diff --git a/CHANGELOG b/CHANGELOG
index e83fc8600d486f04ba3a8f6cd0de7f3468855d4d..bf7d79fe8f2b54752a8d460224dd9459541fd53a 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -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/CMakeLists.txt b/CMakeLists.txt
index c350a53b11f1e83862a563b3f5a9d6c301d588ca..32e8b9d5a0cd668e86a0be542dd92b6048382f82 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -24,8 +24,8 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 3)
-set(PROMOD3_VERSION_MINOR 2)
-set(PROMOD3_VERSION_PATCH 1)
+set(PROMOD3_VERSION_MINOR 3)
+set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
@@ -103,7 +103,7 @@ if(NOT DISABLE_DOCUMENTATION)
# this URL should always point to the latest version of OST
set(OST_DOC_URL "https://www.openstructure.org/docs")
endif()
-find_package(OPENSTRUCTURE 2.3.0 REQUIRED
+find_package(OPENSTRUCTURE 2.4.0 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
if(CMAKE_COMPILER_IS_GNUCXX)
diff --git a/container/Dockerfile b/container/Dockerfile
index d9bb19166ee7b3a49153565200f8326b6ceb999b..247b5f20d931549e0b4424f51400ee13de7e424d 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -1,9 +1,9 @@
-ARG OPENSTRUCTURE_IMAGE_TAG="2.3.0-focal"
+ARG OPENSTRUCTURE_IMAGE_TAG="2.4.0-jammy"
FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
-ARG PROMOD_VERSION="3.2.1"
+ARG PROMOD_VERSION="3.3.0"
ARG SRC_FOLDER="/usr/local/src"
diff --git a/container/Singularity b/container/Singularity
index 11a920f192d13f3040e35f879ae7bead5719cdf0..d66131adf2d38ebab6d27a323c8094cc5d01cb8f 100644
--- a/container/Singularity
+++ b/container/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/promod3:3.2.1-OST2.3.0-focal
+From: registry.scicore.unibas.ch/schwede/promod3:3.3.0-OST2.4.0-jammy
%post
##############################################################################
# POST
diff --git a/doc/cmake.py b/doc/cmake.py
index 6075cf5a75c6a62eba1bf43be6d153cf12c6a653..2bdb01c9dc68dd650bdb4c387d06d0abcfae705a 100644
--- a/doc/cmake.py
+++ b/doc/cmake.py
@@ -2,6 +2,8 @@
# file Copyright.txt or https://cmake.org/licensing for details.
# Team SMNG note: This file comes from here: https://github.com/Kitware/CMake/blob/master/Utilities/Sphinx/cmake.py
+# Team SMNG note: applied patch from here: https://salsa.debian.org/science-team/ycm-cmake-modules/-/blob/master/debian/patches/fix-sphinx-build.patch
+# On Ubuntu 22.04 LTS I needed to additionally install the following package: python3-sphinxcontrib.qthelp
import os
import re
@@ -61,8 +63,12 @@ CMakeLexer.tokens["root"] = [
# Monkey patch for sphinx generating invalid content for qcollectiongenerator
# https://bitbucket.org/birkenfeld/sphinx/issue/1435/qthelp-builder-should-htmlescape-keywords
-from sphinx.util.pycompat import htmlescape
-from sphinx.builders.qthelp import QtHelpBuilder
+import html
+try:
+ from sphinxcontrib.qthelp import QtHelpBuilder
+except ImportError:
+ # sphinx < 4.0
+ from sphinx.builders.qthelp import QtHelpBuilder
old_build_keywords = QtHelpBuilder.build_keywords
def new_build_keywords(self, title, refs, subitems):
old_items = old_build_keywords(self, title, refs, subitems)
@@ -71,7 +77,7 @@ def new_build_keywords(self, title, refs, subitems):
before, rest = item.split("ref=\"", 1)
ref, after = rest.split("\"")
if ("<" in ref and ">" in ref):
- new_items.append(before + "ref=\"" + htmlescape(ref) + "\"" + after)
+ new_items.append(before + "ref=\"" + html.escape(ref) + "\"" + after)
else:
new_items.append(item)
return new_items
diff --git a/doc/conf.py.in b/doc/conf.py.in
index d00634a2a04492443ec1044a9803a8892225649a..c01cff17230e43ad52465d37c2b28baea42714cd 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'2013-2021, 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
@@ -286,7 +286,7 @@ rst_epilog = """
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
-.. |ost_version| replace:: 2.3.0
+.. |ost_version| replace:: 2.4.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
diff --git a/doc/html/_sources/changelog.rst.txt b/doc/html/_sources/changelog.rst.txt
index e83fc8600d486f04ba3a8f6cd0de7f3468855d4d..bf7d79fe8f2b54752a8d460224dd9459541fd53a 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 b36bf5bb77ef1ee30a716469a803e652a4420a5e..c9db60f1f7f57dc8ac74e00d8db94b9cb018c4be 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 ab5b5eb9eec534e44b685fb09571c30ce77ed2a7..400f3737f7389d157300c6bce938acf6abc68353 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 22999c300b2e17707358b76492cab207c4d44548..e42d212690329abb5fb8ac48021c049591f80733 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 c17396d63f79bdf26a29d16e85d25dc278ef95b4..e250c0387d6988e10e2be5816abbe0efd587ed46 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 408223d63c3356f2cbddee7f22175516ff007228..c91acf1bae26aabd3aa6db5cd0a96a241f1178f1 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 d013cbc79d4fb5dd10f9d668518e7e7ce0e40c8b..78cfa9bc845f3fa97dee73903c2fa83f616a231d 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 9f00e07757540e4ddd5bc2b3b7a0a744fcda935f..4f246044f6a6a310bcb9755979772f35199e9251 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 a18b6c781a3bb93cdd4087606e9e03e918e0d8be..403551e94de69196008c9d1a10b20f9fff92efc3 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 efd454dae0676f9373d8fcb8a97239da4e4397d9..70b21e457a6b9ca919f128539fbf7faad29c393a 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 1cd6fb1b509d6a2aa6e8002a02d8a2d63b57c3af..11a0a45b2354ae1755686ac1a1a41870a35825a0 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 61c1dc21108f9c9bc370ce4264333beb34a73f94..79d7f49b1e7d3062d09d3c7938c42060d6d74c0f 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 9f612109a6e472105c26df477282cb25ce8cbf50..1fdfbf12c0a454f631ecf3941e3ed35e522308d3 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 4db119f6e43fd07a28ca388d8630770c5f964dda..7a551e0371800bbc8d785ddae9b5273b80918942 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 1d1d0b3a00098296d63b6421e6f39cdc5e26e41c..6c1b852d7a1cc9d8fcfd2d69506801b6125e8e84 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 6abb2303e27b455c68ba34793f62d6acebf77093..02ce0b8a743df0d8fe0254150ab922cb55ddc4f1 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 551c891176d54176d2663a43965cb80a1a739b21..0a8d27bc7bf0adf0a92aa6f9d71e444b145f25f7 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 ad588482c05bbd2192e5f094c543e73abc327ccb..7547ac6444e2cf93673a1a526152480460c6fba9 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 795b6c9fad6daab07814879961cac843f5caba8e..f22d0b777e665bcae8314cddf1a88860ff34e699 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 f6cbb73e8d60cf848b57bb6bf6609d49473eb9d2..1af7258a0b77d5cb2c5cdfa467db86337f4f8d31 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 2a060c73826e7fe234a7ce2a43e024b9755ff058..5a09c032e65f1f2b17e9d6a8e37176cabad99507 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 7084fedebc67848cc80f6bd2f5f058fe931016ed..91607a8019c11b7066bc5a07ccef624aa6e6bffe 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 5ef68c4bd5228d4b81369271fa83fc79b7cf5f62..5b605538c950d2db69e465bcd77b129727a40f3d 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 80a23c32bac0dd7b3a391415c5fe91aa5ffc6e88..e79788840098db2df078376db7ffd2831adbf510 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 48736a0c783604f8b6d4ffc81ebfacd942b36dd3..94f13fec1f198235bb39ef5e18cb34ce67bbef7f 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 2fa7eaf1e51cfcc2ccd9a981b902d1ebfdb7e3f8..04749084cd6ec9c8e570c832900220e9bf4f9e94 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.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index f27b4188bdce492b5a6be0d1175442ff9542ba6a..5affbe0d808be1eea3e7a49074249b8cca596901 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.
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diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index bc203c9950665a139f17eae99ff48700adbec51c..adc18a285338a31c95c7f84aa7671b3a9efa8ec7 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.
|
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 5ea7d7d40d1528fe32dde6b8137749297f3b63e4..540e0f8c4d81fe33abbcddbfbe19838418f93433 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 3d5bd43d253ffba41578c413e00a7ba26a6c8b0e..51d3acd6a7d7f89955e4b4cdeec8cefbe4ea8376 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 5110342b60f1cb3c51960fa24cbda974c559bf5c..05816c62a4fd69fed419d722ae047bdb5719adcb 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.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 2ce5f6faeef242db1fc6f37ff534d74c46380d12..f5413e9fd7c236b612a8b0182faa7369708076ec 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.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index fa34d776bc15cf23340f75e569d3dbc290de5bc1..0f280d3cb2606eb6b2556717c1f3451e6a2dc6de 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>
<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/algorithms.html b/doc/html/modelling/algorithms.html
index b50786148354be50f4cf7124d841b262debf706d..20a4c6e471c12cc54588a0a1a01adab7b8d7f7a2 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>
<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 - Sidechain Modelling" href="../sidechain/index.html" />
@@ -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>â€).
+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 33480a71923b4579ff5e5d80d23a55595592cbc6..367970a45918d669797c5add095557368852cf1c 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 72df0c020ef76b044551de040d7a72cfdd0944e8..8329bb87acfa8d00d660ea8a1cafae5aaf4ad1fc 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 a04ae292b2ed52770a63c7d47eed174fbcce7f13..98a3289adb73745b06583b32dcc2bb6c1866b3df 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" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Loop Candidates — ProMod3 3.2.1 documentation</title>
+ <title>Handling Loop Candidates — 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="Fitting Loops Into Gaps" href="loop_closing.html" />
@@ -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.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index dfab8aa39dbb0a60f7f0322aea794238a08ceb65..7cd4dcf9b6eb59022a7d70f9071066107d3f0fd9 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" />
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<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 04ece5d3cd50301e608eaf4d6bde84499b465b51..d39b5fe78f18d2c81779a3672c75647d30420458 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.molprobityâ€
+<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.molprobityâ€
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 e05d228440ebf6a0b28b68d3315ff15fd858cc20..e307c44dfc5ba42e349b2bac26a389f36de7ee99 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 184688346f49e5b7d8d9cfdeec85da76417ef6d5..5548082996d7a865a38f946ceb9ca0c9fdb77593 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_backboneâ€
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 980622fd937d01d81b7fc7169cbaa996af57c06d..53ea062ed1d80e4c55f8f08c33b6d87de26fd2bd 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>
<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 Algorithms" href="algorithms.html" />
@@ -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
-[“SCWRL4â€, “SCWRL3â€]</li>
+[“SCWRL4â€, “SCWRL3â€, “VINAâ€]</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.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 4629e19fb62e0b1865a01acd2115ca59fdadce24..e475a666d3eb87b34bb7d67dd2c741520372a872 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index 53ee73f38cf93faae4a3eaef0a682ed27f29dc3c..fb4c10e0697802ef1fe597a5c97a168c14d95452 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 06632bdef08109eb6898181cc0df6a7ebb72ba1c..400d92030f69ae9d638f76c183d330d2c8b79f40 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 c5cfde451fc538649c62098da9c73dc3434b22f5..a7cf963db411916dad7bf40f62986f3848c5c595 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 3e3d467e790f5bf411b0328dc7ff1466db12cd59..de7b370f9fe6a9c4f54473f63f259f8aed3046f2 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 ab4bc1a2ce98e5afc7b5073c5ed553defd7fa3ca..1c6e7ef03738a3a47531008b353601f329acef43 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 ff76e572ea550aa83438163d2af9440503f6bfbe..24f2cd2ef3a9ef6a800d41c8d459d3e848b4d5f9 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 ebc4d6c9bffda1a6c3c14b758a59734dec80e3aa..606b2b56daee011aeca20c3498c8990756b6e429 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 0de14121fe084c5aea2c6ace5fcaf4684ed7c45a..2648f13f707bce27881de467b4c6be0e48baffe9 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 a60fd4630084ef95efe75cbfb5c15432c6e4eb59..0e575bda06a6effc3c18a7919b846566d7248223 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>
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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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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 3d8e50950092529e4ae9bd789e0e12de31fbe8e2..0ab78f1095cb968d4b9a1304c5051b111f246d80 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.
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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 e85a1e8ff373c6e2aaf478b1af6ed7691f9c7397..0c4e69f76d9f06ced8b62d5b0b2c9c280f2a3f94 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 61732485dc5627272f1857dcc88e22d4d5619ba1..cc59c634e77b3fa91f1f7a6d51c173b2fde12acf 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 e6e40a3b78011f7f26bea103c0f5ac16172bc58b..855b5a7cd5b033add84bdc7877e501e409fa439b 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 d54af5fd4e741da4b8dad8ae3bb522993a715f17..a0efe0432eda3eaad35edccfd91602a29bdd5a63 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 e33eb6e988202302ca3ad1bef062b3fb14235bb4..3ae62751fe7a39fba0b3534fddd0e8f218f99341 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 3e5431c2715fae4618854aff7f6ecaed7223de42..fc7229f75dd6e2860034418835fc85037e9fc22b 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_donorâ€, False) and
at.SetBoolProp(“is_hbond_acceptorâ€, 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.
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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 6dd76800bccb8370dbcd92c5bda8d59d0b3edeb4..b2f7c4e36626f8ea03dbea899ead36b5eda4d1d4 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 241f685e465a346f918d7686995e4e0c4d5b4194..c1ae5456ea803a5af66a4d12bbfd122efe321a03 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 44fd3f6c307cb7180f9da374afbe04099aeb5b42..109d865d4bafda395c30bb65af8b2f9c7a6bf7d5 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 81a37ae06ac1e75b57de228030d9f22fde448332..82c3ffa195f703025db6ebc0aa823dcc98d19534 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>
diff --git a/extras/data_generation/afdb_modelling/README.md b/extras/data_generation/afdb_modelling/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..6690891ad1b6dc41868e05201ac22471b92c509d
--- /dev/null
+++ b/extras/data_generation/afdb_modelling/README.md
@@ -0,0 +1,53 @@
+Data generation for AFDB Modelling capabilities in ProMod3
+
+Requires you to download the full proteomes database as described in
+https://github.com/deepmind/alphafold/blob/main/afdb/README.md.
+
+This gives one tar file per proteome which serves as starting point.
+
+In case of sciCORE they're here:
+`/scicore/data/managed/AF_UniProt/frozen_221115T101000/proteomes`
+
+The `afdb_proteom_to_data_chunks.py` script generates one such chunk.
+It reads a list of filenames which needs to be generated manually.
+Something like:
+
+```python
+import os
+files = os.listdir(<AFDB_PROTEOM_DIR>)
+with open("afdb_proteom_files.txt", 'w') as fh:
+ fh.write('\n'.join(files))
+```
+
+`create_commands.py` generates a command file which can be submitted
+as batch job. Carefully check the variables defined on top and adapt to your
+needs. Test to run one of these commands interactively to see whether the
+respective chunk file is created correctly before submitting.
+
+Once all chunks are there, an indexed database can be created with:
+
+```python
+from promod3.modelling import FSStructureServer
+fs_server = FSStructureServer.FromDataChunks("afdb_data_chunks", "afdb_fs")
+```
+
+## Data preparation for PentaMatch
+
+The same data chunks are used to extract the sequences that are searched by
+PentaMatch. `create_pentamatch_sequences.py` generates a Fasta file with all
+sequences of the previously generated FSStructureServer. Execute with:
+
+```bash
+ost create_pentamatch_sequences.py --data_chunks <DATA_CHUNK_DIR> --fs_server <FS_SERVER> --out <PENTAMATCH>.fasta
+```
+
+The searchable PentaMatch object is generated interactively with:
+```python
+from promod3.modelling import PentaMatch
+PentaMatch.FromSeqList("<PENTAMATCH>.fasta", "<PENTAMATCH_DIR>",
+ entries_from_seqnames=True)
+```
+
+Be aware that the command above requires a substantial amount of memory.
+For 200e6 entries, 500GB was sufficient.
+
diff --git a/extras/data_generation/afdb_modelling/afdb_proteom_to_data_chunks.py b/extras/data_generation/afdb_modelling/afdb_proteom_to_data_chunks.py
new file mode 100644
index 0000000000000000000000000000000000000000..895d7e44c8a83c012606e2d465ccb32e6041f88a
--- /dev/null
+++ b/extras/data_generation/afdb_modelling/afdb_proteom_to_data_chunks.py
@@ -0,0 +1,126 @@
+import os
+import tarfile
+import gzip
+import argparse
+import pickle
+
+from ost import io
+
+def parse_args():
+ desc = ("Parses proteom tarballs from AFDB and dumps pickle files ready "
+ "for database creation")
+
+ parser = argparse.ArgumentParser(description = desc)
+ parser.add_argument("--afdb_dir", help="Directory containing the "
+ "tarballs")
+ parser.add_argument("--tarballs", help=" File containing tarball filenames")
+ parser.add_argument("--start", help="idx in that file to start", type=int)
+ parser.add_argument("--end", help="idx in that file to end", type=int)
+ parser.add_argument("--out_file", help="Output file where stuff gets "
+ "pickled")
+ parser.add_argument("--ca_only", help="Whether to use CA-only "
+ "representation", action="store_true")
+ return parser.parse_args()
+
+def iterate_proteom(tarball):
+ """ Helper: iterate over proteome tarball provided by EBI-AFDB
+
+ Yields mmcif data
+ in detail: tuple with types :class:`str`, :class:`ost.mol.EntityHandle`,
+ :class:`ost.io.MMFicInfo` and :class:`ost.seq.SequenceList`
+
+ :param tarball: Path to tarball to iterate
+ :type tarball: :class:`str`
+ :returns: Generator of specified tuple
+ """
+ tf = tarfile.open(tarball)
+ prof = io.profiles.Get("STRICT")
+
+ # hack to correct for corrupt cif files in AFDB
+ corrupt_cit = "_citation.id primary"
+ correct_cit = "_citation.id 1"
+ while True:
+ tar_info = tf.next()
+ if tar_info is None:
+ break # we're done
+ if tar_info.name.endswith("cif.gz"):
+ fh = tf.extractfile(tar_info)
+ mmcif_str = gzip.decompress(fh.read()).decode("utf-8")
+ if corrupt_cit in mmcif_str:
+ mmcif_str = mmcif_str.replace(corrupt_cit, correct_cit)
+ ent, mmcif_info, seqres = io.MMCifStrToEntity(mmcif_str,
+ profile=prof,
+ process=True)
+ yield (tar_info.name, ent, mmcif_info, seqres)
+
+def process_proteom(tarball, ca_only=False):
+ """ Helper: Creates list of entries for one proteom
+
+ :param tarball: Path to proteom tarball
+ :type tarball: :class:`str`
+ :ca_only: Whether to select for only CA positions
+ :type ca_only: :class:`bool`
+ :returns: :class: list of :class:`tuple` in format required by
+ :func:`FromDataChunks`
+ """
+ omf_opts = io.OMFOption.DEFAULT_PEPLIB | io.OMFOption.LOSSY | \
+ io.OMFOption.AVG_BFACTORS | io.OMFOption.ROUND_BFACTORS | \
+ io.OMFOption.SKIP_SS | io.OMFOption.INFER_PEP_BONDS
+
+ entries = list()
+ for entry in iterate_proteom(tarball):
+ uniprot_ac = entry[0].split('-')[1]
+ fragment = entry[0].split('-')[2]
+ version = entry[0].split('-')[3]
+ version = version.split('_')[1]
+ version = version.split('.')[0]
+ ent = entry[1]
+ if ca_only:
+ ent = ent.Select("aname=CA")
+ ent = mol.CreateEntityFromView(ent, False)
+ ent_name = f"{uniprot_ac} {fragment} {version}"
+ ent.SetName(ent_name)
+ omf = io.OMF.FromMMCIF(ent, entry[2], omf_opts)
+ omf = gzip.compress(omf.ToBytes())
+ entries.append([uniprot_ac, fragment, version, omf])
+ return entries
+
+def create_data_chunk(tarballs, afdb_dir, start, end, chunk_out,
+ ca_only=False):
+ """ Create full data chunk
+
+ Requires preprocessing step of creating a text file that lists all
+ proteom tarballs.
+
+ :param tarballs: Path to file where each line corresponds to one proteom
+ tarball, i.e. its filename
+ :type tarballs: :class:`str`
+ :param afdb_dir: Directory containing the tarball files specified in
+ *tarballs*
+ :type afdb_dir: :class:`str`
+ :param start: Start of tarball slice to be added to chunk
+ :type start: :class:`int`
+ :param end: End of tarball slice to be added to chunk (*end* won't be
+ added...)
+ :type end: :class:`str`
+ :param chunk_out: Chunk will be pickled to that file
+ :type chunk_out: :class:`str`
+ :ca_only: Whether to select for only CA positions
+ :type ca_only: :class:`bool`
+ """
+ with open(tarballs, 'r') as fh:
+ tarballs = fh.readlines()
+ entries = list()
+ for tarball in tarballs[start:end]:
+ full_path = os.path.join(afdb_dir, tarball.strip())
+ entries += process_proteom(full_path, ca_only=ca_only)
+ with open(chunk_out, 'wb') as fh:
+ pickle.dump(entries, fh)
+
+def main():
+ args = parse_args()
+ create_data_chunk(args.tarballs, args.afdb_dir, args.start, args.end,
+ args.out_file, ca_only = args.ca_only)
+
+if __name__ == '__main__':
+ main()
diff --git a/extras/data_generation/afdb_modelling/create_commands.py b/extras/data_generation/afdb_modelling/create_commands.py
new file mode 100644
index 0000000000000000000000000000000000000000..f83e41f9be5516d1987d4864c146eb009f086389
--- /dev/null
+++ b/extras/data_generation/afdb_modelling/create_commands.py
@@ -0,0 +1,52 @@
+import os
+
+# path to Singularity container with recent OpenStructure installation
+omf_sif = "<PATH_TO_SIF>"
+
+# path to directory that contains AFDB - one tarball per proteom
+afdb_dir = "/scicore/data/managed/AF_UniProt/frozen_221115T101000/proteomes"
+
+# file with one proteom filename per line - in principle the content of os.listdir(afdb_dir)
+proteom_file = "<WHEREVER>/afdb_proteom_files.txt"
+
+# number of proteoms that end up in one data chunk
+chunk_size = 100
+
+# path to directory where chunks will be dumped
+chunk_out_dir = "<WHEREVER>/afdb_data_chunks"
+
+# path to script that does the job
+fancy_script = "<WHEREVER>/afdb_proteom_to_data_chunks.py"
+
+# whether structures should be reduced to CA only representation
+ca_only = False
+
+# path to file into which the commands are written
+cmd_file = "allatom_commands.cmd"
+
+
+with open(proteom_file, 'r') as fh:
+ proteom_data = fh.readlines()
+N = len(proteom_data)
+
+commands = list()
+chunk_idx = 0
+for i in range(0, N, chunk_size):
+ start = i
+ end = min(N, i+chunk_size)
+ out_file = os.path.join(chunk_out_dir, str(chunk_idx) + ".pkl")
+ cmd = ["singularity", "exec", "--bind", f"{afdb_dir}:{afdb_dir}",
+ omf_sif, "ost", fancy_script,
+ "--afdb_dir", afdb_dir,
+ "--tarballs", proteom_file,
+ "--start", str(start),
+ "--end", str(end),
+ "--out_file", out_file]
+ if ca_only:
+ cmd.append("--ca_only")
+ commands.append(' '.join(cmd))
+ chunk_idx += 1
+
+with open(cmd_file, 'w') as fh:
+ fh.write('\n'.join(commands))
+
diff --git a/extras/data_generation/afdb_modelling/create_pentamatch_sequences.py b/extras/data_generation/afdb_modelling/create_pentamatch_sequences.py
new file mode 100644
index 0000000000000000000000000000000000000000..7f202dbb4f7ad4b421e8e36c1fbab64beab0f06e
--- /dev/null
+++ b/extras/data_generation/afdb_modelling/create_pentamatch_sequences.py
@@ -0,0 +1,58 @@
+import os
+import tarfile
+import gzip
+import argparse
+import pickle
+
+from ost import io
+from promod3.modelling import FSStructureServer
+
+def parse_args():
+ desc = ("Extracts sequences from pickled files generated with "
+ "create_fsserver_data_chunks.py and relates them to entries in an "
+ "FSStructureServer object. I.e. Dumps a sequence list in Fasta "
+ "format with entry indices as sequence names. This file serves as "
+ "starting point for an actual PentaMatch object. Requires faf.py "
+ "to be importable.")
+
+ parser = argparse.ArgumentParser(description = desc)
+ parser.add_argument("--data_chunks", help="Directory with all data chunks "
+ "generated with create_fsserver_data_chunks.py")
+ parser.add_argument("--fs_server", help="Directory containing the files "
+ "for an FSStructureServer object derived from "
+ "data_chunks directory")
+ parser.add_argument("--out", help="Outfile in Fasta format that will "
+ "contain all sequences with their respective index in "
+ "the underlying FSStructureServer object as names")
+ return parser.parse_args()
+
+
+def main():
+ args = parse_args()
+ fs_server = FSStructureServer(args.fs_server)
+ chunk_files = os.listdir(args.data_chunks)
+ outfile = open(args.out, 'w')
+
+ for cf_idx, cf in enumerate(chunk_files):
+ print(f"processing chunk {cf_idx}, {cf}")
+ with open(os.path.join(args.data_chunks, cf), 'rb') as fh:
+ data = pickle.load(fh)
+ for entry in data:
+ uniprot_ac = entry[0]
+ fragment = entry[1]
+ version = entry[2]
+ omf_data = entry[3]
+ idx = fs_server.GetIdx(uniprot_ac, fragment = fragment,
+ version = version)
+ omf = io.OMF.FromBytes(gzip.decompress(omf_data))
+ assert(omf.GetChainNames() == ["A"])
+ sequence = omf.GetSequence("A")
+ outfile.write(f">{idx}\n")
+ seq_chunks = [sequence[i:i+80] for i in range(0, len(sequence), 80)]
+ outfile.write('\n'.join(seq_chunks))
+ outfile.write('\n')
+ outfile.close()
+
+if __name__ == '__main__':
+ main()
+
diff --git a/loop/src/mm_system_creator.cc b/loop/src/mm_system_creator.cc
index d5ec8d66e0b46687b7887dc074d2b85d228fc37b..4a745c2c43e83c5ac2ad327ee98d778f661b30cf 100644
--- a/loop/src/mm_system_creator.cc
+++ b/loop/src/mm_system_creator.cc
@@ -58,7 +58,7 @@ void AddConnectivity_(ost::mol::mm::TopologyPtr top, uint start_idx,
const uint idx2 = GetIndex_<non_contiguous>(info.index_two, start_idx,
start_idx2, split_idx);
const bool fixed_all = atom_masses[idx1] == 0 && atom_masses[idx2] == 0;
- if (!fixed_all) {
+ if (!fixed_all && info.force_constant != 0.0) {
top->AddHarmonicBond(idx1, idx2, info.bond_length, info.force_constant);
}
if (!fixed_all || !inaccurate_pot_energy) {
@@ -76,7 +76,7 @@ void AddConnectivity_(ost::mol::mm::TopologyPtr top, uint start_idx,
start_idx2, split_idx);
const bool fixed_13 = atom_masses[idx1] == 0 && atom_masses[idx3] == 0;
const bool fixed_all = fixed_13 && atom_masses[idx2] == 0;
- if (!fixed_all) {
+ if (!fixed_all && info.force_constant != 0.0) {
top->AddHarmonicAngle(idx1, idx2, idx3, info.angle, info.force_constant);
}
if (!fixed_13 || !inaccurate_pot_energy) {
@@ -95,7 +95,8 @@ void AddConnectivity_(ost::mol::mm::TopologyPtr top, uint start_idx,
start_idx2, split_idx);
const bool fixed_13 = atom_masses[idx1] == 0 && atom_masses[idx3] == 0;
const bool fixed_all = fixed_13 && atom_masses[idx2] == 0;
- if (!fixed_all) {
+ if (!fixed_all && (info.angle_force_constant != 0.0 ||
+ info.bond_force_constant != 0.0)) {
top->AddUreyBradleyAngle(idx1, idx2, idx3,
info.angle, info.angle_force_constant,
info.bond_length, info.bond_force_constant);
@@ -118,7 +119,7 @@ void AddConnectivity_(ost::mol::mm::TopologyPtr top, uint start_idx,
start_idx2, split_idx);
const bool fixed_all = atom_masses[idx1] == 0 && atom_masses[idx2] == 0
&& atom_masses[idx3] == 0 && atom_masses[idx4] == 0;
- if (!fixed_all) {
+ if (!fixed_all && info.force_constant != 0.0) {
top->AddPeriodicDihedral(idx1, idx2, idx3, idx4, info.multiplicity,
info.phase, info.force_constant);
}
@@ -137,7 +138,7 @@ void AddConnectivity_(ost::mol::mm::TopologyPtr top, uint start_idx,
start_idx2, split_idx);
const bool fixed_all = atom_masses[idx1] == 0 && atom_masses[idx2] == 0
&& atom_masses[idx3] == 0 && atom_masses[idx4] == 0;
- if (!fixed_all) {
+ if (!fixed_all && info.force_constant != 0.0) {
top->AddPeriodicImproper(idx1, idx2, idx3, idx4, info.multiplicity,
info.phase, info.force_constant);
}
@@ -156,7 +157,7 @@ void AddConnectivity_(ost::mol::mm::TopologyPtr top, uint start_idx,
start_idx2, split_idx);
const bool fixed_all = atom_masses[idx1] == 0 && atom_masses[idx2] == 0
&& atom_masses[idx3] == 0 && atom_masses[idx4] == 0;
- if (!fixed_all) {
+ if (!fixed_all && info.force_constant != 0.0) {
top->AddHarmonicImproper(idx1, idx2, idx3, idx4,
info.angle, info.force_constant);
}
diff --git a/loop/tests/test_torsion_sampler.cc b/loop/tests/test_torsion_sampler.cc
index 4e021260248ed3885d2f39c2c940550ddd617548..7ea8d40bebd29c59678e140455a2daf62dd78c6c 100644
--- a/loop/tests/test_torsion_sampler.cc
+++ b/loop/tests/test_torsion_sampler.cc
@@ -113,6 +113,7 @@ BOOST_AUTO_TEST_CASE(test_torsion_sampler_general_things){
true,
true,
true,
+ true,
ost::conop::CONOP_SILENT));
processor->Process(test_ent);
diff --git a/modelling/doc/algorithms.rst b/modelling/doc/algorithms.rst
index b36bf5bb77ef1ee30a716469a803e652a4420a5e..c9db60f1f7f57dc8ac74e00d8db94b9cb018c4be 100644
--- a/modelling/doc/algorithms.rst
+++ b/modelling/doc/algorithms.rst
@@ -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/modelling/doc/model_checking.rst b/modelling/doc/model_checking.rst
index ab5b5eb9eec534e44b685fb09571c30ce77ed2a7..400f3737f7389d157300c6bce938acf6abc68353 100644
--- a/modelling/doc/model_checking.rst
+++ b/modelling/doc/model_checking.rst
@@ -35,6 +35,15 @@ Detecting Ring Punches
.. autofunction:: FilterCandidatesWithSC
+
+Detecting Non-Planar Rings
+--------------------------------------------------------------------------------
+
+.. autofunction:: GetNonPlanarRings
+
+.. autofunction:: HasNonPlanarRings
+
+
Model Checking With MolProbity
--------------------------------------------------------------------------------
diff --git a/modelling/pymod/CMakeLists.txt b/modelling/pymod/CMakeLists.txt
index 58e2665c98f6d6ac1e81901a956547ddaa3a2836..63b25b975f4af1a0ac3918c8b8b48b2219d4409c 100644
--- a/modelling/pymod/CMakeLists.txt
+++ b/modelling/pymod/CMakeLists.txt
@@ -11,6 +11,7 @@ set(MODELLING_CPP
export_scoring_weights.cc
export_sidechain_reconstructor.cc
export_motif_finder.cc
+ export_afdb.cc
wrap_modelling.cc
)
@@ -27,6 +28,8 @@ set(MODELLING_PYMOD
_mhandle_helper.py
_alignment_fiddling.py
_raw_model.py
+ _planar_rings.py
+ _afdb_modelling.py
)
pymod(NAME modelling
diff --git a/modelling/pymod/__init__.py b/modelling/pymod/__init__.py
index 6cf9be125390e77c9307fdff5c346c56a2f540c0..c195865ecc45e91a0d314ac107fe9a02c0ccdbc3 100644
--- a/modelling/pymod/__init__.py
+++ b/modelling/pymod/__init__.py
@@ -27,3 +27,5 @@ from ._fragger_handle import *
from ._monte_carlo import *
from ._mhandle_helper import *
from ._raw_model import *
+from ._planar_rings import *
+from ._afdb_modelling import *
diff --git a/modelling/pymod/_afdb_modelling.py b/modelling/pymod/_afdb_modelling.py
new file mode 100644
index 0000000000000000000000000000000000000000..a273d8d80276aed9aaa3cd793831d3b1cc718b15
--- /dev/null
+++ b/modelling/pymod/_afdb_modelling.py
@@ -0,0 +1,709 @@
+# Copyright (c) 2013-2023, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os
+import gzip
+import mmap
+import pickle
+import numpy as np
+import time
+import tarfile
+import glob
+import re
+
+import ost
+from ost import io
+from ost import seq
+from ._raw_model import BuildRawModel
+from ._pipeline import BuildFromRawModel
+from ._modelling import *
+
+class _AFDBLogSink(ost.LogSink):
+ """ To capture all log messages of ProMod3 when modelling
+ """
+ def __init__(self):
+ ost.LogSink.__init__(self)
+ self.messages = list()
+ self.severities = list()
+
+ def LogMessage(self, message, severity):
+ self.messages.append(message)
+ self.severities.append(severity)
+
+class FSStructureServer:
+ """ FSStructureServer - A filesystem based AFDB structure server
+
+ 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.
+
+ Data creation happens with static Create function: :func:`FromDataChunks`.
+ The required preprocessing must be done with external scripts.
+
+ :param db_dir: Directory containing required files. 1) pos.dat (see
+ :attr:`pos`) 2) length.dat (see :attr:`length`)
+ 3) chunk.dat (see :attr:`chunk`) 4) indexer.dat (see
+ :attr:`indexer`) 4) one or several files with pattern
+ fs_data_[x].dat (see :attr:`data`)
+ :type db_dir: :class:`str`
+ """
+ def __init__(self, db_dir):
+ super().__init__()
+
+ self._pos = None
+ self._length = None
+ self._chunk = None
+ self._indexer = None
+ self._search_keys = None
+ self._data = None
+ self._data_fh = None
+ self._n_entries = None
+
+ # only check if required files are there, they're lazy loaded
+ self.pos_file = os.path.join(db_dir, "pos.dat")
+ self.length_file = os.path.join(db_dir, "length.dat")
+ self.chunk_file = os.path.join(db_dir, "chunk.dat")
+ self.search_key_file = os.path.join(db_dir, "search_keys.dat")
+ self.indexer_file = os.path.join(db_dir, "indexer.dat")
+ self.data_files = glob.glob(os.path.join(db_dir, "fs_data_*.dat"))
+ if not os.path.exists(self.pos_file):
+ raise RuntimeError(f"Exp \"pos.dat\" file in db_dir ({db_dir})")
+ if not os.path.exists(self.length_file):
+ raise RuntimeError(f"Exp \"length.dat\" file in db_dir ({db_dir})")
+ if not os.path.exists(self.chunk_file):
+ raise RuntimeError(f"Exp \"chunk.dat\" file in db_dir ({db_dir})")
+ if not os.path.exists(self.indexer_file):
+ raise RuntimeError(f"Exp \"indexer.dat\" file in db_dir ({db_dir})")
+ # there can be one or more data files, just check whether there is at
+ # least one
+ if len(self.data_files) == 0:
+ raise RuntimeError(f"Exp at least one data file in form "
+ f"\"fs_data_[x].dat\" in db_dir ({db_dir})")
+
+ def __del__(self):
+ if self._data:
+ for fh in self._data:
+ fh.close()
+ for fh in self._data_fh:
+ fh.close()
+
+ @property
+ def pos(self):
+ """ Start positions of data in internal linear memory layout
+
+ :type: :class:`np.ndarray` with dtype np.int64
+ """
+ if self._pos is None:
+ with open(self.pos_file, 'rb') as fh:
+ self._pos = np.load(fh)
+ return self._pos
+
+ @property
+ def length(self):
+ """ Lengths of data in internal linear memory layout
+
+ :type: :class:`np.ndarray` with dtype np.int32
+ """
+ if self._length is None:
+ with open(self.length_file, 'rb') as fh:
+ self._length = np.load(fh)
+ return self._length
+
+ @property
+ def chunk(self):
+ """ Chunk, in which entry is stored
+
+ :type: :class:`np.ndarray` with dtype np.int16
+ """
+ if self._chunk is None:
+ with open(self.chunk_file, 'rb') as fh:
+ self._chunk = np.load(fh)
+ return self._chunk
+
+ @property
+ def indexer(self):
+ """ Internal data structure - Relates entries with data indices
+
+ :type: :class:`np.ndarray` with dtype np.int32
+ """
+ if self._indexer is None:
+ with open(self.indexer_file, 'rb') as fh:
+ self._indexer = np.load(fh)
+ return self._indexer
+
+ @property
+ def search_keys(self):
+ """ Internal data structure - Relates entries with data indices
+ """
+ if self._search_keys is None:
+ with open(self.search_key_file, 'rb') as fh:
+ self._search_keys = np.load(fh)
+ return self._search_keys
+
+ @property
+ def data(self):
+ """ Internal binary data in memory mapped files
+
+ :type: :class:`list` of :class:`mmap.mmap`
+ """
+ if self._data is None:
+ self._data = list()
+ self._data_fh = list()
+ tmp = list()
+ for f in self.data_files:
+ idx = int(f.split('_')[-1].replace(".dat", ""))
+ tmp.append((idx, f))
+ tmp.sort()
+ sorted_data_files = [x[1] for x in tmp]
+ for f in sorted_data_files:
+ self._data_fh.append(open(f, 'rb'))
+ self._data.append(mmap.mmap(self._data_fh[-1].fileno(), 0,
+ prot=mmap.PROT_READ))
+ return self._data
+
+ @property
+ def n_entries(self):
+ """ Number of entries
+
+ :type: :class:`int`
+ """
+ if self._n_entries is None:
+ self._n_entries = self.pos.shape[0]
+ return self._n_entries
+
+ def GetIdx(self, uniprot_ac, fragment="F1", version="v4"):
+ """ Get internal idx of stored data
+
+ Can be used for data retrieval with :func:`GetOMFByIdx`
+
+ :param uniprot_ac: Uniprot AC
+ :type uniprot_ac: :class:`str`
+ :param fragment: AFDB entries are potentially split to fragments
+ 99.999% of all entries only have one fragment: F1
+ :type fragment: class:`str`
+ :param version: Version of entry
+ :type version: :class:`str`
+ :returns: Internal idx of that entry
+ :raises: :class:`RuntimeError` if no such entry exists
+ """
+ if not fragment.startswith('F'):
+ raise RuntimeError("expect fragment to start with F")
+ if not version.startswith('v'):
+ raise RuntimeError("expect version to start with v")
+ search_key = CreateAFDBIdx(uniprot_ac, int(fragment[1:]),
+ int(version[1:]))
+ idx = np.searchsorted(self.search_keys, np.uint64(search_key))
+ if idx != len(self.indexer) and self.search_keys[idx] == search_key:
+ return self.indexer[idx]
+ raise RuntimeError(f"No entry for {uniprot_ac} {fragment} "
+ f"{version}")
+
+ def GetOMFByIdx(self, idx):
+ """ Get stored OMF data structure
+
+ :param idx: Internal index which can be derived from :func:`GetIdx`
+ :type idx: :class:`int`
+ :returns: OMF data structure of type :class:`ost.io.OMF`
+ :raises: :class:`RuntimeError` if *idx* is out of range
+ """
+ if idx < 0 or idx >= self.n_entries:
+ raise RuntimeError(f"Invalid idx, must be in [0, {self.n_entries-1}]")
+ pos = self.pos[idx]
+ length = self.length[idx]
+ chunk = self.chunk[idx]
+ omf_data = self.data[chunk][pos:pos+length]
+ return io.OMF.FromBytes(gzip.decompress(omf_data))
+
+ def GetOMF(self, uniprot_ac, fragment="F1", version="v4"):
+ """ Get stored OMF data structure
+
+ :param uniprot_ac: Uniprot AC
+ :type uniprot_ac: :class:`str`
+ :param fragment: AFDB entries are potentially split to fragments
+ 99.999% of all entries only have one fragment: F1
+ :type fragment: class:`str`
+ :param version: Version of entry
+ :type version: :class:`str`
+ :returns: OMF data structure of type :class:`ost.io.OMF`
+ :raises: :class:`RuntimeError` if no such entry exists
+ """
+ idx = self.GetIdx(uniprot_ac, fragment = fragment, version = version)
+ return self.GetOMFByIdx(idx)
+
+ @staticmethod
+ def FromDataChunks(chunk_dir, db_dir, chunk_bytes=None):
+ """ Static method to create new database from preprocessed data
+
+ 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 (:class:`str`)
+ 2) fragment (:class:`str`) 3) version (:class:`str`) 4) structure data
+ (:class:`ost.io.OMF` object which has been written to a bytes object and
+ compressed with gzip)
+
+ The data itself is again stored in chunks of binary data which are
+ indexed.
+
+ :param chunk_dir: Path to directory containing described data chunks
+ :type chunk_dir: :class:`str`
+ :param db_dir: Output directory - Creates all files that are needed for
+ :class:`FSStructureServer`
+ :type db_dir: :class:`str`
+ :param chunk_bytes: Size in bytes of binary data chunks in final
+ database - default None: Everything ends up in one
+ single chunk
+ :type chunk_bytes: :class:`int`
+ :returns: :class:`FSStructureServer` with all data from *chunk_dir*
+ """
+ if not os.path.exists(db_dir):
+ raise RuntimeError(f"{db_dir} does not exist")
+ positions = list()
+ lengths = list()
+ chunks = list()
+ search_keys = list()
+ indexer = list()
+ chunk_files = os.listdir(chunk_dir)
+ chunk_files = [f for f in chunk_files if f.endswith(".pkl")]
+ current_pos = 0
+ current_chunk = 0
+ current_entry = 0
+ data_file = open(os.path.join(db_dir, "fs_data_0.dat"), 'wb')
+ t0 = time.time()
+ for cf_idx, cf in enumerate(chunk_files):
+ print(f"processing chunk {cf_idx}, {cf}")
+ with open(os.path.join(chunk_dir, cf), 'rb') as fh:
+ data = pickle.load(fh)
+ for entry in data:
+ uniprot_ac = entry[0]
+ fragment = entry[1]
+ version = entry[2]
+ data_bytes = entry[3]
+ length = len(data_bytes)
+ data_file.write(data_bytes)
+ positions.append(current_pos)
+ lengths.append(length)
+ chunks.append(current_chunk)
+ k = CreateAFDBIdx(uniprot_ac, int(fragment[1:]),
+ int(version[1:]))
+ search_keys.append(k)
+ indexer.append(current_entry)
+ current_pos += length
+ current_entry += 1
+ if chunk_bytes and current_pos > chunk_bytes:
+ data_file.close()
+ current_chunk += 1
+ f = os.path.join(db_dir, f"fs_data_{current_chunk}.dat")
+ data_file = open(f, 'wb')
+ current_pos = 0
+ data_file.close()
+ print(f"done processing chunks ({round(time.time() - t0, 3)}s)")
+ print("sort indexer matrix")
+ t0 = time.time()
+ # make search keys searchable by bisect search => sort
+ search_keys = np.asarray(search_keys, dtype=np.uint64)
+ indexer = np.asarray(indexer, dtype=np.int32)
+ sort_indices = np.argsort(search_keys)
+ search_keys = search_keys[sort_indices]
+ indexer = indexer[sort_indices]
+
+ with open(os.path.join(db_dir, "search_keys.dat"), 'wb') as fh:
+ np.save(fh, search_keys)
+ with open(os.path.join(db_dir, "indexer.dat"), 'wb') as fh:
+ np.save(fh, indexer)
+ with open(os.path.join(db_dir, "pos.dat"), 'wb') as fh:
+ np.save(fh, np.array(positions, dtype=np.int64))
+ with open(os.path.join(db_dir, "length.dat"), 'wb') as fh:
+ np.save(fh, np.array(lengths, dtype=np.int32))
+ with open(os.path.join(db_dir, "chunk.dat"), 'wb') as fh:
+ np.save(fh, np.array(chunks, dtype=np.int16))
+ fs_server = FSStructureServer(db_dir)
+ return fs_server
+
+
+class PentaMatch:
+ """ Pentamer matching for fast sequence searches
+
+ :class:`PentaMatch` 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.
+
+ :param db_dir: Directory containing all required files (indexer.dat,
+ pos.dat, length.dat, meta.dat). New :class:`PentaMatch`
+ objects can be derived using the static :func:`FromSeqList`
+ creator.
+ :type db_dir: :class:`str`
+ :raises: :class:`RuntimeError` if any required file is missing in *db_dir*
+ """
+ def __init__(self, db_dir):
+ self._indexer = None
+ self._pos = None
+ self._length = None
+ self._N = None
+ self.db_dir = db_dir
+
+ # only check if required files are there, they're lazy loaded
+ self.indexer_file = os.path.join(db_dir, "indexer.dat")
+ self.pos_file = os.path.join(db_dir, "pos.dat")
+ self.length_file = os.path.join(db_dir, "length.dat")
+ self.meta_file = os.path.join(db_dir, "meta.dat")
+
+ if not os.path.exists(self.indexer_file):
+ raise RuntimeError(f"Exp \"indexer.dat\" file in db_dir ({db_dir})")
+ if not os.path.exists(self.pos_file):
+ raise RuntimeError(f"Exp \"pos.dat\" file in db_dir ({db_dir})")
+ if not os.path.exists(self.length_file):
+ raise RuntimeError(f"Exp \"length.dat\" file in db_dir ({db_dir})")
+ if not os.path.exists(self.meta_file):
+ raise RuntimeError(f"Exp \"meta.dat\" file in db_dir ({db_dir})")
+
+ @property
+ def indexer(self):
+ """ Entry indices for pentamers
+
+ Entry data for one pentamer can be extracted with the respective values in
+ :attr:`pos` and :attr:`length`
+
+ :type: memory mapped :class:`np.ndarray` of dtype np.int32
+ """
+ if self._indexer is None:
+ self._indexer = np.memmap(self.indexer_file, dtype=np.int32,
+ mode='r')
+ return self._indexer
+
+ @property
+ def pos(self):
+ """ Start position for each pentamer in :attr:`indexer`
+
+ :type: :class:`np.ndarray` of dtype np.int64 with 3.2E6 entries
+ """
+ if self._pos is None:
+ self._pos = np.fromfile(self.pos_file, dtype=np.int64)
+ return self._pos
+
+ @property
+ def length(self):
+ """ Length for each pentamer in :attr:`indexer`
+
+ :type: :class:`np.ndarray` of dtype np.int32 with 3.2E6 entries
+ """
+ if self._length is None:
+ self._length = np.fromfile(self.length_file, dtype=np.int32)
+ return self._length
+
+ @property
+ def N(self):
+ """ Number of entries in underlying :class:`FSStructureServer`
+
+ :type: :class:`int`
+ """
+ if self._N is None:
+ with open(self.meta_file, 'r') as fh:
+ self._N = int(fh.read()) + 1 # the files stores max idx => +1
+ return self._N
+
+ def TopN(self, N, sequence, return_counts=False, unique_pentamers=True):
+ """ Find top-N matches given *sequence*
+
+ Identifies unique pentamers in *sequence* and counts number of
+ occurences in each entry. Returns the top-N entries with respect
+ to counts.
+
+ :param N: Number of results to return
+ :type N: :class:`int`
+ :param sequence: Sequence to search
+ :type sequence: :class:`str`
+ :param return_counts: Additionally return underlying pentamer counts
+ :type return_counts: :class:`bool`
+ :param unique_pentamers: Set to True if :attr:`indexer` 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.
+ :type unique_pentamers: :class:`bool`
+ :returns: :class:`list` of :class:`int` with length *N* specifying
+ entry indices. If *return_counts* is true, the
+ :class:`list` contains :class:`tuple` with two elements:
+ 1) count 2) index.
+ :raises: :class:`RuntimeError` if N is invalid or sequence is shorter
+ than 5 characters
+ """
+ if N <=0:
+ raise RuntimeError(f"N ({N}) must be larger than 0")
+ if N > self.N:
+ raise RuntimeError(f"N ({N}) larger than actual entries ({self.N})")
+ if len(sequence) < 5:
+ raise RuntimeError(f"sequence must have length >=5, got: {sequence}")
+ pentamers = list()
+ SeqToPentamerIndices(sequence, True, pentamers)
+ # uint16 allows for up to 65535 pentamer matches
+ accumulator = np.zeros(self.N, dtype=np.int32)
+ if unique_pentamers:
+ for p in pentamers:
+ pos = self.pos[p]
+ length = self.length[p]
+ accumulator[self.indexer[pos:pos+length]] += 1
+ else:
+ for p in pentamers:
+ pos = self.pos[p]
+ length = self.length[p]
+ np.add.at(accumulator, self.indexer[pos:pos+length], 1)
+
+ top_n_indices = np.argpartition(accumulator, -N)[-N:]
+ top_n_counts = accumulator[top_n_indices]
+ # top_n_indices is not sorted by counts => sort by counts and return
+ tmp = [(a,b) for a,b in zip(top_n_counts, top_n_indices)]
+ tmp.sort(reverse=True)
+ if return_counts:
+ return tmp
+ else:
+ return [x[1] for x in tmp]
+
+ @staticmethod
+ def FromSeqList(fasta_file, db_dir, entries_from_seqnames=False):
+ """ Creates PentaMatch object from Fasta file
+
+ :param fasta_file: Path to Fasta file with sequences
+ :type fasta_file: :class:`str`
+ :param db_dir: Files required for :class:`PentaMatch` will be dumped
+ here, will be created if non-existent.
+ :type db_dir: :class:`str`
+ :param entries_from_seqnames: If set to False, indices returned by
+ :func:`TopN` refer to position in
+ *fasta_file*. If set to True, integer
+ indices are parsed from sequence name.
+ :type entries_from_seqnames: :class:`bool`
+ :returns: class:`PentaMatch`
+ :raises: :class:`ost.Error` if *entries_from_seqnames* is True but
+ sequence name cannot be casted to int.
+ """
+ slist = io.LoadSequenceList(fasta_file)
+ if not os.path.exists(db_dir):
+ os.makedirs(db_dir)
+ CreatePentaMatch(slist, db_dir, entries_from_seqnames)
+ return PentaMatch(db_dir)
+
+def AFDBTPLSearch(fs_server, pentamatch, trg_seq, pentamatch_n = 100,
+ seqid_thresh = 70, tpl_n = 5):
+ """ Searches *tpl_n* templates in *fs_server*/*pentamatch*
+
+ Step 1: Identifies *pentamatch_n* sequences in *pentamatch* with largest
+ number of matching pentamers with respect to *trg_seq*.
+ Step 2: Generate pairwise alignments with :func:`ost.seq.alg.LocalAlign`
+ and only retain the ones with seqid >= *seqid_thresh*.
+ Step 3: Extract respective templates from *fs_server* and score them by
+ the sum of plDDT of aligned residues divided by *trg_seq* length.
+ Step 4: Return top *tpl_n* (or less)
+
+ :param fs_server: Structure database - The AFDB
+ :type fs_server: :class:`FSStructureServer`
+ :param pentamatch: Pentamatch object specific for *fs_server*
+ :type pentamatch: :class:`PentaMatch`
+ :param trg_seq: Target sequence
+ :type trg_seq: :class:`ost.seq.SequenceHandle`/:class:`str`
+ :pentamatch_n: Number of sequences that are initially searched in
+ *pentamatch*
+ :type pentamatch_n: :class:`int`
+ :param seqid_thresh: Sequence Identity threshold [0-100] that alignment is
+ considered further
+ :type seqid_thresh: :class:`int`
+ :param tpl_n: Number of templates that are finally returned based on
+ described scoring
+ :type tpl_n: :class:`int`
+ :returns: :class:`list` of pairs with first element being the tpl score,
+ the second element being a :class:`ost.seq.AlignmentHandle` with
+ first sequence being *trg_seq* and second sequence the hit found
+ in *fs_server* with structure attached. If *fs_server* 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 *fs_server*.
+ """
+ top_n = pentamatch.TopN(pentamatch_n, str(trg_seq))
+ if isinstance(trg_seq, str):
+ trg_seq = seq.CreateSequence("A", trg_seq)
+ tmp = list()
+ for idx in top_n:
+ omf = fs_server.GetOMFByIdx(idx)
+ assert(omf.GetChainNames() == ["A"])
+ omf_s = omf.GetSequence("A")
+ aln = seq.alg.LocalAlign(trg_seq, seq.CreateSequence("A", omf_s),
+ seq.alg.BLOSUM62)[0]
+ if seq.alg.SequenceIdentity(aln) >= seqid_thresh:
+ bfactors = omf.GetAvgBFactors("A")
+ summed_bfac = 0.0
+ current_pos = aln.GetSequence(1).offset
+ for col in aln:
+ if col[0] != '-' and col[1] != '-':
+ summed_bfac += bfactors[current_pos]
+ if col[1] != '-':
+ current_pos += 1
+ score = summed_bfac / len(trg_seq)
+ tmp.append((score, aln, omf, idx))
+ tmp.sort(reverse=True, key=lambda x: x[0])
+ return_list = list()
+ for item in tmp[:tpl_n]:
+ # the alignments are local, expand the first sequence to
+ # *trg_seq*, i.e. make sure that the offset is 0
+ aln = item[1]
+ if aln.GetSequence(0).offset > 0:
+ s1 = aln.GetSequence(0)
+ s2 = aln.GetSequence(1)
+ s1_prefix = trg_seq[:s1.offset]
+ s2_prefix = '-' * s1.offset
+ new_s1 = seq.CreateSequence(s1.name, s1_prefix + str(s1))
+ new_s2 = seq.CreateSequence(s2.name, s2_prefix + str(s2))
+ new_s2.SetOffset(s2.offset)
+ aln = seq.CreateAlignment(new_s1, new_s2)
+ ent = item[2].GetAUChain("A").CreateFullView()
+ ent.SetName(ent.GetName() + ' ' + str(item[3]))
+ aln.AttachView(1, ent)
+ return_list.append((item[0], aln))
+ return return_list
+
+def _TransferBFactors(messages, aln, model):
+ """ Simple heuristic to transfer plDDT from AFDB model
+
+ Assumes *model* to be monomer. 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 gaps indicated in 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).
+
+ :param messages: List of log messages that you derived during logging
+ of :func:`modelling.BuildFromRawModel`.
+ :type messages: :class:`list` of :class:`str`
+ :param aln: Alignment
+ :type aln: :class:`ost.seq.AlignmentHandle`
+ :param model: Model
+ :type model: :class:`ost.mol.EntityHandle`
+ """
+ assert(model.chain_count == 1)
+ bfactors = [0.0] * len(aln)
+ for col_idx, col in enumerate(aln):
+ if col[0] != '-' and col[1] != '-':
+ r = col.GetResidue(1)
+ bfactors[col_idx] = np.mean([a.GetBFactor() for a in r.atoms])
+
+ # regular expression that finds stuff like: filling A.PRO59-(ESRQG)-A.ILE65
+ # and directly makes stem residue numbers (59 and 65) available as groups
+ cname = model.chains[0].GetName()
+ pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)"
+ for m in messages:
+ if m.startswith("Resolved"):
+ match = re.search(pat, m)
+ assert(match is not None)
+ groups = match.groups()
+ assert(len(groups) == 2)
+ n_stem = int(groups[0]) - 1 # rnum to idx
+ c_stem = int(groups[1]) - 1 # rnum to idx
+ # we have no guarantee that these stems were aligned from the
+ # very beginning. Lets move towards the termini and find the first
+ # non-zero bfactors
+ while n_stem > 0:
+ if bfactors[n_stem] != 0.0:
+ break
+ n_stem -= 1
+ while c_stem < len(bfactors):
+ if bfactors[c_stem] != 0.0:
+ break
+ c_stem += 1
+ n_stem_bfac = bfactors[n_stem]
+ c_stem_bfac = bfactors[c_stem]
+ min_bfac = 0.5*(min(n_stem_bfac, c_stem_bfac))
+ for idx in range(n_stem+1, c_stem):
+ n_stem_d = idx - n_stem
+ c_stem_d = c_stem - idx
+ if n_stem_d < c_stem_d:
+ # closer to n stem
+ n_stem_d = min(4, n_stem_d)
+ weight = 0.25 * n_stem_d
+ bfactors[idx] = weight * min_bfac + (1-weight)*n_stem_bfac
+ else:
+ # closer to c stem (or same d...)
+ c_stem_d = min(4, c_stem_d)
+ weight = 0.25*c_stem_d
+ bfactors[idx] = weight * min_bfac + (1-weight)*c_stem_bfac
+
+ for r in model.residues:
+ rnum = r.GetNumber().GetNum()
+ bfac = bfactors[rnum-1]
+ for a in r.atoms:
+ a.SetBFactor(bfac)
+
+def AFDBModel(fs_server, pentamatch, trg_seq, transfer_bfactors=False):
+ """ Build model with AFDB as template library
+
+ :param fs_server: Structure database - The AFDB
+ :type fs_server: :class:`FSStructureServer`
+ :param pentamatch: Pentamatch object specific for *fs_server*
+ :type pentamatch: :class:`PentaMatch`
+ :param trg_seq: Target sequence
+ :type trg_seq: :class:`ost.seq.SequenceHandle`/:class:`str`
+ :param transfer_bfactors: 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).
+ :returns: :class:`tuple` with 4 elements. 1: The model 2: The model score
+ based on plDDT 3: Pairwise alignment (first seq: *trg_seq*,
+ 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.
+ """
+ tpl_list = AFDBTPLSearch(fs_server, pentamatch, trg_seq, pentamatch_n = 100,
+ seqid_thresh=70, tpl_n = 1)
+ if len(tpl_list):
+ score = tpl_list[0][0]
+ aln = tpl_list[0][1]
+ mhandle = BuildRawModel(aln)
+ if transfer_bfactors:
+ # setup custom logger to fish out logging messages
+ log_sink = _AFDBLogSink()
+ ost.PushLogSink(log_sink)
+ ost.PushVerbosityLevel(3)
+ model = BuildFromRawModel(mhandle)
+ _TransferBFactors(log_sink.messages, aln, model)
+ ost.PopLogSink()
+ ost.PopVerbosityLevel()
+ # let the world know in original log sink
+ orig_log_sink = ost.GetCurrentLogSink()
+ if orig_log_sink:
+ for m,s in zip(log_sink.messages, log_sink.severities):
+ orig_log_sink.LogMessage(m, s)
+ else:
+ model = BuildFromRawModel(mhandle)
+
+ name = aln.GetSequence(1).GetAttachedView().GetName()
+ return (model, score, name, aln)
+ return (None, None, None, None)
+
+__all__ = ('FSStructureServer', 'PentaMatch', 'AFDBTPLSearch', 'AFDBModel')
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 337c281b22c3fee1b9a14cd941fd12e6009b3a55..7e6a730d5cae09ddf81dba6122b0dabfd1a6a95e 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -1047,7 +1047,7 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler=None, max_loops_to_search=6,
ext_step = 0
first_iteration = True
- while found_loops < max_loops_to_search and ext_step < max_extension:
+ while found_loops < max_loops_to_search and ext_step <= max_extension:
# extend the gap
if not first_iteration:
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index a4b5e8709578a0a1b79831442c2d8c93e22dc0e9..db7fc2ad4b7d8cafcf530a17695ee3fae2113f68 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -25,6 +25,7 @@ from ._modelling import *
from ._reconstruct_sidechains import *
from ._closegaps import *
from ._ring_punches import *
+from ._planar_rings import *
from ._mhandle_helper import *
# external
import ost
@@ -255,7 +256,8 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
max_iter_lbfgs=10, use_amber_ff=False,
- extra_force_fields=list()):
+ extra_force_fields=list(),
+ tolerance_sd=1.0, tolerance_lbfgs=1.0):
'''Minimize energy of final model using molecular mechanics.
Uses :mod:`ost.mol.mm` to perform energy minimization.
@@ -290,6 +292,14 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
:param max_iter_lbfgs: Max. number of iterations within LBFGS method
:type max_iter_lbfgs: :class:`int`
+ :param tolerance_sd: Tolerance parameter passed to ApplySD of
+ :class:`ost.mol.mm.Simulation` object.
+ :type tolerance_sd: :class:`float`
+
+ :param tolerance_lbfgs: Tolerance parameter passed to ApplyLBFGS of
+ :class:`ost.mol.mm.Simulation` object.
+ :type tolerance_lbfgs: :class:`float`
+
:param use_amber_ff: if True, use the AMBER force field instead of the def.
CHARMM one (see :meth:`BuildFromRawModel`).
:type use_amber_ff: :class:`bool`
@@ -334,8 +344,8 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
ost.LogInfo("Perform energy minimization "
"(iteration %d, energy: %g)" % (i+1, cur_energy))
try:
- sim.ApplySD(tolerance = 1.0, max_iterations = max_iter_sd)
- sim.ApplyLBFGS(tolerance = 1.0, max_iterations = max_iter_lbfgs)
+ sim.ApplySD(tolerance = tolerance_sd, max_iterations = max_iter_sd)
+ sim.ApplyLBFGS(tolerance = tolerance_lbfgs, max_iterations = max_iter_lbfgs)
sim.UpdatePositions()
except Exception as ex:
# ABORT ON FAIL
@@ -363,8 +373,9 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
ost.PopVerbosityLevel()
# checks above would remove bad atoms
cur_energy = sim.GetEnergy()
- if len(temp_ent_stereo_checked.Select("ele!=H").atoms) \
- == len(temp_ent.Select("ele!=H").atoms):
+ n_checked = len(temp_ent_stereo_checked.Select("ele!=H").atoms)
+ n_tot = len(temp_ent.Select("ele!=H").atoms)
+ if n_checked == n_tot and HasNonPlanarRings(temp_ent) == False:
ost.LogInfo("No more stereo-chemical problems "
"-> final energy: %g" % cur_energy)
break
@@ -396,6 +407,7 @@ def CheckFinalModel(mhandle):
- 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.
+ - Residues that contain non-planar rings.
:param mhandle: Modelling handle for which to perform checks.
:type mhandle: :class:`ModellingHandle`
@@ -477,6 +489,13 @@ def CheckFinalModel(mhandle):
ost.LogInfo(msg)
AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MINOR, [res])
+ # report non-planar rings
+ non_planar_rings = GetNonPlanarRings(mhandle.model)
+ for res in non_planar_rings:
+ msg = "Ring of " + str(res) + " is non-planar!"
+ ost.LogWarning(msg)
+ AddModellingIssue(mhandle, msg, ModellingIssue.Severity.MINOR, [res])
+
def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list(),
model_termini=False):
'''Build a model starting with a raw model (see :func:`BuildRawModel`).
diff --git a/modelling/pymod/_planar_rings.py b/modelling/pymod/_planar_rings.py
new file mode 100644
index 0000000000000000000000000000000000000000..dcb4c28771200f0092be647dcfb7daf5d8a28d49
--- /dev/null
+++ b/modelling/pymod/_planar_rings.py
@@ -0,0 +1,113 @@
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+'''Helper functions to deal with non-planar rings'''
+import ost
+from ost import geom
+
+from promod3 import core
+
+def _GetMaxDist(res):
+ """Get max distance of any atom from ring plane
+
+ None is returned if res.one_letter_code is not in ['Y', 'F', 'W', 'H']
+ or when not all expected ring atoms are present
+
+ :param res: Residue for which you want to get the max dist to ring plane
+ :type res: :class:`~ost.mol.ResidueHandle` or :class:`~ost.mol.ResidueView`
+ :returns: Max distance of any ring atom to optimal ring plane or None if
+ residue contains no ring or not all expected ring atoms are
+ present.
+ """
+ prof = core.StaticRuntimeProfiler.StartScoped("planar_rings::GetMaxDist")
+ if res.one_letter_code in "YF":
+ atom_names = ["CG", "CD1", "CD2", "CE1", "CE2", "CZ"]
+ elif res.one_letter_code == 'W':
+ atom_names = ["CG", "CD1", "NE1", "CD2", "CE2", "CE3", "CZ2", "CZ3",
+ "CH2"]
+ elif res.one_letter_code == 'H':
+ atom_names = ["CG", "CD2", "ND1", "CE1", "NE2"]
+ else:
+ return None
+ positions = geom.Vec3List()
+ for atom_name in atom_names:
+ a = res.FindAtom(atom_name)
+ if a.IsValid():
+ positions.append(a.GetPos())
+ else:
+ return None
+ origin=positions.center
+ normal=positions.principal_axes.GetRow(0)
+ plane = geom.Plane(origin, normal)
+ return max([abs(geom.Distance(plane, pos)) for pos in positions])
+
+def GetNonPlanarRings(ent, max_dist_thresh = 0.1):
+ '''Get list of residues with rings that non-planar in the given structure.
+
+ Only residues with res.one_letter_code in ['Y', 'F', 'W', 'H'] that contain
+ all expected ring atoms are considered.
+
+ 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.
+
+ 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
+ |project| 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).
+
+ :param ent: Structure for which to detect non-planar rings.
+ :type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
+ :param max_dist_thresh: 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.
+ :type max_dist_thresh: :class:`float`
+
+ :return: :class:`list` of residues (:class:`~ost.mol.ResidueHandle`/
+ :class:`~ost.mol.ResidueView`) which have a non-planar ring.
+ '''
+ prof_name = 'ring_punches::GetNonPlanarRings'
+ prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
+ dists = [_GetMaxDist(res) for res in ent.residues]
+ mdt = max_dist_thresh
+ return [r for d, r in zip(dists, ent.residues) if d is not None and d > mdt]
+
+def HasNonPlanarRings(ent, max_dist_thresh = 0.1):
+ '''Check if any ring is non-planar in the given structure.
+
+ Calls :func:`GetNonPlanarRings` with given parameters and returns if any
+ residue is considered non-planar.
+
+ :param ent: Structure for which to detect non-planar rings
+ :type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
+ :param max_dist_thresh: 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.
+ :type max_dist_thresh: :class:`float`
+
+
+ :return: True, if any ring is non-planar
+ :rtype: :class:`bool`
+ '''
+ prof_name = 'ring_punches::HasNonPlanarRings'
+ prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
+ return len(GetNonPlanarRings(ent, max_dist_thresh)) > 0
+
+# these methods will be exported into module
+__all__ = ('GetNonPlanarRings', 'HasNonPlanarRings')
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index 47228fb035ace3aaa80525ba27a5a3077b6724b7..e10f194804c6b6d372fd1b3e9b51148f0391bfea 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -467,7 +467,7 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
:meth:`RotamerGraph.TreeSolve`.
:type graph_intial_epsilon: :class:`float`
:param energy_function: What energy function to use can be any in
- ["SCWRL4", "SCWRL3"]
+ ["SCWRL4", "SCWRL3", "VINA"]
:type energy_function: :class:`str`
'''
prof_name = 'modelling::ReconstructSidechains'
diff --git a/modelling/pymod/export_afdb.cc b/modelling/pymod/export_afdb.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7a9741d7552909274fd0eaa84c667376996a76be
--- /dev/null
+++ b/modelling/pymod/export_afdb.cc
@@ -0,0 +1,46 @@
+// Copyright (c) 2013-2023, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
+#include <boost/python.hpp>
+#include <promod3/modelling/afdb.hh>
+
+using namespace ost;
+using namespace boost::python;
+using namespace promod3::modelling;
+
+namespace {
+ void WrapSeqToPentamerIndices(const String& sequence, bool unique,
+ boost::python::list& l) {
+ std::vector<int> indices;
+ SeqToPentamerIndices(sequence, unique, indices);
+ for(size_t i = 0; i < indices.size(); ++i) {
+ l.append(indices[i]);
+ }
+ }
+}
+
+void export_afdb()
+{
+ def("SeqToPentamerIndices", &WrapSeqToPentamerIndices, (arg("sequence"),
+ arg("unique"),
+ arg("result_list")));
+ def("CreateAFDBIdx", &CreateAFDBIdx, (arg("uniprot_ac"), arg("fragment"),
+ arg("version")));
+
+ def("CreatePentaMatch", &CreatePentaMatch, (arg("seq_list"),
+ arg("db_path"),
+ arg("entries_from_seqnames")));
+}
diff --git a/modelling/pymod/wrap_modelling.cc b/modelling/pymod/wrap_modelling.cc
index 39b82e4f4fbd602ce24cdbdf2e3df0a4e36052fc..21e008507a3a678a80872367d8a9fb98865fbd44 100644
--- a/modelling/pymod/wrap_modelling.cc
+++ b/modelling/pymod/wrap_modelling.cc
@@ -28,6 +28,7 @@ void export_score_container();
void export_scoring_weights();
void export_SidechainReconstructor();
void export_motif_finder();
+void export_afdb();
BOOST_PYTHON_MODULE(_modelling)
{
@@ -43,4 +44,5 @@ BOOST_PYTHON_MODULE(_modelling)
export_scoring_weights();
export_SidechainReconstructor();
export_motif_finder();
+ export_afdb();
}
diff --git a/modelling/src/CMakeLists.txt b/modelling/src/CMakeLists.txt
index 440e65e09b7ae505f125b7cd0088092b7557d4b5..0a618209a8ba5ebb17d40788b619a71b310a6e77 100644
--- a/modelling/src/CMakeLists.txt
+++ b/modelling/src/CMakeLists.txt
@@ -19,6 +19,7 @@ set(MODELLING_SOURCES
sidechain_reconstructor.cc
sidechain_env_listener.cc
motif_finder.cc
+ afdb.cc
)
set(MODELLING_HEADERS
@@ -43,6 +44,7 @@ set(MODELLING_HEADERS
sidechain_env_listener.hh
motif_finder.hh
robin_hood.h
+ afdb.hh
)
module(NAME modelling
diff --git a/modelling/src/afdb.cc b/modelling/src/afdb.cc
new file mode 100644
index 0000000000000000000000000000000000000000..1548de1664ebb78747a0dd753ffe485eaf262059
--- /dev/null
+++ b/modelling/src/afdb.cc
@@ -0,0 +1,295 @@
+// Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#include <algorithm>
+#include <fstream>
+
+#include <ost/log.hh>
+#include <ost/string_ref.hh>
+
+#include <promod3/modelling/afdb.hh>
+
+namespace{
+ inline int CharToIdx(char ch) {
+ switch(ch){
+ case 'A': return 0;
+ case 'C': return 1;
+ case 'D': return 2;
+ case 'E': return 3;
+ case 'F': return 4;
+ case 'G': return 5;
+ case 'H': return 6;
+ case 'I': return 7;
+ case 'K': return 8;
+ case 'L': return 9;
+ case 'M': return 10;
+ case 'N': return 11;
+ case 'P': return 12;
+ case 'Q': return 13;
+ case 'R': return 14;
+ case 'S': return 15;
+ case 'T': return 16;
+ case 'V': return 17;
+ case 'W': return 18;
+ case 'Y': return 19;
+ }
+ std::stringstream ss;
+ ss << "nonstandard olc observed: " << ch;
+ throw ost::Error(ss.str());
+ }
+
+ inline int PentamerToIdx(const char* ptr) {
+ return CharToIdx(ptr[0])*160000 + CharToIdx(ptr[1])*8000 +
+ CharToIdx(ptr[2])*400 + CharToIdx(ptr[3])*20 + CharToIdx(ptr[4]);
+ }
+
+ inline int PentamerToIdx(const int* ptr) {
+ return ptr[0]*160000 + ptr[1]*8000 + ptr[2]*400 + ptr[3]*20 + ptr[4];
+ }
+
+ inline uint64_t AlphaToIdx(char ch) {
+ if(ch == ' ') {
+ return 0;
+ } else {
+ return static_cast<uint64_t>(ch - 'A' + 1);
+ }
+ }
+
+ inline uint64_t NumericToIdx(char ch) {
+ if(ch == ' ') {
+ return 0;
+ } else {
+ return static_cast<uint64_t>(ch - '0' + 1);
+ }
+ }
+
+ inline uint64_t AlphaNumericToIdx(char ch) {
+ if(ch == ' ') {
+ return 0;
+ } else if(ch >= '0' && ch <= '9') {
+ return static_cast<uint64_t>(ch-'0' + 1);
+ } else {
+ return static_cast<uint64_t>(ch-'A' + 1 + 10);
+ }
+ }
+
+ inline bool CheckAlpha(char ch, bool allow_whitespace) {
+ return (ch>='A' and ch<='Z') || (allow_whitespace && ch == ' ');
+ }
+
+ inline bool CheckNumeric(char ch, bool allow_whitespace) {
+ return (ch>='0' and ch<='9') || (allow_whitespace && ch == ' ');
+ }
+
+ inline bool CheckAlphaNumeric(char ch, bool allow_whitespace) {
+ return CheckAlpha(ch, allow_whitespace) ||
+ CheckNumeric(ch, allow_whitespace);
+ }
+}
+
+namespace promod3 { namespace modelling {
+
+
+void SeqToPentamerIndices(const String& seq, bool unique, std::vector<int>& indices) {
+ int N = seq.size();
+ if(N < 5) {
+ std::stringstream ss;
+ ss << "Sequence must have at least length 5, got: " << seq;
+ throw ost::Error(ss.str());
+ }
+ indices.resize(N);
+ for(int i = 0; i < N; ++i) {
+ indices[i] = CharToIdx(seq[i]);
+ }
+ for(int i = 0; i < N-4; ++i) {
+ indices[i] = PentamerToIdx(&indices[i]);
+ }
+ indices.resize(N-4);
+ if(unique) {
+ std::sort(indices.begin(), indices.end());
+ auto last = std::unique(indices.begin(), indices.end());
+ indices.erase(last, indices.end());
+ }
+}
+
+uint64_t CreateAFDBIdx(const String& uniprot_ac, int fragment, int version) {
+
+ // check if uniprot AC has expected size of 6 or 10
+ // https://www.uniprot.org/help/accession_numbers
+ size_t ac_size = uniprot_ac.size();
+ if(ac_size != 6 && ac_size != 10) {
+ std::stringstream ss;
+ ss << "Expect uniprot AC to be of size 6 or 10, got: " << uniprot_ac;
+ throw ost::Error(ss.str());
+ }
+
+ if(!CheckAlpha(uniprot_ac[0], false)) {
+ throw ost::Error("Exp capital alphabetic character at idx 0 of uniprot AC");
+ }
+
+ if(!CheckNumeric(uniprot_ac[1], false)) {
+ throw ost::Error("Exp capital alphabetic character at idx 1 of uniprot AC");
+ }
+
+ if(!CheckAlphaNumeric(uniprot_ac[2], false)) {
+ throw ost::Error("Exp capital alphabetic character at idx 2 of uniprot AC");
+ }
+
+ if(!CheckAlphaNumeric(uniprot_ac[3], false)) {
+ throw ost::Error("Exp capital alphabetic character at idx 3 of uniprot AC");
+ }
+
+ if(!CheckAlphaNumeric(uniprot_ac[4], false)) {
+ throw ost::Error("Exp capital alphabetic character at idx 4 of uniprot AC");
+ }
+
+ if(!CheckNumeric(uniprot_ac[5], false)) {
+ throw ost::Error("Exp capital alphabetic character at idx 5 of uniprot AC");
+ }
+
+ if(ac_size > 6) {
+ if(!CheckAlpha(uniprot_ac[6], true)) {
+ throw ost::Error("Exp capital alphabetic character at idx 6 of uniprot AC");
+ }
+
+ if(!CheckAlphaNumeric(uniprot_ac[7], true)) {
+ throw ost::Error("Exp capital alphabetic character at idx 7 of uniprot AC");
+ }
+
+ if(!CheckAlphaNumeric(uniprot_ac[8], true)) {
+ throw ost::Error("Exp capital alphabetic character at idx 8 of uniprot AC");
+ }
+
+ if(!CheckNumeric(uniprot_ac[9], true)) {
+ throw ost::Error("Exp capital alphabetic character at idx 9 of uniprot AC");
+ }
+ }
+
+ if(fragment < 0 || fragment > 127) {
+ std::stringstream ss;
+ ss << "Expect fragment to be in range [0, 127], got: " << fragment;
+ }
+ if(version < 0 || version > 31) {
+ std::stringstream ss;
+ ss << "Expect version to be in range [0, 31], got: " << version;
+ }
+
+ uint64_t idx = 0;
+ idx += AlphaToIdx(uniprot_ac[0]);
+ idx += NumericToIdx(uniprot_ac[1]) << 5;
+ idx += AlphaNumericToIdx(uniprot_ac[2]) << 9;
+ idx += AlphaNumericToIdx(uniprot_ac[3]) << 15;
+ idx += AlphaNumericToIdx(uniprot_ac[4]) << 21;
+ idx += NumericToIdx(uniprot_ac[5]) << 27;
+ if(ac_size > 6) {
+ idx += AlphaToIdx(uniprot_ac[6]) << 31;
+ idx += AlphaNumericToIdx(uniprot_ac[7]) << 36;
+ idx += AlphaNumericToIdx(uniprot_ac[8]) << 42;
+ idx += NumericToIdx(uniprot_ac[9]) << 48;
+ }
+ idx += static_cast<uint64_t>(fragment) << 52;
+ idx += static_cast<uint64_t>(version) << 59;
+ return idx;
+}
+
+void CreatePentaMatch(const ost::seq::SequenceList& seq_list,
+ const String& db_path,
+ bool entries_from_seqnames) {
+
+ String indexer_path = db_path + "/" + "indexer.dat";
+ String pos_path = db_path + "/" + "pos.dat";
+ String length_path = db_path + "/" + "length.dat";
+ String meta_path = db_path + "/" + "meta.dat";
+
+ std::vector<int> entry_indices;
+ entry_indices.reserve(seq_list.GetCount());
+ if(entries_from_seqnames) {
+ for(int i = 0; i < seq_list.GetCount(); ++i) {
+ const String& sname = seq_list[i].GetName();
+ ost::StringRef s(&sname[0], sname.size());
+ std::pair<bool, int> idx = s.trim().to_int();
+ if(idx.first == false) {
+ std::stringstream ss;
+ ss << "Cannot cast seq name to integer: " << sname;
+ throw ost::Error(ss.str());
+ }
+ entry_indices.push_back(idx.second);
+ }
+ } else {
+ for(int i = 0; i < seq_list.GetCount(); ++i) {
+ entry_indices.push_back(i);
+ }
+ }
+
+ std::vector<std::vector<int32_t> > indexer(3200000);
+ for(int i = 0; i < seq_list.GetCount(); ++i) {
+ int entry_idx = entry_indices[i];
+ std::vector<int> penta_indices;
+ SeqToPentamerIndices(seq_list[i].GetString(), true, penta_indices);
+ for(auto j = penta_indices.begin(); j != penta_indices.end(); ++j) {
+ indexer[*j].push_back(entry_idx);
+ }
+ }
+
+ for(auto i = indexer.begin(); i != indexer.end(); ++i) {
+ std::sort(i->begin(), i->end());
+ }
+
+ std::ofstream indexer_stream(indexer_path, std::ios::binary);
+ if(!indexer_stream) {
+ throw ost::Error("Could not open indexer file: " + indexer_path);
+ }
+ std::vector<int64_t> positions;
+ std::vector<int32_t> lengths;
+ int64_t current_pos = 0;
+ for(auto i = indexer.begin(); i != indexer.end(); ++i) {
+ int size = i->size();
+ if(size > 0) {
+ indexer_stream.write(reinterpret_cast<char*>(&(*i)[0]),
+ size*sizeof(int32_t));
+ }
+ positions.push_back(current_pos);
+ lengths.push_back(size);
+ current_pos += size;
+ }
+ indexer_stream.close();
+
+ std::ofstream pos_stream(pos_path, std::ios::binary);
+ std::ofstream length_stream(length_path, std::ios::binary);
+ std::ofstream meta_stream(meta_path, std::ofstream::out);
+ if(!pos_stream) {
+ throw ost::Error("Could not open pos file: " + pos_path);
+ }
+ if(!length_stream) {
+ throw ost::Error("Could not open length file: " + length_path);
+ }
+ if(!meta_stream) {
+ throw ost::Error("Could not open meta file: " + meta_path);
+ }
+ pos_stream.write(reinterpret_cast<char*>(&positions[0]),
+ positions.size()*sizeof(int64_t));
+ length_stream.write(reinterpret_cast<char*>(&lengths[0]),
+ lengths.size()*sizeof(int32_t));
+ int32_t max_entry_idx = *std::max_element(entry_indices.begin(),
+ entry_indices.end());
+ meta_stream << max_entry_idx;
+ pos_stream.close();
+ length_stream.close();
+ meta_stream.close();
+}
+
+
+
+}} //ns
diff --git a/modelling/src/afdb.hh b/modelling/src/afdb.hh
new file mode 100644
index 0000000000000000000000000000000000000000..551e51d97285707825851f19fdb721fbb0b1687f
--- /dev/null
+++ b/modelling/src/afdb.hh
@@ -0,0 +1,36 @@
+// Copyright (c) 2013-2023, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef PM3_MODELLING_AFDB_HH
+#define PM3_MODELLING_AFDB_HH
+
+#include <ost/mol/mol.hh>
+#include <ost/seq/sequence_list.hh>
+#include <promod3/core/message.hh>
+
+
+namespace promod3 { namespace modelling {
+
+void SeqToPentamerIndices(const String& seq, bool unique,
+ std::vector<int>& indices);
+
+void CreatePentaMatch(const ost::seq::SequenceList& seq_list,
+ const String& db_path,
+ bool entries_from_seqnames);
+
+uint64_t CreateAFDBIdx(const String& uniprot_ac, int fragment, int version);
+}} //ns
+
+#endif
diff --git a/modelling/tests/test_loop_closing.cc b/modelling/tests/test_loop_closing.cc
index 46fb0e97159e233c19bec1ebf4a12d6c156c64b0..f45d55a1df74c0373eb2686397e7982d040ae222 100644
--- a/modelling/tests/test_loop_closing.cc
+++ b/modelling/tests/test_loop_closing.cc
@@ -122,7 +122,7 @@ BOOST_AUTO_TEST_CASE(test_ccd_closing) {
ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
reader.Import(test_ent);
- ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor(false,true,true,true,ost::conop::CONOP_SILENT));
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor(false,true,true,true,true,ost::conop::CONOP_SILENT));
processor->Process(test_ent);
@@ -186,7 +186,7 @@ BOOST_AUTO_TEST_CASE(test_kic_closing) {
ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
reader.Import(test_ent);
- ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor(false,true,true,true,ost::conop::CONOP_SILENT));
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor(false,true,true,true,true,ost::conop::CONOP_SILENT));
processor->Process(test_ent);
String gap_sequence = "PALDFLVEK";