From 43fb8abf18fc21d2f935a7241bc02ae0de8df0ef Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 20 Apr 2023 23:13:27 +0200
Subject: [PATCH] Updated compiled doc.
---
doc/conf.py.in | 2 +-
doc/html/_sources/changelog.rst.txt | 14 +
.../_sources/modelling/algorithms.rst.txt | 31 ++
.../_sources/modelling/model_checking.rst.txt | 9 +
doc/html/_static/documentation_options.js | 2 +-
doc/html/actions/index.html | 9 +-
doc/html/actions/index_dev.html | 7 +-
doc/html/buildsystem.html | 9 +-
doc/html/changelog.html | 20 +-
doc/html/cmake/index.html | 5 +-
doc/html/container/docker.html | 7 +-
doc/html/container/index.html | 5 +-
doc/html/container/singularity.html | 5 +-
doc/html/contributing.html | 5 +-
doc/html/core/geometry.html | 47 +-
doc/html/core/graph_minimizer.html | 5 +-
doc/html/core/helper.html | 5 +-
doc/html/core/index.html | 5 +-
doc/html/core/pm3argparse.html | 7 +-
doc/html/core/runtime_profiling.html | 5 +-
doc/html/core/setcompoundschemlib.html | 5 +-
doc/html/dev_setup.html | 5 +-
doc/html/developers.html | 5 +-
doc/html/genindex.html | 83 ++-
doc/html/gettingstarted.html | 7 +-
doc/html/index.html | 5 +-
doc/html/license.html | 5 +-
doc/html/loop/all_atom.html | 53 +-
doc/html/loop/backbone.html | 71 ++-
doc/html/loop/index.html | 5 +-
doc/html/loop/load_loop_objects.html | 5 +-
doc/html/loop/mm_system_creation.html | 45 +-
doc/html/loop/structure_db.html | 39 +-
doc/html/loop/torsion_sampler.html | 49 +-
doc/html/modelling/algorithms.html | 491 +++++++++++++++++-
doc/html/modelling/gap_handling.html | 21 +-
doc/html/modelling/index.html | 7 +-
doc/html/modelling/loop_candidates.html | 25 +-
doc/html/modelling/loop_closing.html | 23 +-
doc/html/modelling/model_checking.html | 93 +++-
doc/html/modelling/monte_carlo.html | 21 +-
doc/html/modelling/pipeline.html | 66 +--
.../modelling/sidechain_reconstruction.html | 13 +-
doc/html/objects.inv | Bin 7934 -> 8108 bytes
doc/html/portableIO.html | 5 +-
doc/html/py-modindex.html | 5 +-
doc/html/references.html | 5 +-
doc/html/scoring/all_atom_scorers.html | 5 +-
doc/html/scoring/backbone_score_env.html | 19 +-
doc/html/scoring/backbone_scorers.html | 15 +-
doc/html/scoring/index.html | 5 +-
doc/html/scoring/other_scoring_functions.html | 5 +-
doc/html/search.html | 5 +-
doc/html/searchindex.js | 2 +-
doc/html/sidechain/disulfid.html | 17 +-
doc/html/sidechain/frame.html | 5 +-
doc/html/sidechain/graph.html | 5 +-
doc/html/sidechain/index.html | 5 +-
doc/html/sidechain/loading.html | 5 +-
doc/html/sidechain/rotamer.html | 29 +-
doc/html/sidechain/rotamer_constructor.html | 31 +-
doc/html/sidechain/rotamer_lib.html | 9 +-
doc/html/sidechain/subrotamer_optimizer.html | 5 +-
doc/html/user_contributions.html | 5 +-
doc/html/users.html | 5 +-
65 files changed, 1072 insertions(+), 466 deletions(-)
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 21b20cca..c01cff17 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -58,7 +58,7 @@ master_doc = 'index'
# General information about the project.
project = u'ProMod3'
-copyright = u'2013-2022, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
+copyright = u'2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
diff --git a/doc/html/_sources/changelog.rst.txt b/doc/html/_sources/changelog.rst.txt
index e83fc860..bf7d79fe 100644
--- a/doc/html/_sources/changelog.rst.txt
+++ b/doc/html/_sources/changelog.rst.txt
@@ -5,6 +5,20 @@
Changelog
================================================================================
+Release 3.3.0
+--------------------------------------------------------------------------------
+
+* Check for and report non-planar rings in the modelling result. This check is
+ also incorporated in energy minimization, potentially increasing the number
+ of minimization steps.
+* Algorithms using large model databases as template libraries for modelling.
+ Sequence search: PentaMatch, a k-mer based sequence search with extreme speed
+ but low sensitivity (similar implementation as
+ https://www.rbvi.ucsf.edu/chimerax/data/kmer-aug2022/kmer_search.html).
+ Structure storage: FSStructureServer, an OMF (OpenStructure Minimal Format)
+ based structure storage that compresses AFDB v4 (214E6 entries) to 1.4TB.
+* Several minor bug fixes, improvements, and speed-ups.
+
Release 3.2.1
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/modelling/algorithms.rst.txt b/doc/html/_sources/modelling/algorithms.rst.txt
index b36bf5bb..c9db60f1 100644
--- a/doc/html/_sources/modelling/algorithms.rst.txt
+++ b/doc/html/_sources/modelling/algorithms.rst.txt
@@ -326,3 +326,34 @@ iteration.
:returns: All found matches
:rtype: :class:`list` of :class:`MotifMatch`
+
+
+AFDB Modelling
+--------------------------------------------------------------------------------
+
+Template based modelling using AFDB as template library comes with two
+challenges for which |project| provides solutions:
+
+* efficient structure storage for the whole AFDB: :class:`FSStructureServer`
+* fast sequence searches with limited sensitivity: :class:`PentaMatch`
+
+The creation of these two object requires extensive preprocessing. The required
+scripts and documentation are available in
+`<GIT_ROOT>/extras/data_generation/afdb_modelling`.
+
+Basic modelling functionality is available in the following two functions:
+
+* :func:`AFDBTPLSearch`
+* :func:`AFDBModel`
+
+.. autofunction:: AFDBTPLSearch
+
+.. autofunction:: AFDBModel
+
+.. autoclass:: FSStructureServer
+ :members:
+ :member-order: bysource
+
+.. autoclass:: PentaMatch
+ :members:
+ :member-order: bysource
diff --git a/doc/html/_sources/modelling/model_checking.rst.txt b/doc/html/_sources/modelling/model_checking.rst.txt
index ab5b5eb9..400f3737 100644
--- a/doc/html/_sources/modelling/model_checking.rst.txt
+++ b/doc/html/_sources/modelling/model_checking.rst.txt
@@ -35,6 +35,15 @@ Detecting Ring Punches
.. autofunction:: FilterCandidatesWithSC
+
+Detecting Non-Planar Rings
+--------------------------------------------------------------------------------
+
+.. autofunction:: GetNonPlanarRings
+
+.. autofunction:: HasNonPlanarRings
+
+
Model Checking With MolProbity
--------------------------------------------------------------------------------
diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js
index 22999c30..e42d2126 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: '3.2.1',
+ VERSION: '3.3.0',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index c17396d6..e250c038 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Actions — ProMod3 3.2.1 documentation</title>
+ <title>ProMod3 Actions — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Building ProMod3" href="../buildsystem.html" />
@@ -102,7 +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/2.2/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
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.3.1)"><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
@@ -184,7 +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/2.2/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
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.3.1)"><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>
@@ -297,7 +296,7 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 408223d6..c91acf1b 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>test_actions - Testing Actions — ProMod3 3.2.1 documentation</title>
+ <title>test_actions - Testing Actions — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="ProMod3’s Share Of CMake" href="../cmake/index.html" />
@@ -184,7 +183,7 @@ 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/2.2/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
+<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/2.3.1/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.3.1)"><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
@@ -399,7 +398,7 @@ file (also complains if a directory is found instead).</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index d013cbc7..78cfa9bc 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Building ProMod3 — ProMod3 3.2.1 documentation</title>
+ <title>Building ProMod3 — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ProMod3 and Containers" href="container/index.html" />
@@ -37,7 +36,7 @@
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-2.3.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
+2.4.0. 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
@@ -46,7 +45,7 @@ release supporting Python 2.7 is 2.1.0 which also requires OST to be
compiled with Python 2.7.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.3.0</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.4.0</li>
<li><a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a> 7.1.1</li>
<li><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</li>
<li><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</li>
@@ -214,7 +213,7 @@ safely delete the whole source folder.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 9f00e077..4f246044 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Changelog — ProMod3 3.2.1 documentation</title>
+ <title>Changelog — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="References" href="references.html" />
@@ -33,6 +32,21 @@
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-3-3-0">
+<h2>Release 3.3.0<a class="headerlink" href="#release-3-3-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>Check for and report non-planar rings in the modelling result. This check is
+also incorporated in energy minimization, potentially increasing the number
+of minimization steps.</li>
+<li>Algorithms using large model databases as template libraries for modelling.
+Sequence search: PentaMatch, a k-mer based sequence search with extreme speed
+but low sensitivity (similar implementation as
+<a class="reference external" href="https://www.rbvi.ucsf.edu/chimerax/data/kmer-aug2022/kmer_search.html">https://www.rbvi.ucsf.edu/chimerax/data/kmer-aug2022/kmer_search.html</a>).
+Structure storage: FSStructureServer, an OMF (OpenStructure Minimal Format)
+based structure storage that compresses AFDB v4 (214E6 entries) to 1.4TB.</li>
+<li>Several minor bug fixes, improvements, and speed-ups.</li>
+</ul>
+</div>
<div class="section" id="release-3-2-1">
<h2>Release 3.2.1<a class="headerlink" href="#release-3-2-1" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
@@ -238,7 +252,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index a18b6c78..403551e9 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3’s Share Of CMake — ProMod3 3.2.1 documentation</title>
+ <title>ProMod3’s Share Of CMake — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
@@ -364,7 +363,7 @@ target has to be created <strong>before</strong> any action may be attached to i
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index efd454da..70b21e45 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Docker — ProMod3 3.2.1 documentation</title>
+ <title>Docker — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Singularity" href="singularity.html" />
@@ -76,7 +75,7 @@ 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/2.2/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.
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.3.1)"><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
@@ -194,7 +193,7 @@ output when running a Python script with following code in the container:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index 1cd6fb1b..11a0a45b 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 and Containers — ProMod3 3.2.1 documentation</title>
+ <title>ProMod3 and Containers — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Docker" href="docker.html" />
@@ -113,7 +112,7 @@ some sugar on top.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index 61c1dc21..79d7f49b 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Singularity — ProMod3 3.2.1 documentation</title>
+ <title>Singularity — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
@@ -195,7 +194,7 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 9f612109..1fdfbf12 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Contributing — ProMod3 3.2.1 documentation</title>
+ <title>Contributing — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
@@ -651,7 +650,7 @@ contributions to web pages using ProMod3.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 4db119f6..7a551e03 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Geometry functions — ProMod3 3.2.1 documentation</title>
+ <title>Geometry functions — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
@@ -46,14 +45,14 @@
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><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)</li>
-<li><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)</li>
+<li><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/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -69,16 +68,16 @@
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</li>
-<li><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</li>
-<li><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</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -95,9 +94,9 @@ dihedral (A-B-C-D).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
-<li><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</li>
-<li><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</li>
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
<li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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)</li>
<li><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)</li>
<li><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)</li>
@@ -107,7 +106,7 @@ dihedral (A-B-C-D).</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -124,16 +123,16 @@ C-alpha and C atoms.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
-<li><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</li>
-<li><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</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -150,8 +149,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
-<li><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</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -159,7 +158,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
</td>
</tr>
</tbody>
@@ -176,7 +175,7 @@ going through the origin.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -184,7 +183,7 @@ going through the origin.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -201,7 +200,7 @@ going through the origin.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
atoms.</td>
@@ -220,7 +219,7 @@ atoms.</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -366,7 +365,7 @@ angles and one distance and is used in the fragment database for fast lookups.</
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index 1d1d0b3a..6c1b852d 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Graph Minimizer — ProMod3 3.2.1 documentation</title>
+ <title>Graph Minimizer — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
@@ -392,7 +391,7 @@ The second element is the according energy value.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 6abb2303..02ce0b8a 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>helper - Shared Functionality For the Everything — ProMod3 3.2.1 documentation</title>
+ <title>helper - Shared Functionality For the Everything — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Geometry functions" href="geometry.html" />
@@ -256,7 +255,7 @@ script will terminate if a gzip file is found.</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 551c8911..0a8d27bc 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>core - ProMod3 Core Functionality — ProMod3 3.2.1 documentation</title>
+ <title>core - ProMod3 Core Functionality — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
@@ -124,7 +123,7 @@ modeling per se but cover standard programming issues.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index ad588482..7547ac64 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>pm3argparse - Parsing Command Lines — ProMod3 3.2.1 documentation</title>
+ <title>pm3argparse - Parsing Command Lines — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
@@ -256,7 +255,7 @@ target sequences</li>
</ul>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/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>,
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
ordered to match the target sequences.</li>
</ul>
<p>Exit codes related to profile input:</p>
@@ -434,7 +433,7 @@ and with the right constraints.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index 795b6c9f..f22d0b77 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Runtime profiling — ProMod3 3.2.1 documentation</title>
+ <title>Runtime profiling — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
@@ -220,7 +219,7 @@ will fail miserably if timers are currently running.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index f6cbb73e..1af7258a 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>SetCompoundsChemlib() — ProMod3 3.2.1 documentation</title>
+ <title>SetCompoundsChemlib() — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Contributing" href="../user_contributions.html" />
@@ -125,7 +124,7 @@ enabled globally.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 2a060c73..5a09c032 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Setup — ProMod3 3.2.1 documentation</title>
+ <title>ProMod3 Setup — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Contributing" href="contributing.html" />
@@ -287,7 +286,7 @@ modules from there, use the binaries from <code class="file docutils literal not
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 7084fede..91607a80 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Developers — ProMod3 3.2.1 documentation</title>
+ <title>Documentation For Developers — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
@@ -132,7 +131,7 @@ new features.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 5ef68c4b..5b605538 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -7,7 +7,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Index — ProMod3 3.2.1 documentation</title>
+ <title>Index — ProMod3 3.3.0 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>
@@ -15,7 +15,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
@@ -258,6 +257,10 @@
<li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.AddSubrotamerDefinition">AddSubrotamerDefinition() (promod3.sidechain.FRMRotamer method)</a>
</li>
<li><a href="loop/structure_db.html#promod3.loop.Fragger.AddTorsionProbabilityParameters">AddTorsionProbabilityParameters() (promod3.loop.Fragger method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.AFDBModel">AFDBModel() (in module promod3.modelling)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.AFDBTPLSearch">AFDBTPLSearch() (in module promod3.modelling)</a>
</li>
<li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.after">after (promod3.modelling.StructuralGap attribute)</a>
</li>
@@ -268,11 +271,11 @@
<li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer_env">all_atom_scorer_env (promod3.modelling.ModellingHandle attribute)</a>
</li>
<li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_sidechain_env">all_atom_sidechain_env (promod3.modelling.ModellingHandle attribute)</a>
-</li>
- <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.all_pos">all_pos (promod3.loop.AllAtomEnvPositions attribute)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.all_pos">all_pos (promod3.loop.AllAtomEnvPositions attribute)</a>
+</li>
<li><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer">AllAtomClashScorer (class in promod3.scoring)</a>
</li>
<li><a href="loop/all_atom.html#promod3.loop.AllAtomEnv">AllAtomEnv (class in promod3.loop)</a>
@@ -480,6 +483,8 @@
<li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi3">chi3 (promod3.sidechain.RotamerLibEntry attribute)</a>
</li>
<li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.chi4">chi4 (promod3.sidechain.RotamerLibEntry attribute)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.chunk">chunk (promod3.modelling.FSStructureServer attribute)</a>
</li>
<li><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer">ClashScorer (class in promod3.scoring)</a>
</li>
@@ -527,6 +532,8 @@
</li>
<li><a href="modelling/pipeline.html#promod3.modelling.CloseSmallDeletions">CloseSmallDeletions() (in module promod3.modelling)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li>
command
@@ -546,8 +553,6 @@
<li><a href="cmake/index.html#command:pymod"><strong>pymod</strong></a>
</li>
</ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li>
command line option
@@ -650,6 +655,8 @@
<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.data">data (promod3.modelling.FSStructureServer attribute)</a>
+</li>
<li><a href="modelling/pipeline.html#promod3.modelling.DeleteGapCols">DeleteGapCols() (in module promod3.modelling)</a>
</li>
<li><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser">DeNovoCloser (class in promod3.modelling)</a>
@@ -834,10 +841,10 @@
</li>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo">ForcefieldHarmonicImproperInfo (class in promod3.loop)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLJPairInfo">ForcefieldLJPairInfo (class in promod3.loop)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup">ForcefieldLookup (class in promod3.loop)</a>
</li>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldPeriodicDihedralInfo">ForcefieldPeriodicDihedralInfo (class in promod3.loop)</a>
@@ -865,12 +872,18 @@
<li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer">FRMRotamer (class in promod3.sidechain)</a>
</li>
<li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup">FRMRotamerGroup (class in promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.FromDataChunks">FromDataChunks() (promod3.modelling.FSStructureServer static method)</a>
</li>
<li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.FromHHM">FromHHM() (promod3.loop.PsipredPrediction method)</a>
</li>
<li><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.FromHoriz">FromHoriz() (promod3.loop.PsipredPrediction method)</a>
</li>
<li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.FromResidue">FromResidue() (promod3.sidechain.RotamerLibEntry static method)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.FromResidue">[1]</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.PentaMatch.FromSeqList">FromSeqList() (promod3.modelling.PentaMatch static method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer">FSStructureServer (class in promod3.modelling)</a>
</li>
<li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.full_seq">full_seq (promod3.modelling.StructuralGap attribute)</a>
</li>
@@ -1035,6 +1048,8 @@
</li>
</ul></li>
<li><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetIdentifiers">GetIdentifiers() (promod3.modelling.MotifQuery method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.GetIdx">GetIdx() (promod3.modelling.FSStructureServer method)</a>
</li>
<li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetIndex">GetIndex() (promod3.loop.AllAtomPositions method)</a>
@@ -1062,10 +1077,10 @@
</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>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.GetList">GetList() (promod3.modelling.FraggerHandle method)</a>
</li>
<li><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetLoopLengths">GetLoopLengths() (promod3.loop.MmSystemCreator method)</a>
@@ -1087,6 +1102,8 @@
<li><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetName">GetName() (promod3.sidechain.Particle method)</a>
</li>
<li><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.GetNonBondedCutoff">GetNonBondedCutoff() (promod3.modelling.BackboneRelaxer method)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.GetNonPlanarRings">GetNonPlanarRings() (in module promod3.modelling)</a>
</li>
<li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetNumAtoms">GetNumAtoms() (promod3.loop.AllAtomPositions method)</a>
@@ -1130,6 +1147,10 @@
<li><a href="loop/backbone.html#promod3.loop.BackboneList.GetOmegaTorsion">(promod3.loop.BackboneList method)</a>
</li>
</ul></li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.GetOMF">GetOMF() (promod3.modelling.FSStructureServer method)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.GetOMFByIdx">GetOMFByIdx() (promod3.modelling.FSStructureServer method)</a>
+</li>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetOXTIndex">GetOXTIndex() (promod3.loop.ForcefieldLookup method)</a>
</li>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity">GetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
@@ -1275,6 +1296,8 @@
<li><a href="loop/structure_db.html#promod3.loop.FragDB.HasFragLength">HasFragLength() (promod3.loop.FragDB method)</a>
</li>
<li><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.HasFragmentInfos">HasFragmentInfos() (promod3.modelling.LoopCandidates method)</a>
+</li>
+ <li><a href="modelling/model_checking.html#promod3.modelling.HasNonPlanarRings">HasNonPlanarRings() (in module promod3.modelling)</a>
</li>
<li><a href="modelling/model_checking.html#promod3.modelling.HasRingPunches">HasRingPunches() (in module promod3.modelling)</a>
</li>
@@ -1332,6 +1355,14 @@
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two">(promod3.loop.ForcefieldUreyBradleyAngleInfo attribute)</a>
</li>
</ul></li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.indexer">indexer (promod3.modelling.FSStructureServer attribute)</a>
+
+ <ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.PentaMatch.indexer">(promod3.modelling.PentaMatch attribute)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modelling/monte_carlo.html#promod3.modelling.FragmentSampler.Initialize">Initialize() (promod3.modelling.FragmentSampler method)</a>
<ul>
@@ -1342,8 +1373,6 @@
<li><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.Initialize">(promod3.modelling.SoftSampler method)</a>
</li>
</ul></li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.InsertInto">InsertInto() (promod3.loop.AllAtomPositions method)</a>
<ul>
@@ -1405,6 +1434,10 @@
<li><a href="loop/structure_db.html#promod3.loop.FragmentInfo.length">length (promod3.loop.FragmentInfo attribute)</a>
<ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.length">(promod3.modelling.FSStructureServer attribute)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.PentaMatch.length">(promod3.modelling.PentaMatch attribute)</a>
+</li>
<li><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.length">(promod3.modelling.StructuralGap attribute)</a>
</li>
</ul></li>
@@ -1461,11 +1494,11 @@
<li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadCBetaScorer">LoadCBetaScorer() (in module promod3.scoring)</a>
</li>
<li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadCBPackingScorer">LoadCBPackingScorer() (in module promod3.scoring)</a>
-</li>
- <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.LoadCHARMM">LoadCHARMM() (promod3.loop.ForcefieldLookup static method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.LoadCHARMM">LoadCHARMM() (promod3.loop.ForcefieldLookup static method)</a>
+</li>
<li><a href="scoring/all_atom_scorers.html#promod3.scoring.LoadDefaultAllAtomOverallScorer">LoadDefaultAllAtomOverallScorer() (in module promod3.scoring)</a>
</li>
<li><a href="scoring/backbone_scorers.html#promod3.scoring.LoadDefaultBackboneOverallScorer">LoadDefaultBackboneOverallScorer() (in module promod3.scoring)</a>
@@ -1615,10 +1648,14 @@
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.PentaMatch.N">N (promod3.modelling.PentaMatch attribute)</a>
+</li>
<li><a href="core/geometry.html#promod3.core.StemCoords.n_coord">n_coord (promod3.core.StemCoords attribute)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.n_entries">n_entries (promod3.modelling.FSStructureServer attribute)</a>
+</li>
<li><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.NaiveSolve">NaiveSolve() (promod3.core.GraphMinimizer method)</a>
</li>
<li><a href="modelling/monte_carlo.html#promod3.modelling.NTerminalCloser">NTerminalCloser (class in promod3.modelling)</a>
@@ -1652,6 +1689,8 @@
<li><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.Parse">Parse() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
</li>
<li><a href="sidechain/rotamer.html#promod3.sidechain.Particle">Particle (class in promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.PentaMatch">PentaMatch (class in promod3.modelling)</a>
</li>
<li><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.periodic_dihedrals">periodic_dihedrals (promod3.loop.ForcefieldConnectivity attribute)</a>
</li>
@@ -1676,6 +1715,12 @@
</li>
<li><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Pop">Pop() (promod3.scoring.BackboneScoreEnv method)</a>
</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.pos">pos (promod3.modelling.FSStructureServer attribute)</a>
+
+ <ul>
+ <li><a href="modelling/algorithms.html#promod3.modelling.PentaMatch.pos">(promod3.modelling.PentaMatch attribute)</a>
+</li>
+ </ul></li>
<li><a href="loop/structure_db.html#promod3.loop.FragDB.PrintStatistics">PrintStatistics() (promod3.loop.FragDB method)</a>
<ul>
@@ -1684,12 +1729,12 @@
</ul></li>
<li><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.PrintSummary">PrintSummary() (promod3.core.StaticRuntimeProfiler static method)</a>
</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.probability">probability (promod3.sidechain.RotamerLibEntry attribute)</a>
</li>
<li><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.profiles">profiles (promod3.modelling.ModellingHandle attribute)</a>
</li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
<li><a href="core/index.html#module-promod3.core">promod3.core (module)</a>
</li>
<li><a href="core/helper.html#module-promod3.core.helper">promod3.core.helper (module)</a>
@@ -1947,6 +1992,8 @@
<li><a href="sidechain/rotamer.html#promod3.sidechain.SCWRL4ParticleType">SCWRL4ParticleType (class in promod3.sidechain)</a>
</li>
<li><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor">SCWRL4RotamerConstructor (class in promod3.sidechain)</a>
+</li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.FSStructureServer.search_keys">search_keys (promod3.modelling.FSStructureServer attribute)</a>
</li>
<li><a href="loop/structure_db.html#promod3.loop.FragDB.SearchDB">SearchDB() (promod3.loop.FragDB method)</a>
</li>
@@ -2210,6 +2257,8 @@
<li><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.ToFrameResidue">(promod3.sidechain.RRMRotamer method)</a>
</li>
</ul></li>
+ <li><a href="modelling/algorithms.html#promod3.modelling.PentaMatch.TopN">TopN() (promod3.modelling.PentaMatch method)</a>
+</li>
<li><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.ToRRMRotamer">ToRRMRotamer() (promod3.sidechain.FRMRotamer method)</a>
</li>
<li><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler">TorsionSampler (class in promod3.loop)</a>
@@ -2304,7 +2353,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 80a23c32..e7978884 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Getting Started — ProMod3 3.2.1 documentation</title>
+ <title>Getting Started — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ProMod3 Actions" href="actions/index.html" />
@@ -88,7 +87,7 @@ is conserved</li>
<li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> module)</li>
<li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> module)</li>
<li>Minimize energy of final model using molecular mechanics
-(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)</li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</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
@@ -167,7 +166,7 @@ not set, 1 thread will be used by default.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/index.html b/doc/html/index.html
index 48736a0c..94f13fec 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 — ProMod3 3.2.1 documentation</title>
+ <title>ProMod3 — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Documentation For Users" href="users.html" />
@@ -121,7 +120,7 @@ algorithms.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/license.html b/doc/html/license.html
index 2fa7eaf1..04749084 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>License — ProMod3 3.2.1 documentation</title>
+ <title>License — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="References" href="references.html" />
@@ -300,7 +299,7 @@ doc/Copyright_cmake.py.txt
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index f27b4188..5affbe0d 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling All Atom Positions — ProMod3 3.2.1 documentation</title>
+ <title>Handling All Atom Positions — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
@@ -81,8 +80,8 @@ new loop is being added.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><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.</td>
</tr>
</tbody>
@@ -104,7 +103,7 @@ concatenated one after each other (indexing starts at 0)</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -134,7 +133,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
<li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
+<li><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/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
</ul>
</td>
@@ -211,7 +210,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -345,7 +344,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
</ul>
</td>
</tr>
@@ -391,7 +390,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
-<li><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>.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
</ul>
</td>
</tr>
@@ -441,7 +440,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</td>
</tr>
@@ -545,7 +544,7 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</td>
</tr>
@@ -824,9 +823,9 @@ atom (N, CA, C, O).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
-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>.</td>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -846,8 +845,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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</li>
-<li><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</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
</ul>
</td>
</tr>
@@ -940,7 +939,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dt id="promod3.loop.AminoAcidLookup">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
-(<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
+(<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><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="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -953,7 +952,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/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></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -975,7 +974,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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])</li>
<li><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</li>
</ul>
@@ -1005,7 +1004,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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])</li>
<li><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</li>
</ul>
@@ -1034,7 +1033,7 @@ atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
</ul>
</td>
@@ -1062,7 +1061,7 @@ and atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
</ul>
</td>
@@ -1086,7 +1085,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1118,7 +1117,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1151,7 +1150,7 @@ hydrogens of <em>aa</em>.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
@@ -1245,7 +1244,7 @@ when residue is peptide bound.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</td>
</tr>
@@ -1269,7 +1268,7 @@ when residue is N terminal.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</td>
</tr>
@@ -1351,7 +1350,7 @@ when residue is N terminal.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index bc203c99..adc18a28 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Representing Loops — ProMod3 3.2.1 documentation</title>
+ <title>Representing Loops — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
@@ -37,7 +36,7 @@
<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/2.2/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>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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>
@@ -149,7 +148,7 @@ code which is not one of the 20 default amino acids or if
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions and one letter codes
are extracted.</td>
</tr>
@@ -173,7 +172,7 @@ required positions.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
-<li><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
+<li><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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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.</li>
</ul>
</td>
@@ -197,7 +196,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -207,7 +206,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
-<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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>) – </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/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>) – </li>
</ul>
@@ -226,7 +225,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -243,8 +242,8 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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</li>
-<li><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</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
</ul>
</td>
</tr>
@@ -260,7 +259,7 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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>) – </li>
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/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>) – </li>
</ul>
@@ -279,7 +278,7 @@ be replaced, otherwise they will be added to the entity.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/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>) – </td>
</tr>
@@ -383,7 +382,7 @@ actual fragment at specified <em>index</em></p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
atom for residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</td>
</tr>
@@ -408,7 +407,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
-<li><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
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><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.</li>
</ul>
</td>
@@ -460,7 +459,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</td>
</tr>
@@ -477,7 +476,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
-<li><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.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
</ul>
</td>
</tr>
@@ -503,12 +502,12 @@ and set the amino acid type according to the given one letter code.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
-<li><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</li>
-<li><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.</li>
-<li><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.</li>
-<li><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.</li>
-<li><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.</li>
-<li><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.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -578,12 +577,12 @@ to the given one letter code.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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</li>
-<li><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.</li>
-<li><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.</li>
-<li><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.</li>
-<li><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.</li>
-<li><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.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -647,7 +646,7 @@ reconstructed if the residue handle is valid.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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)</td>
</tr>
</tbody>
@@ -664,7 +663,7 @@ element of this backbone list)</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
-<li><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</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -684,7 +683,7 @@ element of this backbone list)</td>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
<li><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).</li>
-<li><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</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -700,7 +699,7 @@ element of this backbone list)</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal 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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
</tr>
</tbody>
</table>
@@ -720,12 +719,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
-<li><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.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
<li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
</ul>
@@ -745,7 +744,7 @@ positions of the N, CA and C atoms.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
list onto CA positions of <em>other</em> backbone list.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
</tr>
@@ -1038,7 +1037,7 @@ backbone list.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 5ea7d7d4..540e0f8c 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>loop - Loop Handling — ProMod3 3.2.1 documentation</title>
+ <title>loop - Loop Handling — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Representing Loops" href="backbone.html" />
@@ -182,7 +181,7 @@ loops. The following example should give you an idea of what can be done:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 3d5bd43d..51d3acd6 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Precomputed Objects — ProMod3 3.2.1 documentation</title>
+ <title>Loading Precomputed Objects — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
@@ -223,7 +222,7 @@ returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" t
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 5110342b..05816c62 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generate ost.mol.mm systems — ProMod3 3.2.1 documentation</title>
+ <title>Generate ost.mol.mm systems — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
@@ -33,8 +32,8 @@
<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/2.2/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
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><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>
@@ -279,7 +278,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. Use this to run
MM simulations.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
</tr>
</tbody>
</table>
@@ -426,7 +425,7 @@ 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="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
<li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -539,7 +538,7 @@ for details.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
</tr>
@@ -655,7 +654,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
-<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>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
</tr>
@@ -671,7 +670,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
-<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>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
</tr>
@@ -686,7 +685,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/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>
@@ -710,7 +709,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/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>
@@ -735,7 +734,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
-(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>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/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>
@@ -760,7 +759,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
-(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>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/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>
@@ -906,7 +905,7 @@ for details.</p>
<dt id="promod3.loop.ForcefieldAminoAcid">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-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,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><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>
@@ -923,7 +922,7 @@ 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/2.2/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>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.3.1)"><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
@@ -1033,7 +1032,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<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>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1095,7 +1094,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<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>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1172,7 +1171,7 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
-(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>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1277,8 +1276,8 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
-<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>
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1382,7 +1381,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<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>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1472,7 +1471,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<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>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1603,7 +1602,7 @@ False, False)</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
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diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 2ce5f6fa..f5413e9f 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Structural Data — ProMod3 3.2.1 documentation</title>
+ <title>Structural Data — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
@@ -116,7 +115,7 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
<dt id="promod3.loop.CoordInfo.shift">
<code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>Translation from original coordinates that has been applied before storing
-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>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -258,7 +257,7 @@ database, you might want to consider two things:</p>
<ol class="arabic simple">
<li>Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)</li>
-<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.3.1)"><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</li>
</ol>
<dl class="class">
@@ -393,11 +392,11 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/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)</li>
<li><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</li>
-<li><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
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><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>.</li>
-<li><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></li>
-<li><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
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><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>.</li>
<li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
connected stretch of residues are all connected
@@ -533,9 +532,9 @@ full entry at <em>coord_idx</em></p>
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
set, the original sequence at specified location in the
database is used.</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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.</li>
</ul>
</td>
@@ -689,7 +688,7 @@ connected stretches of residues in the database.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Solvent accessibility for each residue of <em>fragment</em> or full entry
at <em>coord_idx</em> in square A as calculated by
-<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
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
the database.</p>
</td>
</tr>
@@ -728,7 +727,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
@@ -762,7 +761,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
@@ -803,7 +802,7 @@ containing that data.</li>
probabilities as NULL model.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
@@ -825,7 +824,7 @@ frequencies in entry with <em>coord_idx</em></p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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])</li>
</ul>
@@ -1128,8 +1127,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
-<li><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</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
<li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><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
@@ -1353,7 +1352,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1371,7 +1370,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1842,7 +1841,7 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
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diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index fa34d776..0f280d3c 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sampling Dihedral Angles — ProMod3 3.2.1 documentation</title>
+ <title>Sampling Dihedral Angles — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Structural Data" href="structure_db.html" />
@@ -129,7 +128,7 @@ acids not matching any of the group definitions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
</tr>
</tbody>
</table>
@@ -201,9 +200,9 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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</li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -243,9 +242,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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</li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -281,9 +280,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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</li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -325,9 +324,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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</li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -369,9 +368,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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.</li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><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</li>
</ul>
@@ -415,9 +414,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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.</li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><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</li>
</ul>
@@ -439,9 +438,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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.</li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><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</li>
</ul>
@@ -600,7 +599,7 @@ standard amino acid</td>
<div class="clearer"></div>
</div>
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+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index b5078614..20a4c6e4 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Algorithms — ProMod3 3.2.1 documentation</title>
+ <title>Modelling Algorithms — ProMod3 3.3.0 documentation</title>
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<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -14,7 +14,6 @@
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@@ -85,7 +84,7 @@ of the solutions</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/2.2/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
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
</td>
@@ -103,7 +102,7 @@ onto <strong>bb_list_two</strong></p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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>
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><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</li>
<li><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</li>
@@ -124,9 +123,9 @@ of the solutions</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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/2.2/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>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><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/2.2/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
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
</td>
@@ -163,7 +162,7 @@ of the solutions</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/2.2/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
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
</td>
@@ -226,8 +225,8 @@ Weird things are happening otherwise.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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</li>
-<li><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.</li>
+<li><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/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
<li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li>
<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
<li><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
@@ -319,7 +318,7 @@ want to generate</li>
<li><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
-<li><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
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><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.</li>
<li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
increases the fragment search performance</li>
@@ -611,6 +610,476 @@ matter in this case.</li>
</table>
</dd></dl>
+</div>
+<div class="section" id="afdb-modelling">
+<h2>AFDB Modelling<a class="headerlink" href="#afdb-modelling" title="Permalink to this headline">¶</a></h2>
+<p>Template based modelling using AFDB as template library comes with two
+challenges for which ProMod3 provides solutions:</p>
+<ul class="simple">
+<li>efficient structure storage for the whole AFDB: <a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a></li>
+<li>fast sequence searches with limited sensitivity: <a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a></li>
+</ul>
+<p>The creation of these two object requires extensive preprocessing. The required
+scripts and documentation are available in
+<cite><GIT_ROOT>/extras/data_generation/afdb_modelling</cite>.</p>
+<p>Basic modelling functionality is available in the following two functions:</p>
+<ul class="simple">
+<li><a class="reference internal" href="#promod3.modelling.AFDBTPLSearch" title="promod3.modelling.AFDBTPLSearch"><code class="xref py py-func docutils literal notranslate"><span class="pre">AFDBTPLSearch()</span></code></a></li>
+<li><a class="reference internal" href="#promod3.modelling.AFDBModel" title="promod3.modelling.AFDBModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">AFDBModel()</span></code></a></li>
+</ul>
+<dl class="function">
+<dt id="promod3.modelling.AFDBTPLSearch">
+<code class="descclassname">promod3.modelling.</code><code class="descname">AFDBTPLSearch</code><span class="sig-paren">(</span><em>fs_server</em>, <em>pentamatch</em>, <em>trg_seq</em>, <em>pentamatch_n=100</em>, <em>seqid_thresh=70</em>, <em>tpl_n=5</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AFDBTPLSearch" title="Permalink to this definition">¶</a></dt>
+<dd><p>Searches <em>tpl_n</em> templates in <em>fs_server</em>/<em>pentamatch</em></p>
+<p>Step 1: Identifies <em>pentamatch_n</em> sequences in <em>pentamatch</em> with largest
+number of matching pentamers with respect to <em>trg_seq</em>.
+Step 2: Generate pairwise alignments with <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/alg/seqalg/#ost.seq.alg.LocalAlign" title="(in OpenStructure v2.3.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.seq.alg.LocalAlign()</span></code></a>
+and only retain the ones with seqid >= <em>seqid_thresh</em>.
+Step 3: Extract respective templates from <em>fs_server</em> and score them by
+the sum of plDDT of aligned residues divided by <em>trg_seq</em> length.
+Step 4: Return top <em>tpl_n</em> (or less)</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fs_server</strong> (<a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a>) – Structure database - The AFDB</li>
+<li><strong>pentamatch</strong> (<a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a>) – Pentamatch object specific for <em>fs_server</em></li>
+<li><strong>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><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#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Target sequence</li>
+<li><strong>seqid_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Sequence Identity threshold [0-100] that alignment is
+considered further</li>
+<li><strong>tpl_n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of templates that are finally returned based on
+described scoring</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Pentamatch_n:</th><td class="field-body"><p class="first">Number of sequences that are initially searched in
+<em>pentamatch</em></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of pairs with first element being the tpl score,
+the second element being a <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a> with
+first sequence being <em>trg_seq</em> and second sequence the hit found
+in <em>fs_server</em> with structure attached. If <em>fs_server</em> has been
+generated with the default procedure described in the docs,
+additional info is available in the name of the attached
+structure. That’s accessible with
+aln.GetSequence(1).GetAttachedView().GetName(). That is
+structured as “<UniprotAC> <Fragment> <AFDB version> <Idx>” where
+idx refers to the raw idx of the template in <em>fs_server</em>.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="function">
+<dt id="promod3.modelling.AFDBModel">
+<code class="descclassname">promod3.modelling.</code><code class="descname">AFDBModel</code><span class="sig-paren">(</span><em>fs_server</em>, <em>pentamatch</em>, <em>trg_seq</em>, <em>transfer_bfactors=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AFDBModel" title="Permalink to this definition">¶</a></dt>
+<dd><p>Build model with AFDB as template library</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fs_server</strong> (<a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a>) – Structure database - The AFDB</li>
+<li><strong>pentamatch</strong> (<a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a>) – Pentamatch object specific for <em>fs_server</em></li>
+<li><strong>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><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#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Target sequence</li>
+<li><strong>transfer_bfactors</strong> – Simple heuristic to transfer bfactors (plDDT) to
+model. In case of an aligned residue, bfactor
+(i.e. plDDT) gets simply transferred.
+Gaps are treated with a heuristic. This operates
+on the full stretch of remodelled amino acids and
+not solely on the gap indicated by the alignment.
+We first derive a minimum plDDT which is
+0.5*min(n_stem_plddt, c_stem_plddt). The plDDT
+values of the processed amino acids then linearly
+decreases from the stem towards that minimum with
+a slope of 0.25 (i.e. reach the minimum value when
+they’re 4 residues away).</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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 4 elements. 1: The model 2: The model score
+based on plDDT 3: Pairwise alignment (first seq: <em>trg_seq</em>,
+second seq: tpl seq) 4: Template name (formatted as
+“<uniprot AC> <AFDB_fragment> <AFDB_version> <chain name>”).
+If no appropriate template can be found, all 4 elements are None.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.modelling.FSStructureServer">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">FSStructureServer</code><span class="sig-paren">(</span><em>db_dir</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FSStructureServer" title="Permalink to this definition">¶</a></dt>
+<dd><p>FSStructureServer - A filesystem based AFDB structure server</p>
+<p>Stores OMF data entries in huge binary files and extracts the respective
+binary data blobs with an indexing mechanism. Efficient reading of these
+huge files is delegated to the OS using the Python mmap module.</p>
+<p>Data creation happens with static Create function: <a class="reference internal" href="#promod3.modelling.FSStructureServer.FromDataChunks" title="promod3.modelling.FSStructureServer.FromDataChunks"><code class="xref py py-func docutils literal notranslate"><span class="pre">FromDataChunks()</span></code></a>.
+The required preprocessing must be done with external scripts.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>db_dir</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>) – Directory containing required files. 1) pos.dat (see
+<a class="reference internal" href="#promod3.modelling.FSStructureServer.pos" title="promod3.modelling.FSStructureServer.pos"><code class="xref py py-attr docutils literal notranslate"><span class="pre">pos</span></code></a>) 2) length.dat (see <a class="reference internal" href="#promod3.modelling.FSStructureServer.length" title="promod3.modelling.FSStructureServer.length"><code class="xref py py-attr docutils literal notranslate"><span class="pre">length</span></code></a>)
+3) chunk.dat (see <a class="reference internal" href="#promod3.modelling.FSStructureServer.chunk" title="promod3.modelling.FSStructureServer.chunk"><code class="xref py py-attr docutils literal notranslate"><span class="pre">chunk</span></code></a>) 4) indexer.dat (see
+<a class="reference internal" href="#promod3.modelling.FSStructureServer.indexer" title="promod3.modelling.FSStructureServer.indexer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">indexer</span></code></a>) 4) one or several files with pattern
+fs_data_[x].dat (see <a class="reference internal" href="#promod3.modelling.FSStructureServer.data" title="promod3.modelling.FSStructureServer.data"><code class="xref py py-attr docutils literal notranslate"><span class="pre">data</span></code></a>)</td>
+</tr>
+</tbody>
+</table>
+<dl class="attribute">
+<dt id="promod3.modelling.FSStructureServer.pos">
+<code class="descname">pos</code><a class="headerlink" href="#promod3.modelling.FSStructureServer.pos" title="Permalink to this definition">¶</a></dt>
+<dd><p>Start positions of data in internal linear memory layout</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal notranslate"><span class="pre">np.ndarray</span></code> with dtype np.int64</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.FSStructureServer.length">
+<code class="descname">length</code><a class="headerlink" href="#promod3.modelling.FSStructureServer.length" title="Permalink to this definition">¶</a></dt>
+<dd><p>Lengths of data in internal linear memory layout</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal notranslate"><span class="pre">np.ndarray</span></code> with dtype np.int32</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.FSStructureServer.chunk">
+<code class="descname">chunk</code><a class="headerlink" href="#promod3.modelling.FSStructureServer.chunk" title="Permalink to this definition">¶</a></dt>
+<dd><p>Chunk, in which entry is stored</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal notranslate"><span class="pre">np.ndarray</span></code> with dtype np.int16</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.FSStructureServer.indexer">
+<code class="descname">indexer</code><a class="headerlink" href="#promod3.modelling.FSStructureServer.indexer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Internal data structure - Relates entries with data indices</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal notranslate"><span class="pre">np.ndarray</span></code> with dtype np.int32</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.FSStructureServer.search_keys">
+<code class="descname">search_keys</code><a class="headerlink" href="#promod3.modelling.FSStructureServer.search_keys" title="Permalink to this definition">¶</a></dt>
+<dd><p>Internal data structure - Relates entries with data indices</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.FSStructureServer.data">
+<code class="descname">data</code><a class="headerlink" href="#promod3.modelling.FSStructureServer.data" title="Permalink to this definition">¶</a></dt>
+<dd><p>Internal binary data in memory mapped files</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><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/mmap.html#mmap.mmap" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">mmap.mmap</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.FSStructureServer.n_entries">
+<code class="descname">n_entries</code><a class="headerlink" href="#promod3.modelling.FSStructureServer.n_entries" title="Permalink to this definition">¶</a></dt>
+<dd><p>Number of entries</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.FSStructureServer.GetIdx">
+<code class="descname">GetIdx</code><span class="sig-paren">(</span><em>uniprot_ac</em>, <em>fragment='F1'</em>, <em>version='v4'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FSStructureServer.GetIdx" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get internal idx of stored data</p>
+<p>Can be used for data retrieval with <a class="reference internal" href="#promod3.modelling.FSStructureServer.GetOMFByIdx" title="promod3.modelling.FSStructureServer.GetOMFByIdx"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetOMFByIdx()</span></code></a></p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>uniprot_ac</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>) – Uniprot AC</li>
+<li><strong>fragment</strong> (class:<cite>str</cite>) – AFDB entries are potentially split to fragments
+99.999% of all entries only have one fragment: F1</li>
+<li><strong>version</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>) – Version of entry</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal idx of that entry</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if no such entry exists</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.FSStructureServer.GetOMFByIdx">
+<code class="descname">GetOMFByIdx</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FSStructureServer.GetOMFByIdx" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get stored OMF data structure</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><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>) – Internal index which can be derived from <a class="reference internal" href="#promod3.modelling.FSStructureServer.GetIdx" title="promod3.modelling.FSStructureServer.GetIdx"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetIdx()</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">OMF data structure of type <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.io.OMF</span></code></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if <em>idx</em> is out of range</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.FSStructureServer.GetOMF">
+<code class="descname">GetOMF</code><span class="sig-paren">(</span><em>uniprot_ac</em>, <em>fragment='F1'</em>, <em>version='v4'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FSStructureServer.GetOMF" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get stored OMF data structure</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>uniprot_ac</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>) – Uniprot AC</li>
+<li><strong>fragment</strong> (class:<cite>str</cite>) – AFDB entries are potentially split to fragments
+99.999% of all entries only have one fragment: F1</li>
+<li><strong>version</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>) – Version of entry</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">OMF data structure of type <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.io.OMF</span></code></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if no such entry exists</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="promod3.modelling.FSStructureServer.FromDataChunks">
+<em class="property">static </em><code class="descname">FromDataChunks</code><span class="sig-paren">(</span><em>chunk_dir</em>, <em>db_dir</em>, <em>chunk_bytes=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FSStructureServer.FromDataChunks" title="Permalink to this definition">¶</a></dt>
+<dd><p>Static method to create new database from preprocessed data</p>
+<p>Data preprocessing consists of creating several data chunks that are
+pickled to disk.
+In detail: each chunk is a pickled file containing a list, where each
+entry is a tuple with 4 elements: 1) uniprot_ac (<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>)
+2) fragment (<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>) 3) version (<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>) 4) structure data
+(<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.io.OMF</span></code> object which has been written to a bytes object and
+compressed with gzip)</p>
+<p>The data itself is again stored in chunks of binary data which are
+indexed.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>chunk_dir</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to directory containing described data chunks</li>
+<li><strong>db_dir</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>) – Output directory - Creates all files that are needed for
+<a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a></li>
+<li><strong>chunk_bytes</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Size in bytes of binary data chunks in final
+database - default None: Everything ends up in one
+single chunk</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a> with all data from <em>chunk_dir</em></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.modelling.PentaMatch">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">PentaMatch</code><span class="sig-paren">(</span><em>db_dir</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PentaMatch" title="Permalink to this definition">¶</a></dt>
+<dd><p>Pentamer matching for fast sequence searches</p>
+<p><a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a> has fast sequence searches with low sensitivity as
+use case. Specifically searching the full AFDB. Stores all unique pentamers
+for each search sequence. Given a query sequence, it computes the number of
+matching pentamers with respect to each search sequence and returns the top
+hits.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>db_dir</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>) – Directory containing all required files (indexer.dat,
+pos.dat, length.dat, meta.dat). New <a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a>
+objects can be derived using the static <a class="reference internal" href="#promod3.modelling.PentaMatch.FromSeqList" title="promod3.modelling.PentaMatch.FromSeqList"><code class="xref py py-func docutils literal notranslate"><span class="pre">FromSeqList()</span></code></a>
+creator.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if any required file is missing in <em>db_dir</em></td>
+</tr>
+</tbody>
+</table>
+<dl class="attribute">
+<dt id="promod3.modelling.PentaMatch.indexer">
+<code class="descname">indexer</code><a class="headerlink" href="#promod3.modelling.PentaMatch.indexer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Entry indices for pentamers</p>
+<p>Entry data for one pentamer can be extracted with the respective values in
+<a class="reference internal" href="#promod3.modelling.PentaMatch.pos" title="promod3.modelling.PentaMatch.pos"><code class="xref py py-attr docutils literal notranslate"><span class="pre">pos</span></code></a> and <a class="reference internal" href="#promod3.modelling.PentaMatch.length" title="promod3.modelling.PentaMatch.length"><code class="xref py py-attr docutils literal notranslate"><span class="pre">length</span></code></a></p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body">memory mapped <code class="xref py py-class docutils literal notranslate"><span class="pre">np.ndarray</span></code> of dtype np.int32</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.PentaMatch.pos">
+<code class="descname">pos</code><a class="headerlink" href="#promod3.modelling.PentaMatch.pos" title="Permalink to this definition">¶</a></dt>
+<dd><p>Start position for each pentamer in <a class="reference internal" href="#promod3.modelling.PentaMatch.indexer" title="promod3.modelling.PentaMatch.indexer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">indexer</span></code></a></p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal notranslate"><span class="pre">np.ndarray</span></code> of dtype np.int64 with 3.2E6 entries</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.PentaMatch.length">
+<code class="descname">length</code><a class="headerlink" href="#promod3.modelling.PentaMatch.length" title="Permalink to this definition">¶</a></dt>
+<dd><p>Length for each pentamer in <a class="reference internal" href="#promod3.modelling.PentaMatch.indexer" title="promod3.modelling.PentaMatch.indexer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">indexer</span></code></a></p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal notranslate"><span class="pre">np.ndarray</span></code> of dtype np.int32 with 3.2E6 entries</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.PentaMatch.N">
+<code class="descname">N</code><a class="headerlink" href="#promod3.modelling.PentaMatch.N" title="Permalink to this definition">¶</a></dt>
+<dd><p>Number of entries in underlying <a class="reference internal" href="#promod3.modelling.FSStructureServer" title="promod3.modelling.FSStructureServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FSStructureServer</span></code></a></p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.PentaMatch.TopN">
+<code class="descname">TopN</code><span class="sig-paren">(</span><em>N</em>, <em>sequence</em>, <em>return_counts=False</em>, <em>unique_pentamers=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PentaMatch.TopN" title="Permalink to this definition">¶</a></dt>
+<dd><p>Find top-N matches given <em>sequence</em></p>
+<p>Identifies unique pentamers in <em>sequence</em> and counts number of
+occurences in each entry. Returns the top-N entries with respect
+to counts.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>N</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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 results to return</li>
+<li><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 to search</li>
+<li><strong>return_counts</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>) – Additionally return underlying pentamer counts</li>
+<li><strong>unique_pentamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Set to True if <a class="reference internal" href="#promod3.modelling.PentaMatch.indexer" title="promod3.modelling.PentaMatch.indexer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">indexer</span></code></a> contains only
+unique pentamers for each entry. This way we
+can use faster methods to accumulate counts.
+In detail: accumulator[indices] += 1 is much
+faster than np.add.at(accumulator, indices, 1).
+But the latter is required if there are
+duplicates.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/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> with length <em>N</em> specifying
+entry indices. If <em>return_counts</em> is true, the
+<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> contains <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two elements:
+1) count 2) index.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if N is invalid or sequence is shorter
+than 5 characters</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="promod3.modelling.PentaMatch.FromSeqList">
+<em class="property">static </em><code class="descname">FromSeqList</code><span class="sig-paren">(</span><em>fasta_file</em>, <em>db_dir</em>, <em>entries_from_seqnames=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PentaMatch.FromSeqList" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates PentaMatch object from Fasta file</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fasta_file</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to Fasta file with sequences</li>
+<li><strong>db_dir</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>) – Files required for <a class="reference internal" href="#promod3.modelling.PentaMatch" title="promod3.modelling.PentaMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">PentaMatch</span></code></a> will be dumped
+here, will be created if non-existent.</li>
+<li><strong>entries_from_seqnames</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to False, indices returned by
+<a class="reference internal" href="#promod3.modelling.PentaMatch.TopN" title="promod3.modelling.PentaMatch.TopN"><code class="xref py py-func docutils literal notranslate"><span class="pre">TopN()</span></code></a> refer to position in
+<em>fasta_file</em>. If set to True, integer
+indices are parsed from sequence name.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">class:<cite>PentaMatch</cite></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.Error</span></code> if <em>entries_from_seqnames</em> is True but
+sequence name cannot be casted to int.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
</div>
</div>
@@ -683,7 +1152,7 @@ matter in this case.</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 33480a71..367970a4 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Gaps — ProMod3 3.2.1 documentation</title>
+ <title>Handling Gaps — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
@@ -51,8 +50,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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></li>
-<li><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></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/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></li>
</ul>
</td>
@@ -107,7 +106,7 @@ are valid and:</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -258,13 +257,13 @@ extend the gap past another gap.</p>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
<code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<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><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
<code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.2/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><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -309,7 +308,7 @@ False if no new extension possible.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/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.</li>
+<li><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/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
</ul>
</td>
</tr>
@@ -350,7 +349,7 @@ valid termini.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/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.</li>
+<li><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/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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>If -1, all possible non-terminal gaps are returned.</li>
<li>If >= 0, this restricts the max. gap-length
@@ -403,7 +402,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
<li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
<li><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.</li>
-<li><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.</li>
+<li><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/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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>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).</li>
@@ -662,7 +661,7 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index 72df0c02..8329bb87 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>modelling - Protein Modelling — ProMod3 3.2.1 documentation</title>
+ <title>modelling - Protein Modelling — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Modelling Pipeline" href="pipeline.html" />
@@ -67,6 +66,7 @@ a model fully automatically as follows:</p>
</li>
<li class="toctree-l1"><a class="reference internal" href="model_checking.html">Model Checking</a><ul>
<li class="toctree-l2"><a class="reference internal" href="model_checking.html#detecting-ring-punches">Detecting Ring Punches</a></li>
+<li class="toctree-l2"><a class="reference internal" href="model_checking.html#detecting-non-planar-rings">Detecting Non-Planar Rings</a></li>
<li class="toctree-l2"><a class="reference internal" href="model_checking.html#model-checking-with-molprobity">Model Checking With MolProbity</a></li>
</ul>
</li>
@@ -106,6 +106,7 @@ a model fully automatically as follows:</p>
<li class="toctree-l2"><a class="reference internal" href="algorithms.html#rigid-blocks">Rigid Blocks</a></li>
<li class="toctree-l2"><a class="reference internal" href="algorithms.html#de-novo-modelling">De Novo Modelling</a></li>
<li class="toctree-l2"><a class="reference internal" href="algorithms.html#motif-finder">Motif Finder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="algorithms.html#afdb-modelling">AFDB Modelling</a></li>
</ul>
</li>
</ul>
@@ -179,7 +180,7 @@ a model fully automatically as follows:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index a04ae292..98a3289a 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
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- <title>Handling Loop Candidates — ProMod3 3.2.1 documentation</title>
+ <title>Handling Loop Candidates — ProMod3 3.3.0 documentation</title>
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@@ -14,7 +14,6 @@
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@@ -123,8 +122,8 @@ a fragment database.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
-<li><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</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/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></li>
<li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – The fragment database</li>
@@ -235,9 +234,9 @@ not depending on a metropolis criterium.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/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
@@ -279,9 +278,9 @@ candidate. This leads to an increase in number of loops.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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</li>
<li><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</li>
<li><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</li>
@@ -355,7 +354,7 @@ anything is raised when calculating the scores.</p>
<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
-<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
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.3.1)"><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>
@@ -371,7 +370,7 @@ with this DB).</p>
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></li>
<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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.</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
<li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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>.</li>
</ul>
</td>
@@ -403,8 +402,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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.</li>
-<li><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.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
</ul>
</td>
</tr>
@@ -1149,7 +1148,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index dfab8aa3..7cd4dcf9 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Fitting Loops Into Gaps — ProMod3 3.2.1 documentation</title>
+ <title>Fitting Loops Into Gaps — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
@@ -74,11 +73,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
-<li><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.
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
and phi angle (-1.0472) to evaluate the first angle.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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.
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
psi angle (-0.7854) to evaluate the last angle.</li>
@@ -115,8 +114,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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</li>
-<li><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</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><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></li>
@@ -317,7 +316,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -339,7 +338,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -362,7 +361,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -384,7 +383,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -406,7 +405,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
</ul>
</td>
@@ -651,7 +650,7 @@ the one given in the constructor.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
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diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 04ece5d3..d39b5fe7 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Model Checking — ProMod3 3.2.1 documentation</title>
+ <title>Model Checking — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Handling Gaps" href="gap_handling.html" />
@@ -48,14 +47,14 @@ three of the atoms exist (center and radii are estimated then).</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/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/2.2/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>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><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/2.3.1/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.3.1)"><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/2.2/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>).</td>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</td>
</tr>
</tbody>
</table>
@@ -71,11 +70,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</li>
-<li><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.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
</td>
</tr>
@@ -94,7 +93,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</li>
-<li><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.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
@@ -119,7 +118,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>candidates</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
Offending candidates are removed from this list.</li>
-<li><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.</li>
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
<li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li>
<li><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/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>.</li>
@@ -137,6 +136,74 @@ must have as many elements as <em>candidates</em>.</li>
See <a class="reference internal" href="#promod3.modelling.FilterCandidates" title="promod3.modelling.FilterCandidates"><code class="xref py py-func docutils literal notranslate"><span class="pre">FilterCandidates()</span></code></a>.</p>
</dd></dl>
+</div>
+<div class="section" id="detecting-non-planar-rings">
+<h2>Detecting Non-Planar Rings<a class="headerlink" href="#detecting-non-planar-rings" title="Permalink to this headline">¶</a></h2>
+<dl class="function">
+<dt id="promod3.modelling.GetNonPlanarRings">
+<code class="descclassname">promod3.modelling.</code><code class="descname">GetNonPlanarRings</code><span class="sig-paren">(</span><em>ent</em>, <em>max_dist_thresh=0.1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetNonPlanarRings" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get list of residues with rings that non-planar in the given structure.</p>
+<p>Only residues with res.one_letter_code in [‘Y’, ‘F’, ‘W’, ‘H’] that contain
+all expected ring atoms are considered.</p>
+<p>Planarity is defined by the maximum distance of any ring atom to the optimal
+plane describing the ring. This plane is constructed by defining a point on
+the plane, here the geometric center of the ring atoms and a normal. We
+construct an orthogonal basis [e1, e2, e3]. e1 points in direction with
+lowest variance of ring atoms and e3 in direction with highest variance.
+e1 is thus the plane normal. Internally this is done using a singular value
+decomposition algorithm.</p>
+<p>To put the default threshold of 0.1 in perspective: if you calculate these
+distances on the same non-redundant set of experimental structures as
+ProMod3 used to derive its rotamer libraries, 99.9 % of the residues are
+within 0.065 (HIS), 0.075 (TRP), 0.057 (TYR), 0.060 (PHE).</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect non-planar rings.</li>
+<li><strong>max_dist_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – A residue that contains a ring is considered
+non-planar if the max distance of any ring-atom to
+the optimal ring plane is above this threshold.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a>) which have a non-planar ring.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="function">
+<dt id="promod3.modelling.HasNonPlanarRings">
+<code class="descclassname">promod3.modelling.</code><code class="descname">HasNonPlanarRings</code><span class="sig-paren">(</span><em>ent</em>, <em>max_dist_thresh=0.1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.HasNonPlanarRings" title="Permalink to this definition">¶</a></dt>
+<dd><p>Check if any ring is non-planar in the given structure.</p>
+<p>Calls <a class="reference internal" href="#promod3.modelling.GetNonPlanarRings" title="promod3.modelling.GetNonPlanarRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetNonPlanarRings()</span></code></a> with given parameters and returns if any
+residue is considered non-planar.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect non-planar rings</li>
+<li><strong>max_dist_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – A residue that contains a ring is considered
+non-planar if the max distance of any ring-atom to
+the optimal ring plane is above this threshold.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">True, if any ring is non-planar</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/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>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</div>
<div class="section" id="model-checking-with-molprobity">
<h2>Model Checking With MolProbity<a class="headerlink" href="#model-checking-with-molprobity" title="Permalink to this headline">¶</a></h2>
@@ -184,7 +251,7 @@ with <code class="docutils literal notranslate"><span class="pre">MolProbity</sp
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/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>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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”
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
</td>
</tr>
@@ -201,7 +268,7 @@ executable is not found.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
</tr>
</tbody>
</table>
@@ -293,7 +360,7 @@ executable is not found.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index e05d2284..e307c44d 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generating Loops De Novo — ProMod3 3.2.1 documentation</title>
+ <title>Generating Loops De Novo — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
@@ -496,9 +495,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>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.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/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>
@@ -546,9 +545,9 @@ dihedral angles as it is the case for the <a class="reference internal" href="#p
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
</ul>
</td>
@@ -588,9 +587,9 @@ solutions. The KICCloser simply picks the first one.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
<li><strong>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.</li>
</ul>
@@ -629,7 +628,7 @@ superposing the c_stem with the desired positions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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.</td>
</tr>
</tbody>
@@ -667,7 +666,7 @@ superposing the n_stem with the desired positions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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.</td>
</tr>
</tbody>
@@ -948,7 +947,7 @@ internal counter to 0</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 18468834..55480829 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Pipeline — ProMod3 3.2.1 documentation</title>
+ <title>Modelling Pipeline — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Model Checking" href="model_checking.html" />
@@ -108,7 +107,7 @@ chain follows afterwards.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -134,13 +133,13 @@ Gaps of different chains are appended one after another.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
<code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<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
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -149,7 +148,7 @@ of the target protein.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
<code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<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
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><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
@@ -158,7 +157,7 @@ to fill it manually or even better by the convenient function
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/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></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -345,7 +344,7 @@ 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/2.2/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>
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><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
@@ -375,7 +374,7 @@ as information about insertions and deletions in the gaps list.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><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.</li>
<li><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
@@ -388,7 +387,7 @@ 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/2.2/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>,
+If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><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
@@ -414,7 +413,7 @@ to False.</li>
<li>the second sequence does not have an attached structure</li>
<li>the residues of the template structure do not match with the
alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.3.1)"><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))</li>
<li>the target sequence has a non-zero offset (cannot be honored as
the resulting model will always start its residue numbering at 1)</li>
@@ -458,12 +457,12 @@ return an incomplete model.</p>
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
alignment.</li>
<li><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/2.2/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>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.3.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
with the optional force fields in <cite>extra_force_fields</cite>.</li>
-<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/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
+<li><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/2.3.1/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.3.1)"><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
@@ -484,7 +483,7 @@ limited.</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -659,7 +658,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
<li><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</li>
<li><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</li>
<li><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</li>
-<li><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
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
they’re copied over</li>
</ul>
</td>
@@ -690,7 +689,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</li>
-<li><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
+<li><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/2.3.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
</ul>
</td>
</tr>
@@ -847,7 +846,7 @@ 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/2.2/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>).</li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.3.1)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/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
@@ -1215,9 +1214,9 @@ one is loaded if None.</li>
<dl class="function">
<dt id="promod3.modelling.MinimizeModelEnergy">
-<code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em>, <em>tolerance_sd=1.0</em>, <em>tolerance_lbfgs=1.0</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/2.2/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.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.3.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
<li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
@@ -1243,9 +1242,13 @@ minimization is aborted. This issue is logged and added as a major issue to
<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations for SD+LBFGS</li>
<li><strong>max_iter_sd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within SD method</li>
<li><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</li>
+<li><strong>tolerance_sd</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>) – Tolerance parameter passed to ApplySD of
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> object.</li>
+<li><strong>tolerance_lbfgs</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>) – Tolerance parameter passed to ApplyLBFGS of
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> object.</li>
<li><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>).</li>
-<li><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
+<li><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/2.3.1/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
</ul>
</td>
@@ -1253,7 +1256,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -1278,6 +1281,7 @@ created per unclosed gap and the stems of the gap are added to the issue.</li>
<li>Remaining stereo-chemical problems after energy minimization. The affected
residues will have the boolean property “stereo_chemical_problem_backbone”
set to True, if the problem affects backbone atoms.</li>
+<li>Residues that contain non-planar rings.</li>
</ul>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -1341,8 +1345,8 @@ set to True, if the problem affects backbone atoms.</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/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></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></td>
</tr>
</tbody>
</table>
@@ -1416,17 +1420,17 @@ 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/2.2/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
+and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
sequences.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The processed alignment</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><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></td>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -1468,16 +1472,16 @@ 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/2.2/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>
+attached <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The processed alignment</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><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></td>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -1555,7 +1559,7 @@ attached <a class="reference external" href="https://www.openstructure.org/docs/
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 980622fd..53ea062e 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sidechain Reconstruction — ProMod3 3.2.1 documentation</title>
+ <title>Sidechain Reconstruction — ProMod3 3.3.0 documentation</title>
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@@ -14,7 +14,6 @@
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@@ -37,7 +36,7 @@
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
<li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<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></li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></li>
<li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
and used to reconstruct sidechains of single loops</li>
</ul>
@@ -92,7 +91,7 @@ and used to reconstruct sidechains of single loops</li>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><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.</li>
<li><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
@@ -117,7 +116,7 @@ parametrization.</li>
<li><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Initial epsilon for
<code class="xref py py-meth docutils literal notranslate"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</li>
<li><strong>energy_function</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – What energy function to use can be any in
-[“SCWRL4”, “SCWRL3”]</li>
+[“SCWRL4”, “SCWRL3”, “VINA”]</li>
</ul>
</td>
</tr>
@@ -204,7 +203,7 @@ environment before calling this!</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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.</li>
+<li><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/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
<li><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.</li>
<li><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.</li>
@@ -450,7 +449,7 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index 53ee73f3..fb4c10e0 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Using Binary Files In ProMod3 — ProMod3 3.2.1 documentation</title>
+ <title>Using Binary Files In ProMod3 — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="License" href="license.html" />
@@ -473,7 +472,7 @@ in the <code class="file docutils literal notranslate"><span class="pre">extras/
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 06632bde..400d9203 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Python Module Index — ProMod3 3.2.1 documentation</title>
+ <title>Python Module Index — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
@@ -146,7 +145,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/references.html b/doc/html/references.html
index c5cfde45..a7cf963d 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>References — ProMod3 3.2.1 documentation</title>
+ <title>References — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Changelog" href="changelog.html" />
@@ -227,7 +226,7 @@ Fragments. Proteins.</td></tr>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 3e3d467e..de7b370f 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>All Atom Scorers — ProMod3 3.2.1 documentation</title>
+ <title>All Atom Scorers — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
@@ -679,7 +678,7 @@ of residues in the input loop. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index ab4bc1a2..1c6e7ef0 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Score Environment — ProMod3 3.2.1 documentation</title>
+ <title>Backbone Score Environment — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
@@ -59,8 +58,8 @@ task.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><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/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><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.</td>
</tr>
</tbody>
@@ -97,7 +96,7 @@ structural data was already set, all the existing data gets cleared first.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -121,7 +120,7 @@ positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
+<li><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/2.3.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
</ul>
</td>
@@ -270,7 +269,7 @@ providing lists of integers.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -377,7 +376,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><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</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
or CB atoms</li>
</ul>
@@ -392,7 +391,7 @@ or CB atoms</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached.</td>
</tr>
@@ -517,7 +516,7 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index ff76e572..24f2cd2e 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Scorers — ProMod3 3.2.1 documentation</title>
+ <title>Backbone Scorers — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
@@ -371,7 +370,7 @@ called for every type of amino acids and for every <em>count</em> <= <em>max_
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
<li><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.</li>
</ul>
@@ -505,8 +504,8 @@ SetEnergy(aa2, aa1, bin, energy).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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.</li>
-<li><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.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
<li><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.</li>
</ul>
@@ -685,8 +684,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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.</li>
-<li><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.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
<li><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.</li>
<li><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.</li>
@@ -1390,7 +1389,7 @@ of residues to be scored. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index ebc4d6c9..606b2b56 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>scoring - Loop Scoring — ProMod3 3.2.1 documentation</title>
+ <title>scoring - Loop Scoring — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
@@ -171,7 +170,7 @@ scorers to it and finally score some loops:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 0de14121..2648f13f 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Other Scoring Functions — ProMod3 3.2.1 documentation</title>
+ <title>Other Scoring Functions — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
@@ -170,7 +169,7 @@ construction algorithm <a class="reference internal" href="../references.html#ca
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/search.html b/doc/html/search.html
index a60fd463..0e575bda 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Search — ProMod3 3.2.1 documentation</title>
+ <title>Search — ProMod3 3.3.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -15,7 +15,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<script type="text/javascript" src="_static/searchtools.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="#" />
@@ -100,7 +99,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index ab93b18c..9c6db87e 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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v:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:37,categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[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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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:[3,8],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,findpython:3,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:[0,2,3,4,8,10,11,13,22,26,28,35,36,49,50],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:[14,20,24,25,26,30,35,40,49,51],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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Actions","<code class=\"docutils literal notranslate\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3\u2019s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal notranslate\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop 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egin:[1,8,21,22,28,34,40],behalf:20,behav:[1,51],behaviour:[0,13,39,40,49,50,51],behind:8,being:[3,5,8,10,21,26,28,31,34,35,44,51],believ:53,bell:8,belong:[3,4,16,21,22,26,29,31,34,35,36,39,40,41,45,49,50],belov:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,bfactor:28,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:[1,4,8,16,17,25,26,27,28,39,41,51],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,blob:28,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:[1,8,10,11,13,14,21,22,25,26,28,29,31,32,33,34,35,36,37,39,41,44,49,50,51],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_plddt:28,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:[8,22,26,27,28,31,32,33,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,33,34,35,36,37,39,40,41,49,50,51],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:[0,8,13,20,25,26,27,28,29,35,37,39,41,48,49,50,51],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:[28,37],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],challeng:28,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:[13,20,26,28,35],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,chimerax:3,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],chunk:28,chunk_byt:28,chunk_dir:28,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],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Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"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=\"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=\"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,afdb:28,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:[33,51],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],planar:33,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 3d8e5095..0ab78f10 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Disulfid Bond Evaluation — ProMod3 3.2.1 documentation</title>
+ <title>Disulfid Bond Evaluation — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
@@ -67,10 +66,10 @@ rotamers to the result of the geometric expression.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
<li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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</li>
-<li><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</li>
-<li><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</li>
-<li><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</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
</ul>
</td>
</tr>
@@ -103,8 +102,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
-<li><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</li>
-<li><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</li>
+<li><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/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/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/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
<li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><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
@@ -199,7 +198,7 @@ describe the optimal rotamers in the according rotamer groups.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index e85a1e8f..0c4e69f7 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Frame - The Rigid Part — ProMod3 3.2.1 documentation</title>
+ <title>Frame - The Rigid Part — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
@@ -180,7 +179,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index 61732485..cc59c634 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Graph — ProMod3 3.2.1 documentation</title>
+ <title>Rotamer Graph — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
@@ -139,7 +138,7 @@ conformations for every amino acid position.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index e6e40a3b..855b5a7c 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>sidechain - Sidechain Modelling — ProMod3 3.2.1 documentation</title>
+ <title>sidechain - Sidechain Modelling — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
@@ -233,7 +232,7 @@ pipelines available in the modelling module.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index d54af5fd..a0efe043 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Rotamer Libraries — ProMod3 3.2.1 documentation</title>
+ <title>Loading Rotamer Libraries — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
@@ -178,7 +177,7 @@ incomplete if the last problem gets triggered.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index e33eb6e9..3ae62751 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.2.1 documentation</title>
+ <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Frame - The Rigid Part" href="frame.html" />
@@ -90,7 +89,7 @@ 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/2.2/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
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><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">
@@ -115,12 +114,12 @@ 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/2.2/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>
+defined in <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
</tr>
@@ -218,7 +217,7 @@ evaluated by the underlying scoring function.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The position of the particle</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/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></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -276,7 +275,7 @@ function</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
<li><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
<li><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
@@ -285,7 +284,7 @@ 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.</li>
-<li><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,
+<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><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
@@ -317,7 +316,7 @@ function</p>
<li><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</li>
<li><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.</li>
-<li><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</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
</ul>
</td>
</tr>
@@ -429,7 +428,7 @@ function</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
<li><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
</ul>
</td>
</tr>
@@ -507,7 +506,7 @@ in this process.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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></li>
<li><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
@@ -783,7 +782,7 @@ No atoms are removed from <strong>res</strong> in this process.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
<li><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
@@ -1183,7 +1182,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
<li><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
@@ -1317,7 +1316,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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</li>
<li><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
@@ -1460,7 +1459,7 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 3e5431c2..fc7229f7 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Constructor — ProMod3 3.2.1 documentation</title>
+ <title>Rotamer Constructor — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
@@ -69,7 +68,7 @@ an interface implemented by scoring function specific constructors
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
@@ -124,7 +123,7 @@ don’t show up in a rotamer).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
@@ -167,7 +166,7 @@ you observe in a rotamer).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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</li>
@@ -255,7 +254,7 @@ any rotamers for ALA and GLY.</td>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">
<code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<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>.
+<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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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
@@ -265,7 +264,7 @@ skipped.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
</ul>
@@ -281,7 +280,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">
<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<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
+<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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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
@@ -299,10 +298,10 @@ as in the <code class="xref py py-class docutils literal notranslate"><span clas
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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.</li>
-<li><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</li>
+<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
</ul>
</td>
</tr>
@@ -462,7 +461,7 @@ to be assigned</li>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>res</em>, <em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<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
+<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/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><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
@@ -480,7 +479,7 @@ 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/2.2/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
+properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.3.1)"><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>.</li>
@@ -504,7 +503,7 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></li>
<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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></li>
</ul>
@@ -526,7 +525,7 @@ as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerCons
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td>
@@ -546,7 +545,7 @@ contains the atoms from <em>residue</em>.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td>
@@ -629,7 +628,7 @@ contains the atoms from <em>residue</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 6dd76800..b2f7c4e3 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Library — ProMod3 3.2.1 documentation</title>
+ <title>Rotamer Library — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Rotamer Graph" href="graph.html" />
@@ -434,7 +433,7 @@ NaN.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/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</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></td>
</tr>
@@ -458,7 +457,7 @@ are NaN.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><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</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></li>
</ul>
</td>
@@ -728,7 +727,7 @@ valid and non rotameric, INVALID otherwise.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 241f685e..c1ae5456 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Subrotamer Optimization — ProMod3 3.2.1 documentation</title>
+ <title>Subrotamer Optimization — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="../_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
@@ -145,7 +144,7 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index 44fd3f6c..109d865d 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Contributing — ProMod3 3.2.1 documentation</title>
+ <title>Contributing — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Documentation For Developers" href="developers.html" />
@@ -111,7 +110,7 @@ information on that matter in the developer section of the documentation
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/users.html b/doc/html/users.html
index 81a37ae0..82c3ffa1 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Users — ProMod3 3.2.1 documentation</title>
+ <title>Documentation For Users — ProMod3 3.3.0 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>
@@ -14,7 +14,6 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/language_data.js"></script>
- <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Getting Started" href="gettingstarted.html" />
@@ -178,7 +177,7 @@ scripts using the functionality of this library.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2023, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
--
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