diff --git a/CHANGELOG b/CHANGELOG
index 2a1fc7b16a30e197ded81d00c08fd93af3e11b6b..822063549d01bf3e67763c25232f558673ce1aa0 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,7 +5,7 @@
Changelog
================================================================================
-Release 3.2.x
+Release 3.2.0
--------------------------------------------------------------------------------
* Remove outdated configuration scripts (Fedora 19 / ancient Mac)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3f3886fd5dd292e7a444005ebe294d7a10a4a97b..b58f41d3c278297e6258ca22b316692daf6c1f12 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,8 +24,8 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 3)
-set(PROMOD3_VERSION_MINOR 1)
-set(PROMOD3_VERSION_PATCH 1)
+set(PROMOD3_VERSION_MINOR 2)
+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})
@@ -103,7 +103,7 @@ if(NOT DISABLE_DOCUMENTATION)
# this URL should always point to the latest version of OST
set(OST_DOC_URL "https://www.openstructure.org/docs")
endif()
-find_package(OPENSTRUCTURE 2.1.0 REQUIRED
+find_package(OPENSTRUCTURE 2.2.0 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 b4d82a2f011ea011ec36bd1bb583f738cc1250db..20a1c805c7d3b0d6ffbd7bfe929fec6dd7ff2034 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -1,9 +1,9 @@
-ARG OPENSTRUCTURE_IMAGE_TAG="2.1.0-bionic"
+ARG OPENSTRUCTURE_IMAGE_TAG="2.2.0-focal"
FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
-ARG PROMOD_VERSION="3.1.1"
+ARG PROMOD_VERSION="3.2.0"
ARG SRC_FOLDER="/usr/local/src"
diff --git a/container/Singularity b/container/Singularity
index 2b9f8f1fee08920e12d46138000dc05af4585b86..ccb464c7d6ce0fcbc58a7ef5db54a1eb4a068e79 100644
--- a/container/Singularity
+++ b/container/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/promod3:3.1.1-OST2.1.0-bionic
+From: registry.scicore.unibas.ch/schwede/promod3:3.2.0-OST2.2.0-focal
%post
##############################################################################
# POST
@@ -42,7 +42,7 @@ cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
"-m", "ipykernel",
"-f", "{connection_file}",
"--InteractiveShellApp.exec_PYTHONSTARTUP=False",
- "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.6/site-packages/ost/ost_startup.py']"
+ "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.8/site-packages/ost/ost_startup.py']"
],
"env": {
}
@@ -200,7 +200,7 @@ and goes to CWD. Thus this sould work as expected out of the box.
# NOTEBOOK ENV
##############################################################################
export DNG_ROOT=$OST_ROOT
-export DNG_INITDIR=${DNG_ROOT}/lib64/python3.6/site-packages/ost
+export DNG_INITDIR=${DNG_ROOT}/lib64/python3.8/site-packages/ost
%apprun IPython
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 08c65e05183e857dd016281843395d512b1bc7f9..4840eb328a28a1201185757fcb089242d1f322c6 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -286,7 +286,7 @@ rst_epilog = """
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
-.. |ost_version| replace:: 2.1.0
+.. |ost_version| replace:: 2.2.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
diff --git a/doc/html/_sources/buildsystem.rst.txt b/doc/html/_sources/buildsystem.rst.txt
index 5960348cf6d2e6cb2598440d7ffa10784a63ef2e..136280e2453d1e1f49ba7de58d9afd36d98f6c2b 100644
--- a/doc/html/_sources/buildsystem.rst.txt
+++ b/doc/html/_sources/buildsystem.rst.txt
@@ -65,7 +65,7 @@ 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``.
+``Python_ROOT_DIR`` and ``EIGEN3_INCLUDE_DIR``.
Here is a list of more options used within |project|:
@@ -165,7 +165,7 @@ safely delete the whole source folder.
.. _python: https://www.python.org/
.. _boost: https://www.boost.org/
.. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page
-.. _openmm: http://openmm.org
+.. _openmm: https://github.com/openmm/openmm
.. LocalWords: cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html
.. LocalWords: doctest linkcheck qmean DQMEAN eigen CMakeCache
diff --git a/doc/html/_sources/changelog.rst.txt b/doc/html/_sources/changelog.rst.txt
index bcfe0e157fa1a99532d33e26cf714e9951345177..822063549d01bf3e67763c25232f558673ce1aa0 100644
--- a/doc/html/_sources/changelog.rst.txt
+++ b/doc/html/_sources/changelog.rst.txt
@@ -5,6 +5,18 @@
Changelog
================================================================================
+Release 3.2.0
+--------------------------------------------------------------------------------
+
+* Remove outdated configuration scripts (Fedora 19 / ancient Mac)
+* Construct CB atoms if only N,CA and C atoms are present in
+ ReconstructSidechains input structure.
+* Detect Python using functionality provided by CMake instead of our own code.
+ You might have to adapt CMake flags when building ProMod3 to variables
+ specified here: https://cmake.org/cmake/help/latest/module/FindPython.html
+* Several minor bug fixes, improvements, and speed-ups.
+
+
Release 3.1.1
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/sidechain/rotamer.rst.txt b/doc/html/_sources/sidechain/rotamer.rst.txt
index 7e87093f6e637bc336cd96a4f5c10d44c883914b..c729b48e792d3ee17eca63d68e3ffa10187fc26b 100644
--- a/doc/html/_sources/sidechain/rotamer.rst.txt
+++ b/doc/html/_sources/sidechain/rotamer.rst.txt
@@ -254,7 +254,7 @@ Details can be found in the relevant publication [canutescu2003]_.
The VINA scoring function
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-The VINA scoring function is a combination of scores that are named
+The VINA scoring function is a combination of functional forms 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
@@ -263,6 +263,43 @@ 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 functional forms are linearly combined with the default weights from
+the Autodock Vina Software. They're set as global variables and can be
+extracted with:
+
+.. method:: GetVINAWeightGaussian1
+
+
+.. method:: GetVINAWeightGaussian2
+
+
+.. method:: GetVINAWeightRepulsion
+
+
+.. method:: GetVINAWeightHydrophobic
+
+
+.. method:: GetVINAWeightHBond
+
+You can set custom weights. A call to the following functions overwrites
+according weights globally which affects any subsequent score evaluation:
+
+.. method:: SetVINAWeightGaussian1(w)
+
+
+.. method:: SetVINAWeightGaussian2(w)
+
+
+.. method:: SetVINAWeightRepulsion(w)
+
+
+.. method:: SetVINAWeightHydrophobic(w)
+
+
+.. method:: SetVINAWeightHBond(w)
+
+
+
The VINA scoring function differentiates between the following particle types:
.. class:: VINAParticleType
diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js
index 64a0640507439eaf96ea9479493c555be9e9adce..42c91446bcb95d168a9e3f067debdc598e518dc9 100644
--- a/doc/html/_static/documentation_options.js
+++ b/doc/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '3.1.1',
+ VERSION: '3.2.0',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index f8482376318926a09800444d23f50f62b8d18401..03acc8c078ac24d3ae060b4247b3658346ecdff9 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>ProMod3 Actions — ProMod3 3.1.1 documentation</title>
+ <title>ProMod3 Actions — ProMod3 3.2.0 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>
@@ -101,7 +101,7 @@ Example:</p>
</li>
</ul>
<p>Structures can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
<code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>. At least one structure must be
given and you cannot mix file formats. Multiple structures can be given and each
@@ -128,7 +128,7 @@ to the corresponding target sequences. This has an impact on loop scoring with
the database approach.
The profiles can be provided as plain files or gzipped. Following file
extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
-Consider to use <a class="reference external" href="https://www.openstructure.org/docs/2.0/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+Consider to use <code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code> if you have a
file in a3m format at hand.</p>
<ul class="simple">
<li><p>The profiles are mapped based on exact matches towards the gapless
@@ -183,7 +183,7 @@ detects and models disulfid bonds and reconstructs all sidechains with the
flexible rotamer model. The result is stored as <code class="file docutils literal notranslate"><span class="pre">out.pdb</span></code>.
The output filename can be controlled with the <code class="docutils literal notranslate"><span class="pre">-o</span></code> flag.</p>
<p>A structure can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
<code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>.</p>
<p>Several flags control the modelling behaviour:</p>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 63efba74b11ff525b6f2376e61bb5940f0f06106..35c893b404ddcfc8d33fcb0c1e49ea75a90a83cf 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>test_actions - Testing Actions — ProMod3 3.1.1 documentation</title>
+ <title>test_actions - Testing Actions — ProMod3 3.2.0 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>
@@ -185,7 +185,7 @@ happens if a user throws dirty input data in.</p>
</div>
<div class="section" id="making-the-script-executable">
<h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>’s <a class="reference external" href="https://www.openstructure.org/docs/2.0/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>’s <a class="reference external" href="https://www.openstructure.org/docs/2.2/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s
<a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
as a script:</p>
<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 21f67d724cc474aad4828460f8491ff47e2905e3..bb112e4cd94fc8a049138175171891ebc7fd8d46 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Building ProMod3 — ProMod3 3.1.1 documentation</title>
+ <title>Building ProMod3 — ProMod3 3.2.0 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>
@@ -38,8 +38,8 @@
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-2.1.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
-use <a class="reference external" href="http://openmm.org">OpenMM</a>. To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same
+2.2.0. 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="https://github.com/openmm/openmm">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. We do not provide backwards compatibility to Python 2.7. The last
@@ -47,8 +47,8 @@ release supporting Python 2.7 is 2.1.0 which also requires OST to be
compiled with Python 2.7.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><p><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.1.0</p></li>
-<li><p><a class="reference external" href="http://openmm.org">OpenMM</a> 7.1.1</p></li>
+<li><p><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.2.0</p></li>
+<li><p><a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a> 7.1.1</p></li>
<li><p><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</p></li>
<li><p><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</p></li>
<li><p><a class="reference external" href="https://www.boost.org/">Boost</a> 1.68.0</p></li>
@@ -75,7 +75,7 @@ headers would be located in <code class="docutils literal notranslate"><span cla
<p>Similarly, one can specify folders for Boost, Python and Eigen 3
if multiple versions exist and/or they are not installed in a default location.
These are set with the <code class="docutils literal notranslate"><span class="pre">BOOST_ROOT</span></code> (make sure that’s the same as for OST),
-<code class="docutils literal notranslate"><span class="pre">PYTHON_ROOT</span></code> and <code class="docutils literal notranslate"><span class="pre">EIGEN3_INCLUDE_DIR</span></code>.</p>
+<code class="docutils literal notranslate"><span class="pre">Python_ROOT_DIR</span></code> and <code class="docutils literal notranslate"><span class="pre">EIGEN3_INCLUDE_DIR</span></code>.</p>
<p>Here is a list of more options used within ProMod3:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code> Don’t build documentation, don’t search for Sphinx</p></li>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 7218355aad831c79052b719d7821dae9832026fe..4a4a2b2289b4f433726fef935582650615500669 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Changelog — ProMod3 3.1.1 documentation</title>
+ <title>Changelog — ProMod3 3.2.0 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>
@@ -34,6 +34,18 @@
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-3-2-0">
+<h2>Release 3.2.0<a class="headerlink" href="#release-3-2-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>Remove outdated configuration scripts (Fedora 19 / ancient Mac)</p></li>
+<li><p>Construct CB atoms if only N,CA and C atoms are present in
+ReconstructSidechains input structure.</p></li>
+<li><p>Detect Python using functionality provided by CMake instead of our own code.
+You might have to adapt CMake flags when building ProMod3 to variables
+specified here: <a class="reference external" href="https://cmake.org/cmake/help/latest/module/FindPython.html">https://cmake.org/cmake/help/latest/module/FindPython.html</a></p></li>
+<li><p>Several minor bug fixes, improvements, and speed-ups.</p></li>
+</ul>
+</div>
<div class="section" id="release-3-1-1">
<h2>Release 3.1.1<a class="headerlink" href="#release-3-1-1" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 6befa7a6af0daf22f5b8f958843e3dfbf236553f..094a5faeed083f11e84f969ed968e06283c38205 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>ProMod3’s Share Of CMake — ProMod3 3.1.1 documentation</title>
+ <title>ProMod3’s Share Of CMake — ProMod3 3.2.0 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>
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index 366b0e48a631e7c0ffece72846b7bf4233b353c1..6156b9d2c9ba9ed6431261ddae3bc4cce325433c 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Docker — ProMod3 3.1.1 documentation</title>
+ <title>Docker — ProMod3 3.2.0 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>
@@ -77,7 +77,7 @@ pdbs/struct.pdb
</div>
<div class="section" id="the-compound-library">
<span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
-<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal 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/2.2/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">CompoundLib</span></code></a> is generated.
Compound libraries contain information on chemical compounds, such as their
connectivity, chemical class and one-letter-code. The compound library has
several uses, but the most important one is to provide the connectivy
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index 05ee8d6ca11dbe12a90213b4fbdd0c9b964d5246..8f18ef708af1893ddc04fea96707bd006e19ac2d 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>ProMod3 and Containers — ProMod3 3.1.1 documentation</title>
+ <title>ProMod3 and Containers — ProMod3 3.2.0 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>
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index e1adf82aed4a1ee6aac3a6520e44753b37e7512d..c0ea15a885d5e61fdfdb2c388429c0a6be6c0924 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Singularity — ProMod3 3.1.1 documentation</title>
+ <title>Singularity — ProMod3 3.2.0 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>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index d9f46848eb77534aaa0d7a766ba8f5d3244ebcce..10ae1b3f0a57744e8807439af15d061638a5b985 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Contributing — ProMod3 3.1.1 documentation</title>
+ <title>Contributing — ProMod3 3.2.0 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>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 3d3d48d0eded6e7120dd2612e133609454db8f92..e379e2db97aca62d73a13378197745c0ea22dd75 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Geometry functions — ProMod3 3.1.1 documentation</title>
+ <title>Geometry functions — ProMod3 3.2.0 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>
@@ -45,14 +45,14 @@
<dd class="field-odd"><ul class="simple">
<li><p><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Gromacs rule</p></li>
<li><p><strong>number</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</p></li>
-<li><p><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</p></li>
+<li><p><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Constructed <em>number</em> positions.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -64,16 +64,16 @@
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Positions of O and OXT atoms.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -86,9 +86,9 @@ dihedral (A-B-C-D).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</p></li>
-<li><p><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</p></li>
-<li><p><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</p></li>
+<li><p><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</p></li>
+<li><p><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</p></li>
+<li><p><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</p></li>
<li><p><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bond length (C-D)</p></li>
<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (B-C-D)</p></li>
<li><p><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</p></li>
@@ -98,7 +98,7 @@ dihedral (A-B-C-D).</p>
<dd class="field-even"><p>Position of atom D</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -111,16 +111,16 @@ C-alpha and C atoms.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Position of C-beta atom</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -133,8 +133,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
-<li><p><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</p></li>
+<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
+<li><p><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</p></li>
<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
</ul>
</dd>
@@ -142,7 +142,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<dd class="field-even"><p>Transformation matrix</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -155,7 +155,7 @@ going through the origin.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
+<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
</ul>
</dd>
@@ -163,7 +163,7 @@ going through the origin.</p>
<dd class="field-even"><p>Rotation matrix</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -176,7 +176,7 @@ going through the origin.</p>
<dd><p>Simple container class to store N, CA and C coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</p>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
@@ -193,7 +193,7 @@ atoms.</p>
<dd><p>Position of nitrogen / alpha carbon / carbon atom.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index 7400bd5ea186025d8bc895f2dd18be80b6887142..e3a5609a7a8cba0076dcb4fe4cf0753493ca3bf6 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Graph Minimizer — ProMod3 3.1.1 documentation</title>
+ <title>Graph Minimizer — ProMod3 3.2.0 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>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index bbbadede7dea5558dbbb5e04b972f70bebcaa347..acf81f09fe5d27a9609f33bce5d22cfccca0ef21 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>helper - Shared Functionality For the Everything — ProMod3 3.1.1 documentation</title>
+ <title>helper - Shared Functionality For the Everything — ProMod3 3.2.0 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>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 520f3e50899fb5789c102e38d200a71059d422ae..1684e67ea84430a56d7fa9beb69d517c65b820bc 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>core - ProMod3 Core Functionality — ProMod3 3.1.1 documentation</title>
+ <title>core - ProMod3 Core Functionality — ProMod3 3.2.0 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>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index dbdf78f2bf0769f1ce5bc7c2821e065c7dfe975b..0cbcfccb1194e13f1628445e9fa7241b6250f7b8 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>pm3argparse - Parsing Command Lines — ProMod3 3.1.1 documentation</title>
+ <title>pm3argparse - Parsing Command Lines — ProMod3 3.2.0 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>
@@ -233,7 +233,7 @@ 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
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code> if you have a file
in a3m format at hand.</p></li>
</ul>
<p>Notes:</p>
@@ -247,7 +247,7 @@ target sequences</p></li>
</ul>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
ordered to match the target sequences.</p></li>
</ul>
<p>Exit codes related to profile input:</p>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index 582468d7f5dc3c6264b06baf0f3e75ffa7d8c18d..aa9651473d8c7dbe31a910ab31729f28accd08f8 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Runtime profiling — ProMod3 3.1.1 documentation</title>
+ <title>Runtime profiling — ProMod3 3.2.0 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>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 1d70eb8ef4e399229e0f50fa86da6976d9f135e0..cabf318b8994fff813783df478b5cfc4dcc4189a 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>SetCompoundsChemlib() — ProMod3 3.1.1 documentation</title>
+ <title>SetCompoundsChemlib() — ProMod3 3.2.0 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>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 2fbffee7db4c76ed82c28399265785a34c4ca09e..5d173da4203c8e761982eb05bc75ab63ff3d49ad 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>ProMod3 Setup — ProMod3 3.1.1 documentation</title>
+ <title>ProMod3 Setup — ProMod3 3.2.0 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>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index ab1e42355b429ad3c73807a44dbeacabd2ab44f3..40fba96583f81dcf40fe8b37169ff05ef060119f 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Documentation For Developers — ProMod3 3.1.1 documentation</title>
+ <title>Documentation For Developers — ProMod3 3.2.0 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>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 1677805e2e2dbb9ebd1aff421fce54cf8e316f07..f18ed2b4690f6241a3b4224e93eb75afbf7b54a7 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -5,7 +5,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Index — ProMod3 3.1.1 documentation</title>
+ <title>Index — ProMod3 3.2.0 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>
@@ -1059,12 +1059,12 @@
<li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor">(promod3.sidechain.RRMRotamer method)</a>
</li>
</ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.GetLargestCluster">GetLargestCluster() (promod3.modelling.LoopCandidates method)</a>
</li>
<li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetLastIndex">GetLastIndex() (promod3.loop.AllAtomPositions method)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.GetLength">GetLength() (promod3.modelling.StructuralGap method)</a>
</li>
<li><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.GetList">GetList() (promod3.modelling.FraggerHandle method)</a>
@@ -1242,6 +1242,16 @@
</li>
</ul></li>
<li><a href="loop/backbone.html#promod3.loop.BackboneList.GetTransform">GetTransform() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.GetTransform">[1]</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.GetVINAWeightGaussian1">GetVINAWeightGaussian1() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.GetVINAWeightGaussian2">GetVINAWeightGaussian2() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.GetVINAWeightHBond">GetVINAWeightHBond() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.GetVINAWeightHydrophobic">GetVINAWeightHydrophobic() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.GetVINAWeightRepulsion">GetVINAWeightRepulsion() (in module promod3.sidechain)</a>
</li>
<li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetWeights">GetWeights() (promod3.modelling.ScoringWeights static method)</a>
</li>
@@ -2001,14 +2011,14 @@
<li><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.SetEnergy">(promod3.scoring.TorsionScorer method)</a>
</li>
</ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv.SetEnvironment">SetEnvironment() (promod3.loop.AllAtomEnv method)</a>
<ul>
<li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetEnvironment">(promod3.scoring.BackboneScoreEnv method)</a>
</li>
</ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetEpsilons">SetEpsilons() (promod3.loop.ForcefieldLookup method)</a>
</li>
<li><a href="modelling/pipeline.html#promod3.modelling.SetFraggerHandles">SetFraggerHandles() (in module promod3.modelling)</a>
@@ -2098,6 +2108,16 @@
<li><a href="modelling/pipeline.html#promod3.modelling.SetupDefaultBackboneScoring">SetupDefaultBackboneScoring() (in module promod3.modelling)</a>
</li>
<li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.SetupSystem">SetupSystem() (promod3.loop.MmSystemCreator method)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.SetVINAWeightGaussian1">SetVINAWeightGaussian1() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.SetVINAWeightGaussian2">SetVINAWeightGaussian2() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.SetVINAWeightHBond">SetVINAWeightHBond() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.SetVINAWeightHydrophobic">SetVINAWeightHydrophobic() (in module promod3.sidechain)</a>
+</li>
+ <li><a href="sidechain/rotamer.html#promod3.sidechain.SetVINAWeightRepulsion">SetVINAWeightRepulsion() (in module promod3.sidechain)</a>
</li>
<li><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.SetWeights">SetWeights() (promod3.modelling.ScoringWeights static method)</a>
</li>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 8fba122262a8eed50b127feb14beb80ea9a93a39..20ff1b4fa4b46126008093a01b22123b95d630cd 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Getting Started — ProMod3 3.1.1 documentation</title>
+ <title>Getting Started — ProMod3 3.2.0 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>
@@ -85,7 +85,7 @@ is conserved</p></li>
<li><p>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> module)</p></li>
<li><p>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> module)</p></li>
<li><p>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</p></li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</p></li>
</ul>
<p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
diff --git a/doc/html/index.html b/doc/html/index.html
index 90ecac33833d41e08f0775ae0397144035079adb..54aac08070a269cd5e98cd508a5c2fa2828a04f6 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>ProMod3 — ProMod3 3.1.1 documentation</title>
+ <title>ProMod3 — ProMod3 3.2.0 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>
diff --git a/doc/html/license.html b/doc/html/license.html
index 5631dc84db1225f2ebba1fe37ad759121728e5fe..63f69948957f005fda4e9602f3788ed4fbe5b2f5 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>License — ProMod3 3.1.1 documentation</title>
+ <title>License — ProMod3 3.2.0 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>
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index b7382adf6aa68462f23eb9ad6e1de17c874a6cfc..606df70990b579ae9dc000f6eeca585cc72d47cf 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Handling All Atom Positions — ProMod3 3.1.1 documentation</title>
+ <title>Handling All Atom Positions — ProMod3 3.2.0 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>
@@ -80,8 +80,8 @@ process with all known positions and then update the environment whenever a
new loop is being added.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
</dd>
</dl>
@@ -100,7 +100,7 @@ concatenated one after each other (indexing starts at 0)</p></li>
<dd><p>Sets full environment. Existing data is cleared first.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</p>
</dd>
@@ -128,7 +128,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
<li><p><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</p></li>
<li><p><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</p></li>
<li><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
</ul>
</dd>
@@ -194,7 +194,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -313,7 +313,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -351,7 +351,7 @@ out of bounds or if residues in the two containers are inconsistent
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Set position at that index.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -394,7 +394,7 @@ out of bounds or if residues in the two containers are inconsistent
<dd class="field-odd"><p>Position at given index.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</p>
@@ -494,7 +494,7 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
<dd class="field-odd"><p>Amino acid type of residue at index <em>res_index</em>.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
@@ -744,10 +744,10 @@ atom (N, CA, C, O).</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</p>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -764,8 +764,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</p></li>
+<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -850,7 +850,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dt id="promod3.loop.AminoAcidLookup">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal 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
+(<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and
hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -863,7 +863,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
</dl>
</dd></dl>
@@ -882,7 +882,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
@@ -908,7 +908,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
@@ -933,7 +933,7 @@ atom.</p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
</dd>
@@ -957,7 +957,7 @@ and atom.</p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
</dd>
@@ -979,7 +979,7 @@ hydrogens of <em>aa</em>.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
</dl>
</dd></dl>
@@ -1008,7 +1008,7 @@ hydrogens of <em>aa</em>.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
</dl>
</dd></dl>
@@ -1036,7 +1036,7 @@ hydrogens of <em>aa</em>.</p>
<dd class="field-odd"><p>Amino acid type of the given heavy atom type</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
@@ -1122,7 +1122,7 @@ when residue is peptide bound.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</p>
@@ -1146,7 +1146,7 @@ when residue is N terminal.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</p>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 45a0992aa4b3a2b8aae53a1d73803f1bbcefd28a..f8d64017e6e5f84a550406d6af13dd62434f3ce4 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Representing Loops — ProMod3 3.1.1 documentation</title>
+ <title>Representing Loops — ProMod3 3.2.0 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>
@@ -38,7 +38,7 @@
<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
-converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -142,7 +142,7 @@ code which is not one of the 20 default amino acids or if
<em>residues</em>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<dd class="field-odd"><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><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.</p>
</dd>
@@ -164,7 +164,7 @@ required positions.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p></li>
-<li><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<li><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions are extracted.</p></li>
</ul>
</dd>
@@ -185,14 +185,14 @@ a residue not providing all necessary positions.</p>
<dd class="field-odd"><p>The whole backbone list converted to a density map.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
-<li><p><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </p></li>
+<li><p><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </p></li>
<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
</ul>
@@ -208,7 +208,7 @@ a residue not providing all necessary positions.</p>
<dd class="field-odd"><p>The whole backbone list converted to an OST entity.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -222,8 +222,8 @@ be replaced, otherwise they will be added to the entity.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</p></li>
+<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</p></li>
</ul>
</dd>
</dl>
@@ -235,7 +235,7 @@ be replaced, otherwise they will be added to the entity.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </p></li>
+<li><p><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </p></li>
<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
</ul>
@@ -251,7 +251,7 @@ be replaced, otherwise they will be added to the entity.</p>
<dd class="field-odd"><p></p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p>
@@ -344,7 +344,7 @@ actual fragment at specified <em>index</em></p>
atom for residue at given index.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
@@ -367,7 +367,7 @@ atom for residue at given index.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
/ oxygen atom to this.</p></li>
</ul>
</dd>
@@ -411,7 +411,7 @@ atom for residue at given index.</p>
<dd class="field-odd"><p>Amino acid type of the residue at given index.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
@@ -426,7 +426,7 @@ atom for residue at given index.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -448,12 +448,12 @@ and set the amino acid type according to the given one letter code.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
-<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
-<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
+<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
+<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
</ul>
</dd>
@@ -512,12 +512,12 @@ to the given one letter code.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
-<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
-<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
+<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
+<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
</ul>
</dd>
@@ -571,7 +571,7 @@ depends on the residue following the C stem. The position is only
reconstructed if the residue handle is valid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+<dd class="field-odd"><p><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
element of this backbone list)</p>
</dd>
</dl>
@@ -585,7 +585,7 @@ element of this backbone list)</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
</ul>
</dd>
</dl>
@@ -601,7 +601,7 @@ element of this backbone list)</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start index.</p></li>
<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
</ul>
</dd>
</dl>
@@ -613,7 +613,7 @@ element of this backbone list)</p>
<dd><p>Applies a transformation to all positions of this list.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p>
+<dd class="field-odd"><p><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p>
</dd>
</dl>
</dd></dl>
@@ -630,12 +630,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</p></li>
<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p></li>
<li><p><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</p></li>
</ul>
@@ -652,7 +652,7 @@ positions of the N, CA and C atoms.</p>
list onto CA positions of <em>other</em> backbone list.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 3eaed6a826ff477cf623a1bcbf8fce0b5f0b61f0..0ec568e810b7056234b8ed36fa586907e744b477 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>loop - Loop Handling — ProMod3 3.1.1 documentation</title>
+ <title>loop - Loop Handling — ProMod3 3.2.0 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>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 39b2f7824021f896a9c4195dbc4d42ad7ca5c53c..8564b0a91585176ba7ed6416e434cb0fca56c2d5 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Loading Precomputed Objects — ProMod3 3.1.1 documentation</title>
+ <title>Loading Precomputed Objects — ProMod3 3.2.0 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>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index c3a57978ee3dd7bd2f5779a36f4407a397bf2823..e3fd0c60adc0127c59ee9e992a79bb02fceb47ea 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Generate ost.mol.mm systems — ProMod3 3.1.1 documentation</title>
+ <title>Generate ost.mol.mm systems — ProMod3 3.2.0 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>
@@ -34,8 +34,8 @@
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) and a
specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>).</p>
<p>The example below showcases the creation and use of an MM system:</p>
@@ -259,7 +259,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
MM simulations.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -388,7 +388,7 @@ 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="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
<li><p>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -491,7 +491,7 @@ for details.</p>
<dd class="field-odd"><p>Amino acid type for given <em>ff_aa</em></p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p>
@@ -589,7 +589,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
@@ -603,7 +603,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
@@ -616,7 +616,7 @@ for details.</p>
<code class="sig-name descname">GetMasses</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetMasses" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+<dd class="field-odd"><p>Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -636,7 +636,7 @@ for details.</p>
<code class="sig-name descname">GetCharges</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetCharges" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+<dd class="field-odd"><p>Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -657,7 +657,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Sigma in nm for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -678,7 +678,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -812,7 +812,7 @@ for details.</p>
<dt id="promod3.loop.ForcefieldAminoAcid">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal 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/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
(<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
types. The full list of values is:</p>
@@ -830,7 +830,7 @@ types. The full list of values is:</p>
<dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
are the combination of all bonds and 1,3 pairs of angles and are not stored
separately). Each type of connectivity has it’s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
= <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal 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
@@ -919,7 +919,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -969,7 +969,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1031,7 +1031,7 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1115,8 +1115,8 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1199,7 +1199,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1271,7 +1271,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
<code class="sig-name 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 0d038160140c4e48f9c6fcbfab2bd0860137d21e..0c036f7842f4c5ee804f04fd9136a81a083f15a6 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Structural Data — ProMod3 3.1.1 documentation</title>
+ <title>Structural Data — ProMod3 3.2.0 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>
@@ -117,7 +117,7 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
<dt id="promod3.loop.CoordInfo.shift">
<code class="sig-name descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>Translation from original coordinates that has been applied before storing
-structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal 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/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -255,7 +255,7 @@ database, you might want to consider two things:</p>
<ol class="arabic simple">
<li><p>Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)</p></li>
-<li><p>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+<li><p>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
running in parallel</p></li>
</ol>
<dl class="class">
@@ -382,11 +382,11 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
<dd class="field-odd"><ul class="simple">
<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</p></li>
<li><p><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
as specified by <em>chain_name</em>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</p></li>
<li><p><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
connected stretch of residues are all connected
@@ -509,9 +509,9 @@ full entry at <em>coord_idx</em></p>
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
set, the original sequence at specified location in the
database is used.</p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
superposed onto.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
superposed onto.</p></li>
</ul>
</dd>
@@ -645,7 +645,7 @@ connected stretches of residues in the database.</p>
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Solvent accessibility for each residue of <em>fragment</em> or full entry
at <em>coord_idx</em> in square A as calculated by
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
the database.</p>
</dd>
<dt class="field-even">Return type</dt>
@@ -680,7 +680,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
@@ -710,7 +710,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
@@ -747,7 +747,7 @@ containing that data.</p></li>
probabilities as NULL model.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
@@ -765,7 +765,7 @@ frequencies in entry with <em>coord_idx</em></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</p></li>
<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p></li>
</ul>
@@ -1045,8 +1045,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</p></li>
<li><p><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues of the fragment</p></li>
<li><p><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
<em>extra_bins</em> additional bins surrounding the bin given by
@@ -1244,7 +1244,7 @@ linked to this object.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
</ul>
</dd>
</dl>
@@ -1258,7 +1258,7 @@ linked to this object.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
</ul>
</dd>
</dl>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index b3013277af5c1b5549b8d9f62df8a1919d2834af..cdb56db84434b425bc4dec86202d2c0c57c0a0a0 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Sampling Dihedral Angles — ProMod3 3.1.1 documentation</title>
+ <title>Sampling Dihedral Angles — ProMod3 3.2.0 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>
@@ -124,7 +124,7 @@ acids not matching any of the group definitions.</p>
<dd><p>Extracts backbone torsion angles from the structure and adds them to the appropriate histograms in the sampler.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</p>
+<dd class="field-odd"><p><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</p>
</dd>
</dl>
</dd></dl>
@@ -187,9 +187,9 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -224,9 +224,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -256,9 +256,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</p></li>
</ul>
</dd>
@@ -292,9 +292,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</p></li>
</ul>
</dd>
@@ -328,9 +328,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
@@ -366,9 +366,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
@@ -386,9 +386,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 9e4ac5d084cf1166434dc1e7706723fa4138d6a2..52fbe89c8cf0175e4df0be3faf5572b2c74428ba 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Modelling Algorithms — ProMod3 3.1.1 documentation</title>
+ <title>Modelling Algorithms — ProMod3 3.2.0 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>
@@ -84,7 +84,7 @@ of the solutions</p></li>
indices of the common subsets (rigid blocks) relative
to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
</dd>
@@ -98,7 +98,7 @@ onto <strong>bb_list_two</strong></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
+<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
objects from which the positions are extracted</p></li>
<li><p><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
positions will be extracted</p></li>
@@ -119,9 +119,9 @@ of the solutions</p></li>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
</dd>
@@ -154,7 +154,7 @@ of the solutions</p></li>
indices of the common subsets (rigid blocks) relative
to the input <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code> objects
and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
</dd>
@@ -217,8 +217,8 @@ Weird things are happening otherwise.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</p></li>
-<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</p></li>
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</p></li>
+<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</p></li>
<li><p><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</p></li>
<li><p><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</p></li>
<li><p><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
@@ -301,7 +301,7 @@ want to generate</p></li>
<li><p><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></p></li>
-<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
+<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
fragment search performance.</p></li>
<li><p><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
increases the fragment search performance</p></li>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 2fb66babc2f89ea3f53639d525dde37dbe8d04c6..bb636cf987354b08e0b3e1e1aefcceb68d1a73cb 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Handling Gaps — ProMod3 3.1.1 documentation</title>
+ <title>Handling Gaps — ProMod3 3.2.0 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>
@@ -50,8 +50,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></p></li>
<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seq</span></code></a></p></li>
</ul>
</dd>
@@ -99,7 +99,7 @@ are valid and:</p>
<dd class="field-odd"><p>Chain, the gap is belonging to</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -233,13 +233,13 @@ extend the gap past another gap.</p>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
<code class="sig-name descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
<code class="sig-name descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -282,7 +282,7 @@ False if no new extension possible.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -317,7 +317,7 @@ valid termini.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
<li><p>If -1, all possible non-terminal gaps are returned.</p></li>
<li><p>If >= 0, this restricts the max. gap-length
@@ -364,7 +364,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
<li><p><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for length of gap.</p></li>
<li><p><strong>penalties</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
<li><p>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a>
(i.e. it stops at gaps and termini).</p></li>
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index b0f4a3f384cf9e6df550d58a4a956a296c5bd696..de2b0d1641736d17426af9034b2dddd4c67b6072 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>modelling - Protein Modelling — ProMod3 3.1.1 documentation</title>
+ <title>modelling - Protein Modelling — ProMod3 3.2.0 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>
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 5f918e03198370377d2581288bc971fb02845ee3..89ab41a29956cbc4a906d61a083d476712b298cf 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Handling Loop Candidates — ProMod3 3.1.1 documentation</title>
+ <title>Handling Loop Candidates — ProMod3 3.2.0 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>
@@ -119,8 +119,8 @@ a fragment database.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</p></li>
<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
<em>n_stem</em> and <em>c_stem</em></p></li>
<li><p><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – The fragment database</p></li>
@@ -221,9 +221,9 @@ not depending on a metropolis criterium.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
@@ -261,9 +261,9 @@ candidate. This leads to an increase in number of loops.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match</p></li>
<li><p><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First pivot residue</p></li>
<li><p><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Second pivot residue</p></li>
@@ -331,7 +331,7 @@ anything is raised when calculating the scores.</p>
<code class="sig-name descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal 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/2.2/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
details, <em>prof.null_model</em> is used for weighting).</p>
<p>Note that for profile scores a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
@@ -345,7 +345,7 @@ with this DB).</p>
<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
<li><p><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a></p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</p></li>
<li><p><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</p></li>
</ul>
</dd>
@@ -373,8 +373,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index 2c5c328c7c86d8d86ff0a7fced103c4cdce1947c..eaed142d036c9382c1daaba0f9f6769b56a265d7 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Fitting Loops Into Gaps — ProMod3 3.1.1 documentation</title>
+ <title>Fitting Loops Into Gaps — ProMod3 3.2.0 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>
@@ -73,11 +73,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
and phi angle (-1.0472) to evaluate the first angle.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
psi angle (-0.7854) to evaluate the last angle.</p></li>
@@ -110,8 +110,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</p></li>
<li><p><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</p></li>
<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
be closed has RMSD below the given <em>c_stem</em></p></li>
@@ -288,7 +288,7 @@ size or sequence as the initial one.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -306,7 +306,7 @@ size or sequence as the initial one.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -325,7 +325,7 @@ doesn’t do anything if specified residue is a glycine</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -343,7 +343,7 @@ doesn’t do anything if specified residue is a glycine</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -361,7 +361,7 @@ doesn’t do anything if specified residue is a glycine</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 9905519bfada6b68f7a73066a1f215f45ff3591a..7ecf5c3eda588565d42bc15174a31539d2ad37bf 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Model Checking — ProMod3 3.1.1 documentation</title>
+ <title>Model Checking — ProMod3 3.2.0 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>
@@ -47,15 +47,15 @@ A ring is only added if all ring-atoms exist or if it is a proline and
three of the atoms exist (center and radii are estimated then).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</p>
+<dd class="field-odd"><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
tuple with:
-center (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
radius (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</p>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</p>
</dd>
</dl>
</dd></dl>
@@ -68,11 +68,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
</dd>
</dl>
@@ -87,7 +87,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -108,7 +108,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<dd class="field-odd"><ul class="simple">
<li><p><strong>candidates</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
Offending candidates are removed from this list.</p></li>
-<li><p><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</p></li>
+<li><p><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</p></li>
<li><p><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</p></li>
<li><p><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
must have as many elements as <em>candidates</em>.</p></li>
@@ -169,7 +169,7 @@ with <code class="docutils literal notranslate"><span class="pre">MolProbity</sp
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></p>
</dd>
<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
</dd>
</dl>
@@ -182,7 +182,7 @@ executable is not found.</p>
<p>See <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal notranslate"><span class="pre">RunMolProbity()</span></code></a> for details.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</p>
+<dd class="field-odd"><p><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</p>
</dd>
</dl>
</dd></dl>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index f33b8de0ad23d5621a34f0dd3bae0adf0f4ec7ce..4a9cf7bbedf72da08008e9c0821ca753f4f9dd7b 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Generating Loops De Novo — ProMod3 3.1.1 documentation</title>
+ <title>Generating Loops De Novo — ProMod3 3.2.0 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>
@@ -448,9 +448,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</p></li>
<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
@@ -490,9 +490,9 @@ dihedral angles as it is the case for the <a class="reference internal" href="#p
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</p></li>
</ul>
</dd>
@@ -524,9 +524,9 @@ solutions. The KICCloser simply picks the first one.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p></li>
<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</p></li>
</ul>
@@ -557,7 +557,7 @@ adapt.</p></li>
superposing the c_stem with the desired positions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<dd class="field-odd"><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p>
</dd>
</dl>
@@ -588,7 +588,7 @@ here.</p></li>
superposing the n_stem with the desired positions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<dd class="field-odd"><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p>
</dd>
</dl>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index c513f54c9fa73d280c0c92df96811a6d15ea6434..59e416f6890acd8b8e90a74b7c38d802c2d44d7a 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Modelling Pipeline — ProMod3 3.1.1 documentation</title>
+ <title>Modelling Pipeline — ProMod3 3.2.0 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>
@@ -107,7 +107,7 @@ and <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqre
chain follows afterwards.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -129,11 +129,11 @@ Gaps of different chains are appended one after another.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
<code class="sig-name descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -141,14 +141,14 @@ of the target protein.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
<code class="sig-name descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please note, that this
attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have
to fill it manually or even better by the convenient function
<a class="reference internal" href="#promod3.modelling.SetSequenceProfiles" title="promod3.modelling.SetSequenceProfiles"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetSequenceProfiles()</span></code></a>, to ensure consistency with the seqres.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -305,7 +305,7 @@ alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
<p>Each alignment handle must contain exactly two sequences and the second
sequence is considered the template sequence, which must have a
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
<p>Before extracting the coordinates, the alignments are pre-processed
according to <em>aln_preprocessing</em>.</p>
<p>This is a basic protein core modelling algorithm that copies backbone
@@ -333,7 +333,7 @@ as information about insertions and deletions in the gaps list.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
list of alignment handles for raw model with multiple chains.</p></li>
<li><p><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
searches for ligands in all OST handles of the views
@@ -346,7 +346,7 @@ in SMTL). All ligands are added to a new chain named
(chains are consecutively named according to
characters in
‘ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz’).
-If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>,
+If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>,
<em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>.
If <em>aln</em> is of type <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentList</span></code>,
<em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
@@ -372,7 +372,7 @@ to False.</p></li>
<li><p>the second sequence does not have an attached structure</p></li>
<li><p>the residues of the template structure do not match with the
alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
template sequence (but not for the target))</p></li>
<li><p>the target sequence has a non-zero offset (cannot be honored as
the resulting model will always start its residue numbering at 1)</p></li>
@@ -412,12 +412,12 @@ return an incomplete model.</p>
<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
alignment.</p></li>
<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
with the optional force fields in <cite>extra_force_fields</cite>.</p></li>
-<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
+<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
@@ -438,7 +438,7 @@ limited. Termini of length 1 won’t be modelled.</p></li>
<dd class="field-even"><p>Delivers the model as an OST entity.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -596,7 +596,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
<li><p><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</p></li>
<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue of the copied stretch</p></li>
<li><p><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
they’re copied over</p></li>
</ul>
</dd>
@@ -623,7 +623,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</p></li>
-<li><p><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</p></li>
+<li><p><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -764,7 +764,7 @@ 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
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.0.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</p></li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</p></li>
<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>. Also works in combination
with <cite>use_scoring_extender</cite>. This allows the gap
@@ -1109,7 +1109,7 @@ one is loaded if None.</p></li>
<dt id="promod3.modelling.MinimizeModelEnergy">
<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">max_iterations=12</em>, <em class="sig-param">max_iter_sd=20</em>, <em class="sig-param">max_iter_lbfgs=10</em>, <em class="sig-param">use_amber_ff=False</em>, <em class="sig-param">extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.0.0)"><code class="xref py py-mod docutils literal 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/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
<li><p>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</p></li>
@@ -1135,7 +1135,7 @@ minimization is aborted. This issue is logged and added as a major issue to
<li><p><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</p></li>
<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
-<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
</ul>
</dd>
@@ -1143,7 +1143,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<dd class="field-even"><p>The model including all oxygens as used in the minimizer.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -1214,8 +1214,8 @@ set to True, if the problem affects backbone atoms.</p></li>
<dd><p>List of residues affected by issue (or empty list if global issue).</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -1282,17 +1282,17 @@ attribute yet, it is added.</p>
<p>Columns that only contain gaps (‘-‘) are removed. If no such column can be
identified, the input alignment gets returned. A new alignment gets
constructed otherwise. The sequences of the new alignment retain name, offset
-and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
+and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
sequences.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The processed alignment</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -1333,16 +1333,16 @@ ATOMSEQ: ABCDEFGHI...
<p>given a <em>min_terminal_anchor_size</em>>2. If no shift can be performed, the
input alignment gets returned. A new alignment gets constructed otherwise.
The sequences of the new alignment retain name, offset and the potentially
-attached <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
+attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The processed alignment</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 819560fe1d078cf746d0514356c01d2229018e0d..cf1a4a3d2e32e1bf2da14921995031cdaff486f6 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Sidechain Reconstruction — ProMod3 3.1.1 documentation</title>
+ <title>Sidechain Reconstruction — ProMod3 3.2.0 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>
@@ -38,7 +38,7 @@
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
<li><p>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p></li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p></li>
<li><p>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
and used to reconstruct sidechains of single loops</p></li>
</ul>
@@ -91,7 +91,7 @@ and used to reconstruct sidechains of single loops</p></li>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
reconstruction gets directly applied on the structure itself.</p></li>
<li><p><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
containing all required atoms) should be kept rigid
@@ -195,7 +195,7 @@ environment before calling this!</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</p></li>
<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop.</p></li>
<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</p></li>
<li><p><strong>start_resnum_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Starts of loops.</p></li>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 2edbb8c2019816293136aa6a0b53aa7aaa558d89..18ab416e6de12e24f5323a72ac410ca1e282bbd4 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index dcdb306338c2e39a7d64ae4c39f6f40f35d802d9..84ec5377cf7cefde90c2f61eecd82ab2517e53a8 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Using Binary Files In ProMod3 — ProMod3 3.1.1 documentation</title>
+ <title>Using Binary Files In ProMod3 — ProMod3 3.2.0 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>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 3e99095b3f8111ae5d8dcb0e5eaddbcbdd7ba74a..6ddff087213a19145e54caa4d81778254493b245 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Python Module Index — ProMod3 3.1.1 documentation</title>
+ <title>Python Module Index — ProMod3 3.2.0 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>
diff --git a/doc/html/references.html b/doc/html/references.html
index 2eed9037df971bd421ad3653f05f66c7d6858777..ba8c49687f2c8cd175676f134fe85c2cf46afe25 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>References — ProMod3 3.1.1 documentation</title>
+ <title>References — ProMod3 3.2.0 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>
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 7c390c0801c1dd9c0ef412b940b39650fc2a8d7d..7724c7078731bdeee33cc4350fadb20f7697559d 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>All Atom Scorers — ProMod3 3.1.1 documentation</title>
+ <title>All Atom Scorers — ProMod3 3.2.0 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>
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 32a0e128bc841d2bdaba2551d06a9a962ec1f7fe..145b8ca99c90a973d9ebe0c83a959427d2c4dc14 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Backbone Score Environment — ProMod3 3.1.1 documentation</title>
+ <title>Backbone Score Environment — ProMod3 3.2.0 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>
@@ -58,8 +58,8 @@ at some point you want to restore the original state. The
task.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
</dd>
</dl>
@@ -91,7 +91,7 @@ attached</p>
structural data was already set, all the existing data gets cleared first.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</p>
</dd>
@@ -113,7 +113,7 @@ positions.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
</ul>
</dd>
@@ -241,7 +241,7 @@ providing lists of integers.</p>
<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -336,7 +336,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</p></li>
<li><p><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
or CB atoms</p></li>
</ul>
@@ -347,7 +347,7 @@ or CB atoms</p></li>
<code class="sig-name descname">AddStructuralInfo</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AddStructuralInfo" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached.</p>
</dd>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index c04f69dbbc0b50c22759b1fa7265bc8777d4d366..aebb68b2beed7d10b16c167114ff95fa9d2da67a 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Backbone Scorers — ProMod3 3.1.1 documentation</title>
+ <title>Backbone Scorers — ProMod3 3.2.0 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>
@@ -336,7 +336,7 @@ called for every type of amino acids and for every <em>count</em> <= <em>max_
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</p></li>
<li><p><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</p></li>
<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
@@ -455,8 +455,8 @@ SetEnergy(aa2, aa1, bin, energy).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
-<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
+<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
+<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
<li><p><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
@@ -614,8 +614,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
-<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
+<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
+<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
<li><p><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
<li><p><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</p></li>
<li><p><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</p></li>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index 0c77470050da4a5292176740595012f205b660c4..f123fcfb603869474f368d4c16c89441124db4dd 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>scoring - Loop Scoring — ProMod3 3.1.1 documentation</title>
+ <title>scoring - Loop Scoring — ProMod3 3.2.0 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>
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index ddf537dcee086399955e71e2001852608a04287c..c08269ec5d9a8b8d2a6543e912bb67fdb1fdde09 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Other Scoring Functions — ProMod3 3.1.1 documentation</title>
+ <title>Other Scoring Functions — ProMod3 3.2.0 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>
diff --git a/doc/html/search.html b/doc/html/search.html
index ab70ca2d779af8b23aa3a431e35f32b4f9cfe350..f7798e62a96be319378692b7be00baf0e62abe9a 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Search — ProMod3 3.1.1 documentation</title>
+ <title>Search — ProMod3 3.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 4448039b7fd9119e7893a37b8082624151d7344d..3000dc92e1c757f089c9d49457a0eb0d1ae50705 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:37,categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[8,14,15,17,18,20,54],cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,6,7,8,11,13,14,15,16,17,18,19,20,21,22,26,27,33,35,47,49,53],codetest:[4,8],coil:[24,28],collect:[11,14,21,28,40],collis:49,column:[26,28,35],combin:[20,25,26,27,28,31,34,35,38,39,41,44,49,51],come:[1,3,4,8,11,13,35,36,42,46,51],command:[0,1,7,8,11,12,16,18,54],commandlin:13,comment:[16,20],commerci:[8,20],commit:[3,8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib:50,compar:[3,8,22,23,26,31,32,51],comparison:[35,38,51],compat:[2,3,16,25,37],compensatori:22,compil:[1,2,3,4,8,14,16,18,20,37,54],complain:1,complaint:16,complet:[14,16,22,25,32,34,35,36,51],complex:[8,16,36,44,49,52],compli:20,complianc:20,complib_dir_contain:[5,7],complib_dir_localhost:[5,7],compon:[5,7,10,15,26,33,41,50],compound:[3,15,50],compoundlib:[5,50],compress:[11,26],comput:[3,8,19,20,31,33,38,39,41],concaten:21,concept:8,concern:8,condit:[8,20,27],conf:[2,8],confid:[26,41],config:[4,8],config_head:4,configur:[2,8,10,16,20,31,47],conflict:16,conform:[26,32,34,38,46,51],connect:[4,5,7,10,16,21,25,26,31],connectivi:5,conop:[5,21,22,25,27,41,49,50],conquer:8,consecut:[26,27,35,41],consequenti:20,conserv:[18,29],consid:[0,4,8,10,13,14,16,21,22,26,27,28,31,32,34,35,36,39,40,41,44,47,49,50,51,53],consider_all_nod:10,consider_hydrogen:49,consider_ligand:36,consist:[3,8,20,21,25,28,29,31,32,34,35,36,37,40,44,49,51],conspicu:20,constant:[3,25,32,39,41,52],constitut:20,constraint:[13,26,32,34,40],constraintfunct:40,constru:20,construct:[0,3,9,21,22,26,28,29,34,35,37,42,43,45,49,50,51],constructatompo:9,constructbackboneframeresidu:[47,50],constructcbetapo:9,constructcterminaloxygen:9,constructetd:10,constructframeresidu:50,constructframeresidueheurist:50,constructfrmrotamergroup:[47,50],constructfrmrotamerheurist:50,constructor:[21,25,28,29,32,34,37,40,41,47,49,54],constructrrmrotamergroup:50,constructrrmrotamerheurist:50,constructsidechainframeresidu:50,contact:[40,53],contactfunct:40,contain:[0,1,2,3,4,5,7,8,9,11,13,16,18,19,20,21,22,24,25,26,27,28,31,34,35,36,39,40,41,42,44,45,47,49,50,51,54],content:[8,12,17,20,23,26,42,47,54],contigu:[25,36,37],continu:[1,21,29,32,47],contract:20,contrast:45,contribut:[4,10,16,17,19,20,54],contributor:20,contributori:20,control:[0,3,8,10,20,31,34,36,40,49,50,51,52],conveni:[1,8,18,28,31,34,35,42,49,50,51],convent:[1,49],converg:[28,31,32,34],convers:[20,37],convert:[4,5,22,25,26,27,35,37,39,41,51,52],convert_module_data:4,convertbasetyp:37,cooler:[3,30,31],coolerbas:34,cooling_factor:[10,34],coord:[26,31],coord_idx:26,coordin:[3,9,26,28,31,32,34,35,38,39,47],coordinfo:26,cope:16,copi:[2,3,4,8,16,18,20,21,22,28,29,31,34,35,40],copyright:20,copyright_cmak:20,core:[0,8,9,10,11,13,14,19,35,37,46,53,54],correct:[5,25,50],correctli:35,correspond:[0,10,16,21,22,25,26,27,28,31,37,49,50,51],corrupt:[21,40],could:[1,4,5,8,13,16,25,26,35],couldn:35,count:[14,28,29,34,35,39,41],countenclosedgap:29,countenclosedinsert:29,counter:[28,34],counterclaim:20,counterpart:[31,41,50],coupl:[1,8,16,35],cours:8,coutsia:38,coutsias2005:[32,38],coval:49,cover:[0,1,8,12,13,14,21,25,28,30,34,35],coverag:[0,3,35],cparticl:49,cpp:4,cpr:[49,51],cpu:[18,25,35],cpu_platform_support:25,crambin:[26,31,34],crash:47,creat:[2,4,5,7,8,9,10,13,16,17,21,22,23,26,27,28,30,34,35,39,41,47,48,49,50,51],createalign:[31,35],createemptyview:28,createentityfromview:[28,36,47],createfromfrmlist:[46,47],createfromrrmlist:46,createfullview:[30,31,35],createscwrl3particl:49,createscwrl4particl:49,createsequ:[26,31,35],createvinaparticl:49,creation:[25,32,49],creator:[25,32],criteria:36,criterion:[10,34],criterium:31,croak:16,cross:[20,28],crucial:8,crude:[0,35],cryst:38,cterminalclos:34,cumul:50,current:[2,4,5,8,10,14,16,21,22,25,26,31,34,35,37,40,41,42,49,50,52],custom:[8,26,34,35,36,37,48,49],customari:20,cutoff:[24,25,31,32,36,39,41],cycl:29,cyclic:[31,32,38],cyd:[49,51],cyh:[49,51],cys_hb3:21,cys_sg:21,cystein:[25,36,44,47,49],d_bin:41,dai:11,damag:20,dampen:25,danc:38,dare:4,dat:[26,37],data1:4,data2:4,data:[0,1,3,4,8,16,17,21,23,24,25,28,29,30,31,32,34,35,36,40,42,47,49,54],data_:37,data_gener:[3,37,48],data_to_stor:26,data_typ:26,databas:[0,9,23,24,28,31,35],databs:26,datatyp:26,date:[5,7,16,20],davi:38,davis2006:[22,38],dbg:8,dcmake_install_prefix:2,deactiv:10,dead:[10,38],deal:[35,36],debug:[8,10,21],decent:15,decid:[3,8,32,50],decis:27,declar:[4,8,16],decod:13,decompos:[3,10],decomposit:[10,28,46],decreas:34,dedic:[4,8,16],dee:10,deep:[22,35],def:[1,8,21,35],def_angl:21,defend:20,defin:[1,4,8,9,13,14,15,20,21,22,23,24,25,28,29,31,32,34,35,36,37,39,40,41,44,49,50,51],definem:8,definit:[8,20,26,27,31,41,49],degre:[22,26,27],delet:[0,2,8,22,35,49],deletegapcol:35,deliber:20,deliv:[1,26,34,35],delta_scor:34,demand:35,demonstr:26,denovoclos:34,densiti:[22,32,38],dep1:4,dep2:4,dep:4,depend:[0,3,4,8,10,13,18,22,25,26,27,28,31,35,36,37,38,39,40,41,47,48,49,54],dependency1:4,dependency2:4,depends_on:4,depth:[26,38],deriv:[1,20,26,38,43,44],descend:35,descent:[31,32,38],describ:[0,4,7,8,10,11,17,20,21,22,26,28,29,30,32,33,37,39,41,44,47,48,49,50,51,54],descript:[0,5,13,16,20,34,35,51],descriptor:[26,28],descsrib:10,design:[1,3,19,20],desir:[9,18,25,26,31,32,34,35,39,40,41],despit:3,detail:[0,3,9,13,16,20,25,26,27,31,33,34,35,39,41,48,49,51],detect:[0,11,28,30,38,44],determin:[8,11,20,25,26,31,34,40,41],determinist:28,deuterium:[35,50],develop:[1,3,8,16,19,53],deviat:[22,33,34,51],devot:12,dict:[4,28,31,33,34,39,41],dictionari:[4,5,13,15,33,38],did:[8,26,31,35],didn:[7,28],didnt:5,diff:10,differ:[1,2,4,7,8,10,15,16,20,21,26,28,29,31,35,39,41,47,49,51],differenti:49,dihedr:[7,9,18,22,23,25,26,32,34,35,41,50,51,54],dihedral_angl:22,dihedral_bin:41,dihedral_idx:51,dihedral_pair:27,dihedralconfigur:51,dill:38,dimens:27,dimension:38,dir:[4,8,18],direct:[8,20,22,24,26,41,49,50],directli:[8,10,18,26,31,35,36,40,44,49,51,53],directori:[1,2,4,5,7,8,17,26,48],dirti:1,dirtyccdclos:34,disabl:[1,16,35],disable_doctest:2,disable_document:2,disable_linkcheck:2,discard:26,disclaim:20,discocontain:40,disconnect:3,discret:[28,39,41],discuss:[20,26],disk:[8,25,28,39,41,51],displai:[7,11,13,14,20],displaystyl:10,dissimilar:28,dist:41,dist_bin:41,dist_bin_s:26,distanc:[7,9,22,26,28,31,35,36,39,40,41,43,49],distance_thresh:28,distant:40,distinct:[21,28,36,51],distinguish:[3,23,25,37,39,41,51],distribut:[1,8,20,25,26,27,34,37,39,41,48,51],disulfid:[0,25,32,36,43,47,49,51,54],disulfid_bridg:[25,36],disulfid_score_thresh:36,disulfidscor:[36,44],dive:[16,35],diverg:8,divers:[26,28],dng:18,do_it:[39,41],doc:[2,4,8,16,20],dock:38,docker:[3,6,7,54],dockerfil:[5,7],docstr:13,doctest:[2,8,16],document:[1,2,7,16,20,26,53],doe:[1,3,4,8,9,10,11,13,15,16,20,22,26,30,31,34,35,37,40,48],doesn:[8,16,29,32,34,35,51],doesnt:51,doexternalscor:[39,41],doing:[1,5,16,28],dointernalscor:[39,41],domain:28,domin:10,don:[2,10,20,31,35,50],done:[1,8,11,13,16,23,25,27,31,34,35,37],donor:[41,49,50],donorm:[39,41],dont:[0,34],dont_write_bytecod:1,dost_root:2,doubl:28,doubt:13,down:[13,22,26,28,34],download:5,dpm3_runtime_profiling_level:14,draw:[22,27,34],drawback:8,drawn:[27,34],drawphigivenpsi:27,drawpsigivenphi:27,drop:[3,8],dssp:[3,26,41],dssp_state:41,due:[0,26,31,32,35,44],dump:[28,51],dunbrack:[3,38,48],duplic:6,dure:[1,3,21,32,35,37,45,51],dynam:51,dynamicspatialorgan:3,e_cut:10,e_thresh:[10,35],e_tresh:10,each:[0,7,8,10,13,14,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,41],earli:3,earlier:2,easi:8,easier:[1,8,20],easili:[4,16,35],echo:8,edg:[10,28],edge_idx:10,editor:1,editori:20,editxc:28,educ:8,effect:[4,8,10,25,36,44],effici:[21,28,34,38,42],egg:26,eigen3_include_dir:2,eigen:[2,3],either:[0,7,8,13,16,18,20,21,22,27,29,31,32,34,35,36,37,39,40,41,45,49,51],elabor:[8,20],electron:20,electrostat:[25,32],element:[1,10,21,22,26,28,31,33,37,40,44,50],elimin:[10,38],els:[8,16,36,37],emerg:1,empir:[43,44],emploi:16,empti:[8,11,13,22,26,28,31,35,49],enabl:[1,2,3,11,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,52],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,28,33,35,42,47],entityhandl:[13,21,22,26,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,31,32,33,36,41,47,50],entrypoint:5,enumer:[8,10,21,25,26,28,31,35,40,47,49,50,51],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39,41,42,54],epsilon:[10,25,36,52],equal:[28,34,39,41,44,50],equidist:51,equip:5,equival:[28,35,39,41],error:[0,11,13,14,26,32,35,37],especi:28,estim:[10,28,33,34,35,38,41,44,49,50,51],etc:[1,3,8,16,22,26,31,40],evalu:[4,8,32,35,39,40,41,46,47,49,51,54],evaluategromacsposrul:9,even:[2,8,10,20,22,25,29,35],event:[20,28],eventu:13,ever:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,51,52],everyth:[1,2,3,7,8,12,13,16,32,35,36,37,39,54],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,49],exampl:[0,1,2,3,8,11,13,16,17,18,20,21,23,25,26,27,28,30,32,34,35,36,42,47,48,49],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35],exclud:[8,20,26],exclus:[1,8,20,25],execut:[0,2,3,4,7,8,16,18,20,26,33,35],exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,31,32,33,34,35,37,39,40,41,48,49,51],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:[10,34],expect:[1,3,7,21,25,26,35,36,40,44,50,52],expens:26,experiment:35,explain:[1,8],explan:8,explicit:2,explicitli:20,explor:[5,38],exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28,30,31,35,41,46],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,29,35],extension_penalti:29,extent:26,extern:[3,4,5,8,34],external_script:[3,8],extra:[2,3,8,16,22,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:[22,28],eye:1,f_i:26,f_idx:40,f_vinaparticl:49,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,35,51],fall:32,fallback:51,fals:[1,8,10,11,13,22,25,26,29,31,34,35,36,44,47,49,50],fantast:8,far:[31,35],fast:[0,9,18,19,21,25,26,27,37,39,40,41,51],fasta:[0,13,30,35],faster:[10,25,26,32,33,40],fastest:[32,35],favor:33,favourit:1,featur:[16,17,23,28,31,35,37,38,53],fed:[4,16],fedora:8,fee:20,feed:[4,21,31],feel:[8,16],fellow:8,fetch:[13,16,18,28],few:[2,8,16,25,37,42],ff_aa:25,ff_aa_on:25,ff_aa_two:25,ff_ala:25,ff_arg:25,ff_asn:25,ff_asp:25,ff_cy:25,ff_cys2:25,ff_gln:25,ff_glu:25,ff_gly:25,ff_hisd:25,ff_hise:25,ff_ile:25,ff_leu:25,ff_lookup:[25,32,35],ff_lookup_charmm:37,ff_ly:25,ff_met:25,ff_phe:25,ff_pro:25,ff_ser:25,ff_thr:25,ff_trp:25,ff_tyr:25,ff_val:25,ff_xxx:25,fiddl:30,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,7,8,12,13,15,16,17,18,20,25,26,27,28,33,39,41,48,51],filecheck:16,fileexist:11,fileextens:11,filegzip:11,filenam:[0,8,11,13,25,26,27,28,37,39,41,48,51],filenotfound:33,fill:[4,8,13,16,23,26,29,30,31,33,35],fillfromdatabas:[31,35],fillfrommontecarlosampl:[31,35],fillloopsbydatabas:35,fillloopsbymontecarlo:35,filo:40,filtercandid:33,filtercandidateswithsc:33,final_model:[30,35],find:[3,4,7,8,10,16,21,23,28,31,32,35,44,46,48,51,53],findatom:28,findchain:42,findeigen3:20,finder:30,findmotif:28,findwithin:[8,28],fine:8,finish:52,fire:[1,7],first:[0,1,3,8,10,13,16,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,20,22,26,30,31,34,54],fix:[3,8,11,16,25,32,35,36,37,39,41],fix_cterm:32,fix_nterm:32,fix_surrounding_hydrogen:25,flag1:4,flag2:4,flag:[0,2,4,8,10,11,13,22,26,28,35,36,49,50],flanking_rot_angle_on:22,flanking_rot_angle_two:22,fletch:[26,47],fletcher:35,flexibl:[0,19,36,44,47,49,50,52],flip:51,flood:26,fluorin:49,flush:[1,16],fold:38,folder:[2,4,8,16,18,37],follow:[0,1,2,4,5,7,8,10,11,16,18,20,22,23,25,26,28,29,30,31,35,36,37,39,41,47,49,50,51],fontsiz:27,forbidden:8,forc:[25,32,35],force_const:[25,32],forcefield:[23,32,35],forcefieldaminoacid:25,forcefieldbondinfo:25,forcefieldconnect:25,forcefieldharmonicangleinfo:25,forcefieldharmonicimproperinfo:25,forcefieldljpairinfo:25,forcefieldlookup:[25,32,35,37],forcefieldperiodicdihedralinfo:25,forcefieldureybradleyangleinfo:25,forg:16,forget:[1,8],form:[14,20,24,25,26,30,35,40,51],formal:[31,32,49,51],format:[0,5,13,20,26,48],formula:33,forward:16,found:[1,3,4,8,11,13,16,19,21,23,26,28,31,32,33,34,35,36,44,46,49,51],foundat:1,four:[9,34],frac:10,fraction:[26,28,32,34],frag_db:[23,26,31,37],frag_length:[23,26,28],frag_map:26,frag_po:[23,26,28],frag_residu:[23,26],frag_seq:[23,26],frag_siz:26,fragdb:[23,24,26,31,35,37],fragger:[13,23,26,28,34,35],fragger_handl:[13,35],fragger_map:26,fraggerhandl:[0,13,26,28,35],fraggermap:[26,28],fragment:[0,3,9,13,22,23,24,28,31,32,34,35,38,47],fragment_db:35,fragment_handl:28,fragment_info:26,fragment_length:[26,28],fragmentinfo:[26,31],fragments_per_posit:28,fragmentsampl:34,frame:[3,16,35,36,46,47,49,50,52,54],frame_energi:49,frame_residu:[45,47],frameresidu:[45,49,50],framework:[8,19,38],free:[0,8,20,35,49,51],frequenc:[26,34],frm:36,frmrotam:[44,49,50,52],frmrotamergroup:[44,46,49,50],from:[0,1,2,3,4,5,6,7,8,9,10,11,13,16,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,46,47,49,50,51],fromhhm:26,fromhoriz:26,fromresidu:51,front:[1,11,16],fstream:37,fudg:25,fulfil:[26,51],full:[0,1,3,8,10,21,25,26,28,29,30,31,34,35,36,47,49,50],full_queri:28,full_seq:[29,31],fullgapextend:[29,35],fulli:[8,16,21,22,26,29,30,36],function_typ:40,functions_specific_to_your_act:8,fundament:37,funni:[2,8],further:[10,28,29,35,36,37,50],furthermor:[37,50],futur:[3,25,26],gamma:[40,41,44],gamma_bin:41,gap:[0,3,9,18,24,25,30,31,33,35,36,54],gapextend:[29,35],gapfre:26,gapless:[0,13],gather:[4,12,16,26,28,47,49,51],gauc:51,gauch:51,gauche_minu:51,gauche_plu:51,gaussian1:49,gaussian2:49,gciiipgatcpgdyan:[31,35],gener:[0,1,2,3,5,7,8,10,13,14,16,18,19,20,23,24,26,27,28,30,31,32,33,35,36,37,39,40,41,48,49,50,51,54],generatedenovotrajectori:28,generatestructureprofil:26,geom:[21,22,25,26,28,32,35,44,49],geometr:[3,9,23,28,31,38,44],geometri:[12,23,26,31,54],geoom:43,get:[0,1,2,8,16,19,21,22,23,25,26,28,30,31,32,33,34,35,36,37,39,40,41,44,47,48,51,52,54],getaa:[21,22,25],getaaa:21,getaah:21,getactivesubrotam:49,getallatomposit:[21,32,36],getallatomscoringkei:31,getallatomweight:31,getanchoratomindex:21,getangl:47,getangularbins:26,getatomcount:8,getatomnam:21,getatomnameamb:21,getatomnamecharmm:21,getaveragescor:31,getbackbonelist:[23,26],getbackbonescoringkei:31,getbackboneweight:31,getbins:27,getbinsperdimens:27,getbound:22,getc:22,getca:22,getcb:22,getchain:29,getchainindex:29,getchainnam:29,getchains:8,getcharg:25,getclust:31,getclusteredcandid:31,getcollisiondist:49,getconfid:26,getcoordidx:26,getcoordinfo:26,getcpuplatformsupport:25,getcreationd:5,getdefault:[25,32,35],getdefaultlib:5,getdihedralangl:26,getdihedralconfigur:51,getdistbins:26,getdisulfidbridg:25,getdisulfidconnect:25,getdsspstat:26,getel:21,getenviron:21,getenvsetdata:8,getepsilon:25,getfirstindex:21,getforcefieldaminoacid:25,getfragmentinfo:[26,31],getframeenergi:49,getfudgelj:25,getfudgeqq:25,geth1index:21,geth2index:21,geth3index:21,getheavyindex:25,gethistogramindex:[22,27],gethistogram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Actions","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3\u2019s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"xref py py-func docutils literal notranslate\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For 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25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:37,categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[3,8,14,15,17,18,20,54],cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,6,7,8,11,13,14,15,16,17,18,19,20,21,22,26,27,33,35,47,49,53],codetest:[4,8],coil:[24,28],collect:[11,14,21,28,40],collis:49,column:[26,28,35],combin:[20,25,26,27,28,31,34,35,38,39,41,44,49,51],come:[1,3,4,8,11,13,35,36,42,46,51],command:[0,1,7,8,11,12,16,18,54],commandlin:13,comment:[16,20],commerci:[8,20],commit:[3,8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib:50,compar:[3,8,22,23,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:20,increas:[0,10,28,31,32,35,50],increment:28,incur:20,indemn:20,indemnifi:20,independ:[0,3,25,36,48],index:[8,10,21,22,25,26,27,28,29,31,32,33,34,35,39,40,41,45,49,50,51],index_four:25,index_on:25,index_thre:25,index_two:25,indic:[8,10,11,13,20,21,22,25,26,27,28,29,31,32,35,36,40,44,47,49],indirect:20,individu:[7,20,39,41],inf:[10,32,35],infin:32,infinit:32,influenc:[13,28,40,50],info:[26,31,35,40],inform:[0,5,7,8,13,16,20,22,23,26,28,29,31,34,35,38,40,41,42,53],infring:20,inherit:[1,39,40,41,46],init:16,init_bb_list:34,init_frag:34,initi:[3,10,21,22,26,28,31,32,34,35,36,39,40,41,46,49,50,51],initial_bb:31,initial_epsilon:[10,52],initialis:1,inlin:37,inner:14,input:[0,1,3,13,16,18,25,26,27,28,32,34,35,36,39,40,41,44,48,52],insert:[21,22,29,31,34,35,52],insertinto:[21,22,31],insertloop:[29,35],insertloopcleargap:[29,31,35],insid:[1,4],insight:16,instal:[8,16,37,54],instanc:[3,8,13,24,25,37,53],instead:[0,1,2,3,4,8,11,26,28,29,31,34,35,50],institut:20,instruct:2,int16_t:37,int32_t:37,int_32_t:37,integ:[8,13,21,40],integr:[4,8,38],intend:[1,8,34,49],intent:26,intention:20,interact:[3,8,25,32,39,40,41,43,44,45,49],intercept:[39,41],interest:[1,10,25,26,34,37,49,51],interfac:[0,3,4,8,20,50],intermedi:8,intern:[0,1,3,4,5,8,16,21,24,25,26,27,28,31,32,34,35,36,37,38,39,40,41,46,49,50,52],internal_e_prefac:50,internal_e_prefactor:49,internal_energi:49,internet:8,interpl:51,interpol:[40,51],interpret:[8,11],intervent:8,intrins:2,introduc:[1,3,4,8,16,32,35],introduct:[12,17],invalid:[8,21,25,26,29,32,35,36,39,40,41,45,49,51],invalid_vinaparticl:49,invok:[2,4,8,15,16],involv:[16,30,44,49],iodin:49,ios:37,iostream:37,ipython:7,irrevoc:20,is_c_ter:[25,36],is_cter:25,is_hbond_acceptor:50,is_hbond_donor:50,is_major:35,is_n_ter:[25,36],is_nter:25,isallatomscoringsetup:[31,35],isallset:21,isanyset:21,isbackbonescoringsetup:35,isctermin:29,isempti:31,isen:14,isntermin:29,isoleucin:49,isset:21,issimilar:51,issourc:37,issu:[3,12,16,17,20,32,35,37],istermin:29,isvalid:47,item:[1,8,16,21,22,25,26,35,40],iter:[10,26,27,28,31,32,34,35,49],its:[0,1,2,4,5,8,11,16,20,25,26,30,31,33,34,35,41,48,49,50,51],itself:[3,4,8,16,26,34,36,37,39,41],januari:20,job:[8,26,34,35],johner:38,join:[8,21,23,26,31,32,34,36],jone:[38,49],jones1999:[26,38],journal:38,json:[0,13],jupyt:7,just:[1,2,8,13,15,16,23,25,26,28,29,31,35,50],kabsch1983:[26,38],kabsch:38,keep:[0,1,2,4,5,8,13,16,28,30,35,47],keep_non_converg:31,keep_sidechain:[8,36],kei:[0,13,26,28,31,34,35,39,40,41],kept:[8,16,25,31,32,36,45,49],kernel:[7,38],keyword:27,kic:[30,31,34],kicclos:34,kick:13,kill_electrostat:25,kind:[1,8,20],kinemat:32,know:[2,51],knowledg:51,known:[4,11,21,40,50],krivov2009:[10,38,47,49],krivov:38,kwarg:1,l_e:49,lab:48,label:[16,25],lack:35,languag:[4,20],larg:[5,27,32,35],larger:[10,14,22,26,28,35,50],largest:[28,31,44],last:[1,2,3,4,21,22,25,29,31,32,34,35,40,41,48],last_psi:22,later:[1,8,10,21,28,47],latest:[2,3,5,8],latter:[0,5,16,35],launcher:[4,8],law:20,lawsuit:20,layer:44,layout:[26,37],lbfg:35,lddt:7,leach1998:[10,38],leach:38,lead:[0,8,9,11,22,25,31,32,36,39,41,48],learn:28,least:[0,2,4,8,10,16,20,22,25,26,35,39,41,44],leav:1,left:[10,11,32],legal:[8,20],lemon:38,len:[22,23,25,26,28,31,35,36,41,47],length:[0,9,10,21,24,25,26,27,28,29,31,32,34,35,36,37,39,40,44],length_dep_weight:35,length_depend:31,lennard:49,less:[0,10,16,22,25,26,27,31,35,39,41,50,51],let:[1,8,22,26,28,31,47],letter:[3,5,21,22,26,27,34,49],leu:49,leu_h:21,leucin:49,level:[2,3,8,14,15,16,30,35],lexicograph:35,liabil:20,liabl:20,lib64:8,lib:[5,7,37],libexec:[4,8],libpromod3_nam:4,librari:[0,3,4,8,15,36,38,47,50,54],library1:4,library2:4,licenc:48,licens:[3,17,19],licensor:20,lies:26,life:16,ligand:[3,35,36,49,50],like:[0,1,4,8,16,35,37,48],limit:[0,3,20,26,32,35],line:[0,1,7,8,9,12,16,27,41,54],linear:[26,28,31,34,39,40,41],linear_weight:[31,34,39,41],linearcombin:31,linearli:49,linearscor:34,link:[0,2,4,8,16,20,21,25,26,28,34,36,39,40,41,42],link_cmd:4,linkcheck:[2,8,16],linker:[4,35],linker_length:35,list:[0,1,2,3,4,7,8,9,10,11,13,20,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,45,46,47,49,50,51,52],listen:8,literalinclud:8,litig:20,littl:[4,8,16,37],live:[4,8],lj_pair:25,load:[1,8,13,15,21,23,25,26,27,28,31,32,35,36,37,39,41,42,47,51,54],loadalign:[30,35],loadallatominteractionscor:39,loadallatompackingscor:39,loadamberforcefield:35,loadbb:26,loadbbdeplib:[0,36,47,48],loadcach:28,loadcbetascor:[31,34,41,42],loadcbpackingscor:41,loadcharmm:25,loadcharmmforcefield:35,loaddefaultallatomoverallscor:39,loaddefaultbackboneoverallscor:41,loadent:[0,13],loadfragdb:[23,24,31,35],loadhbondscor:41,loadlib:[0,36,48],loadpdb:[8,21,23,25,26,28,30,31,32,34,35,36,42,47],loadport:[25,26,27,37,39,41,51],loadreducedscor:41,loadsequenceprofil:[13,26,31],loadssagreementscor:41,loadstructuredb:[23,24,26,31,35],loadtorsionsampl:[22,24,27,34],loadtorsionsamplercoil:[24,31,35],loadtorsionsamplerextend:24,loadtorsionsamplerhel:24,loadtorsionscor:41,local:[2,5,7,25,26,27,39,41,51],localhost:7,locat:[2,3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Actions","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3\u2019s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"xref py py-func docutils literal notranslate\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],For:[4,11,17,54],Into:32,The:[1,5,7,16,21,22,26,27,31,35,36,45,49,50,51],Using:[2,37],With:33,acid:[21,25,27],action:[0,1,4,5,8],actiontestcas:1,algorithm:28,align:35,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,app:7,argument:13,atom:[21,32,39],avail:7,backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:[1,5],exisit:37,extend:29,featur:[8,26],fiddl:35,file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:5,instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:51,novo:[28,34],object:[24,34,45],optim:52,ost:25,other:43,output:1,own:[5,8],pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,5,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,registri:5,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 75517390cc3c8e174d9c62a7a7c63652fe6d36a7..2d8800954685db9e06127789b0d5d5b5a88287f7 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Disulfid Bond Evaluation — ProMod3 3.1.1 documentation</title>
+ <title>Disulfid Bond Evaluation — ProMod3 3.2.0 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>
@@ -66,10 +66,10 @@ rotamers to the result of the geometric expression.</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</p></li>
<li><p><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</p></li>
-<li><p><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</p></li>
-<li><p><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</p></li>
-<li><p><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</p></li>
-<li><p><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</p></li>
+<li><p><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</p></li>
+<li><p><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</p></li>
+<li><p><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</p></li>
+<li><p><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -98,8 +98,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</p></li>
-<li><p><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</p></li>
-<li><p><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</p></li>
+<li><p><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</p></li>
+<li><p><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</p></li>
<li><p><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
as a disulfid bond</p></li>
<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index c9d5c91db3abb0803acb37180af1bcd14fa32216..528c859ef98f26d0a2534ddadf1f3c9edab16cb8 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Frame - The Rigid Part — ProMod3 3.1.1 documentation</title>
+ <title>Frame - The Rigid Part — ProMod3 3.2.0 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>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index cc392291aa2bec8486007c41713a5fe53d67fa72..deda2927ca84a31f1c03e2212d2c1081c1193514 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Rotamer Graph — ProMod3 3.1.1 documentation</title>
+ <title>Rotamer Graph — ProMod3 3.2.0 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>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index d74fe72a81522f2b4d1b1d248f32f1594f14d23b..58f4b468a3882dbc95e82d7297ab04dd23e75820 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>sidechain - Sidechain Modelling — ProMod3 3.1.1 documentation</title>
+ <title>sidechain - Sidechain Modelling — ProMod3 3.2.0 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>
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index e5087c03d885199a9cd22308eaf01cef0aa2ef7d..84357123fcc616a047076060cbdc293c8c0cabd2 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Loading Rotamer Libraries — ProMod3 3.1.1 documentation</title>
+ <title>Loading Rotamer Libraries — ProMod3 3.2.0 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>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 0fbcb9adc832aace334453193da8dfb179e30b24..4201fcc72369bf35b5c80dda56cd9c426d1e87e1 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.1.1 documentation</title>
+ <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.2.0 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>
@@ -91,7 +91,7 @@ or as <code class="docutils literal notranslate"><span class="pre">promod3.sidec
<div class="section" id="how-can-i-get-an-id">
<h3>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h3>
<p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal 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/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
or from amino acid three letter codes.</p>
<dl class="method">
<dt id="promod3.sidechain.TLCToRotID">
@@ -114,10 +114,10 @@ exactly the naming convention defined above.</p>
<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
to generate special IDs this way
(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
-defined in <a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+defined in <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</p>
@@ -210,7 +210,7 @@ evaluated by the underlying scoring function.</p>
<dd class="field-odd"><p>The position of the particle</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -263,7 +263,7 @@ function</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
<li><p><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
<li><p><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
bond term</p></li>
<li><p><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
@@ -272,7 +272,7 @@ 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.</p></li>
-<li><p><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+<li><p><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
relevant for the hydrogen bond term. If set, the
particle is a potential hydrogen bond donor. An
example would be the Serine HG hydrogen. The
@@ -300,7 +300,7 @@ function</p>
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
<li><p><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
repulsion term.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
</ul>
</dd>
</dl>
@@ -309,7 +309,7 @@ repulsion term.</p></li>
</div>
<div class="section" id="the-vina-scoring-function">
<span id="vina-scoring-function"></span><h3>The VINA scoring function<a class="headerlink" href="#the-vina-scoring-function" title="Permalink to this headline">¶</a></h3>
-<p>The VINA scoring function is a combination of scores that are named
+<p>The VINA scoring function is a combination of functional forms that are named
gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
software <a class="reference internal" href="../references.html#trott2010" id="id3"><span>[trott2010]</span></a>. VINA only evaluates heavy atoms. Gaussian1, gaussian2
and repulsion are evaluated for all pairs of particles. Hydrophobic is only
@@ -317,6 +317,61 @@ evaluated between C_VINAParticle <a class="reference internal" href="#promod3.si
evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
are intended to evaluate sidechain-sidechain interactions in proteins,
VINA is mainly targeted at interactions between sidechains and ligands.</p>
+<p>The functional forms are linearly combined with the default weights from
+the Autodock Vina Software. They’re set as global variables and can be
+extracted with:</p>
+<dl class="method">
+<dt id="promod3.sidechain.GetVINAWeightGaussian1">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightGaussian1</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightGaussian1" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetVINAWeightGaussian2">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightGaussian2</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightGaussian2" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetVINAWeightRepulsion">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightRepulsion</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightRepulsion" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetVINAWeightHydrophobic">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightHydrophobic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightHydrophobic" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetVINAWeightHBond">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightHBond</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightHBond" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<p>You can set custom weights. A call to the following functions overwrites
+according weights globally which affects any subsequent score evaluation:</p>
+<dl class="method">
+<dt id="promod3.sidechain.SetVINAWeightGaussian1">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightGaussian1</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightGaussian1" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.SetVINAWeightGaussian2">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightGaussian2</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightGaussian2" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.SetVINAWeightRepulsion">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightRepulsion</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightRepulsion" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.SetVINAWeightHydrophobic">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightHydrophobic</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightHydrophobic" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.SetVINAWeightHBond">
+<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightHBond</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightHBond" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
<p>The VINA scoring function differentiates between the following particle types:</p>
<dl class="class">
<dt id="promod3.sidechain.VINAParticleType">
@@ -353,7 +408,7 @@ function</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
<li><p><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
</ul>
</dd>
</dl>
@@ -419,7 +474,7 @@ in this process.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
<strong>res</strong></p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
@@ -644,7 +699,7 @@ No atoms are removed from <strong>res</strong> in this process.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -973,7 +1028,7 @@ particles of the same residue.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1085,7 +1140,7 @@ particles of the same residue.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 3b3b1ea0dd9bb85bb8d9e3a829e65ed204d41441..188163de022b7e2fd1ec974874720da82ef954a3 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Rotamer Constructor — ProMod3 3.1.1 documentation</title>
+ <title>Rotamer Constructor — ProMod3 3.2.0 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>
@@ -68,7 +68,7 @@ an interface implemented by scoring function specific constructors
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</p></li>
<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</p></li>
<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the required backbone atoms</p></li>
@@ -119,7 +119,7 @@ don’t show up in a rotamer).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</p></li>
@@ -158,7 +158,7 @@ you observe in a rotamer).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</p></li>
@@ -237,7 +237,7 @@ any rotamers for ALA and GLY.</p>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">
<code class="sig-name descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
This can be useful to mark a region occupied by a ligand. Note, that
there won’t be any parametrization of hbonds in this function. All heavy
atoms of the residue will be represented as carbons and hydrogens are
@@ -245,7 +245,7 @@ skipped.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
</ul>
@@ -259,7 +259,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">
<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms based on the passed compounds library.
This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ConstructFrameResidue()</span></code></a>,
which will be called by this function if the residue is not known by the given
@@ -275,10 +275,10 @@ as in the <code class="xref py py-class docutils literal notranslate"><span clas
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
-<li><p><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</p></li>
+<li><p><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -418,7 +418,7 @@ to be assigned</p></li>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms. It is important that the residue has
proper bonds assigned, as they influence the atom typing procedure.
Furthermore, you need hydrogens to automatically estimate the correct
@@ -436,7 +436,7 @@ If the atom has the bool properties “is_hbond_acceptor” AND
in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
every oxygen is assumed to be an hbond acceptor. But only an hbond donor
if its bound to a hydrogen (or deuterium). You can set the generic
-properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
+properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
at.SetBoolProp(“is_hbond_donor”, False) and
at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
@@ -458,7 +458,7 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
</ul>
@@ -476,7 +476,7 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></p>
</dd>
<dt class="field-even">Return type</dt>
@@ -494,7 +494,7 @@ constructed <a class="reference internal" href="rotamer.html#promod3.sidechain.F
contains the atoms from <em>residue</em>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></p>
</dd>
<dt class="field-even">Return type</dt>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 31ee974e5b03d01d997ac62c563bccc59ce18988..382c4eb5bbba3e9620b278c6b47bd2ce09aebba7 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Rotamer Library — ProMod3 3.1.1 documentation</title>
+ <title>Rotamer Library — ProMod3 3.2.0 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>
@@ -401,7 +401,7 @@ all not required chi angles with their corresponding standard deviations to
NaN.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p>
@@ -424,7 +424,7 @@ are NaN.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.0/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.0.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p></li>
<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p></li>
</ul>
</dd>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 4b570a0c38d886bc95da5a261b6f4b0a32f55789..beaa0201cd26c3269fe78e36e5acbb20da232c9b 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Subrotamer Optimization — ProMod3 3.1.1 documentation</title>
+ <title>Subrotamer Optimization — ProMod3 3.2.0 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>
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index 483876a4d0d5c592e330f84c73d5012edb202c10..3bd565408368560b2ee4457d62ac1f4ea9a628a2 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Contributing — ProMod3 3.1.1 documentation</title>
+ <title>Contributing — ProMod3 3.2.0 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>
diff --git a/doc/html/users.html b/doc/html/users.html
index e2705ef0a7a2e9aec0f538a07b6102331cdd230e..d7adae8e715467dedc94de90210651b332effc39 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -4,7 +4,7 @@
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
- <title>Documentation For Users — ProMod3 3.1.1 documentation</title>
+ <title>Documentation For Users — ProMod3 3.2.0 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>