pairwise
+>>>>>>> develop
 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 notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
@@ -169,6 +217,7 @@ you observe in a rotamer).</p>
 <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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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</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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
@@ -176,6 +225,15 @@ 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 notranslate"><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 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
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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>) &#8211; To extract the backbone positions</li>
+<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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>) &#8211; Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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&#8217;t want to calculate a pairwise
+>>>>>>> develop
 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 notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
@@ -211,8 +269,13 @@ to the energy function specific constructors to override that behaviour.</p>
 <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 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</li>
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+=======
+<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>) &#8211; Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; The index of the residue which is represented by
+>>>>>>> develop
 <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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
@@ -257,7 +320,11 @@ any rotamers for ALA and GLY.</td>
 <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>
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+>>>>>>> develop
 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
 atoms of the residue will be represented as carbons and hydrogens are
@@ -267,9 +334,15 @@ skipped.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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>.</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 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.</li>
+=======
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -283,7 +356,11 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
 <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>
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+>>>>>>> develop
 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 notranslate"><span class="pre">ConstructFrameResidue()</span></code></a>,
 which will be called by this function if the residue is not known by the given
@@ -301,10 +378,17 @@ as in the <code class="xref py py-class docutils literal notranslate"><span clas
 <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">
+<<<<<<< HEAD
 <li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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>.</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 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.</li>
 <li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
+=======
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) &#8211; OST compound library to use</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -447,8 +531,127 @@ is already called at construction and the energies are properly assigned.</p>
 <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 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</li>
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+=======
+<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>) &#8211; Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Whether the residue is c-terminal</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</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>
+<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
+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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; 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
+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&#8217;t generate
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
+<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>.
+Takes the rotamer group and assigns every single rotamer its internal
+energy based on the probabilistic approach used by SCWRL3.
+=&gt; -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+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>) &#8211; 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>) &#8211; Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Whether the residue is c-terminal</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</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>
+<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
+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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; 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
+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&#8217;t generate
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
+<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>.
+Takes the rotamer group and assigns every single rotamer its internal
+energy based on the probabilistic approach used by SCWRL3/SCWRL4.
+=&gt; -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+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>) &#8211; 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>) &#8211; Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; The index of the residue which is represented by
+>>>>>>> develop
 <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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
@@ -464,7 +667,11 @@ to be assigned</li>
 <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>
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+>>>>>>> develop
 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
@@ -473,6 +680,7 @@ 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">
+<<<<<<< HEAD
 <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 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 notranslate"><span class="pre">VINAParticleType</span></code></a>.</li>
@@ -500,12 +708,42 @@ M_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechai
 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>.</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 notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
+=======
+<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
+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 &#8220;is_hbond_acceptor&#8221; AND
+&#8220;is_hbond_donor&#8221; 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,
+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/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
+at.SetBoolProp(&#8220;is_hbond_donor&#8221;, False) and
+at.SetBoolProp(&#8220;is_hbond_acceptor&#8221;, 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.
+If the atom has the bool properties &#8220;is_hbond_acceptor&#8221; AND
+&#8220;is_hbond_donor&#8221; 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
+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 [&#8220;MG&#8221;, &#8220;MN&#8221;, &#8220;ZN&#8221;, &#8220;CA&#8221;, &#8220;FE&#8221;] 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 [&#8220;S&#8221;, &#8220;P&#8221;, &#8220;F&#8221;, &#8220;CL&#8221;, &#8220;BR&#8221;, &#8220;I&#8221;] 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>
+>>>>>>> develop
 </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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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></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 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></li>
@@ -513,6 +751,15 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
 </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 notranslate"><span class="pre">FrameResidue</span></code></a></p>
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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>
+</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>
+>>>>>>> develop
 </td>
 </tr>
 </tbody>
@@ -522,16 +769,28 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
 <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>
+<<<<<<< HEAD
 <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>
+=======
+<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>
+>>>>>>> develop
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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></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 notranslate"><span class="pre">RRMRotamer</span></code></a></td>
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -540,18 +799,31 @@ as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerCons
 <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>
+<<<<<<< HEAD
 <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
+=======
+<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
+>>>>>>> develop
 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">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><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></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 notranslate"><span class="pre">FRMRotamer</span></code></a></td>
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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>
+>>>>>>> develop
 </tr>
 </tbody>
 </table>
@@ -569,6 +841,7 @@ contains the atoms from <em>residue</em>.</p>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
+<<<<<<< HEAD
 <h1 class="logo"><a href="../index.html">ProMod3</a></h1>
 
 
@@ -592,6 +865,13 @@ contains the atoms from <em>residue</em>.</p>
 <li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="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="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>
+=======
+  <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>
+>>>>>>> develop
 </ul>
 </li>
 </ul>
@@ -607,7 +887,11 @@ contains the atoms from <em>residue</em>.</p>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
   <li><a href="../users.html">Documentation For Users</a><ul>
+<<<<<<< HEAD
   <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+=======
+  <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+>>>>>>> develop
       <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>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 54fe48a8fa1df551cfb80468404d3ab1b75359e1..63a20c973bec9c01a7534268be90be73159dd172 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Rotamer Library &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Rotamer Library &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Rotamer Graph" href="graph.html" />
     <link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
    
@@ -107,8 +131,13 @@ for details.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</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>) &#8211; 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>) &#8211; the rotamer to be added</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -136,7 +165,11 @@ special <em>id</em> requests.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</td>
+=======
+<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>) &#8211; Identity of rotamer of interest</td>
+>>>>>>> develop
 </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 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</td>
@@ -229,6 +262,7 @@ for details.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Configuration of chi2</li>
@@ -237,6 +271,16 @@ for details.</p>
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</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>) &#8211; Identity of rotamer to be added</li>
+<li><strong>r1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Configuration of chi1</li>
+<li><strong>r2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Configuration of chi2</li>
+<li><strong>r3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Configuration of chi3</li>
+<li><strong>r4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Configuration of chi4</li>
+<li><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Phi backbone dihedral description</li>
+<li><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; 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>) &#8211; the rotamer to be added</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -276,9 +320,15 @@ special <em>id</em> requests.</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle in range [-pi,pi[</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>) &#8211; Identity of rotamer of interest</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Phi backbone dihedral angle in range [-pi,pi[</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Psi backbone dihedral angle in range [-pi,pi[</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -300,11 +350,19 @@ found</p>
 <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">
+<<<<<<< HEAD
 <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 notranslate"><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 notranslate"><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 notranslate"><span class="pre">RotamerID</span></code></a> must
+=======
+<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
+>>>>>>> develop
 be consistent across all phi/psi bins</li>
 </ul>
 <table class="docutils field-list" frame="void" rules="none">
@@ -427,8 +485,13 @@ functionalities.</p>
 <dl class="staticmethod">
 <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>
+<<<<<<< HEAD
 <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
+=======
+<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
+>>>>>>> develop
 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>
@@ -436,12 +499,21 @@ NaN.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
+<<<<<<< HEAD
 <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/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
+=======
+<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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Source of dihedral angles</td>
+>>>>>>> develop
 </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 notranslate"><span class="pre">RotamerLibEntry</span></code></a></td>
 </tr>
+<<<<<<< HEAD
 <tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><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
+=======
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> 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
+>>>>>>> develop
 are present in <em>res</em>.</td>
 </tr>
 </tbody>
@@ -460,8 +532,13 @@ are NaN.</p>
 <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">
+<<<<<<< HEAD
 <li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/1.11/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.11.0)"><code class="xref py py-class docutils literal notranslate"><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 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></li>
+=======
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; 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>) &#8211; 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>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -520,7 +597,11 @@ the chi2 is checked for its actual value, but also for its flipped state.</p>
 <li><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</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 notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
 considered similar</li>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</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>) &#8211; Identity of the entries to be compared</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -578,7 +659,11 @@ for its actual value, but also for its flipped state.</p>
 (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 notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
 considered similar</li>
+<<<<<<< HEAD
 <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 notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</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>) &#8211; Identity of the entries to be compared</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -643,9 +728,15 @@ to also return NON_ROTAMERIC (e.g. chi2 for ASN).</p>
 <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">
+<<<<<<< HEAD
 <li><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</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 notranslate"><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 notranslate"><span class="pre">int</span></code></a>) – Specifies angle (0 =&gt; chi1, …, 3 =&gt; chi4)</li>
+=======
+<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>) &#8211; 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>) &#8211; Identity of rotamer</li>
+<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Specifies angle (0 =&gt; chi1, ..., 3 =&gt; chi4)</li>
+>>>>>>> develop
 </ul>
 </td>
 </tr>
@@ -706,7 +797,11 @@ valid and non rotameric, INVALID otherwise.</p>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
   <li><a href="../users.html">Documentation For Users</a><ul>
+<<<<<<< HEAD
   <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+=======
+  <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+>>>>>>> develop
       <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>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 150150090a8ec3035c37936b00d880f2cd7a8e30..23010bcaa63ad70cafe3e4516d7b6828ba675773 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Subrotamer Optimization &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Subrotamer Optimization &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
+    <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
     <link rel="prev" title="Loading Rotamer Libraries" href="loading.html" />
    
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index b9333e6b2efb886796caa4c0d024a308111035fb..fd5efd52966642e3f171f6175eb9f4c809cdedb2 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Contributing &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,29 @@
     <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" />
+=======
+    
+    <title>Contributing &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+    <link rel="up" title="Documentation For Users" href="users.html" />
+>>>>>>> develop
     <link rel="next" title="Documentation For Developers" href="developers.html" />
     <link rel="prev" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
    
diff --git a/doc/html/users.html b/doc/html/users.html
index 1e1cb07cd79c8316060d74d18c5fdd69c5084ad1..4fd90e479b17d92b8cf3626c680d7753e20fbc93 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -6,6 +6,7 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<<<<<<< HEAD
     <title>Documentation For Users &#8212; ProMod3 2.0.0 documentation</title>
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -16,6 +17,28 @@
     <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" />
+=======
+    
+    <title>Documentation For Users &mdash; ProMod3 2.1.0 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:     '2.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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>
+    <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
+>>>>>>> develop
     <link rel="next" title="Getting Started" href="gettingstarted.html" />
     <link rel="prev" title="ProMod3" href="index.html" />
    
@@ -74,7 +97,11 @@ 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>
+<<<<<<< HEAD
 <li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+=======
+<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>
+>>>>>>> develop
 <li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Representing Sidechains - Rotamers &amp; 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>