diff --git a/doc/html/_sources/changelog.rst.txt b/doc/html/_sources/changelog.rst.txt index bf7d79fe8f2b54752a8d460224dd9459541fd53a..da700eca24229ad11c6919ec01e5213589252b26 100644 --- a/doc/html/_sources/changelog.rst.txt +++ b/doc/html/_sources/changelog.rst.txt @@ -5,6 +5,12 @@ Changelog ================================================================================ +Release 3.3.1 +-------------------------------------------------------------------------------- + +* Bugfix release: Updates OpenStructure dependency to 2.5.0 and fixes issues + with Singularity container. + Release 3.3.0 -------------------------------------------------------------------------------- diff --git a/doc/html/_sources/modelling/algorithms.rst.txt b/doc/html/_sources/modelling/algorithms.rst.txt index c9db60f1f7f57dc8ac74e00d8db94b9cb018c4be..5545a9acfd90270e035ef0cbf2c45b6ffe5a1088 100644 --- a/doc/html/_sources/modelling/algorithms.rst.txt +++ b/doc/html/_sources/modelling/algorithms.rst.txt @@ -308,7 +308,7 @@ iteration. .. method:: FindMotifs(query, target_positions, hash_tresh=0.4, \ distance_thresh=1.0, refine_thresh=0.7, \ - flags=list()) + flags=list(), swap_thresh=False) Performs the detection and refinement stages of the geometric hashing algorithm. @@ -322,6 +322,10 @@ iteration. constructor. If you didn't provide anything there, this can be ignored. Only the actual coordinates matter in this case. + :param swap_thresh: *hash_thresh* and *refine_thresh* refer to fraction of + covered positions in *query*. When setting this to + True, they refer to the fraction of covered positions + in *target_positions*. :returns: All found matches diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js index e42d212690329abb5fb8ac48021c049591f80733..4c289d9b2f01108607b8c0c3e562001137c59bde 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: '3.3.0', + VERSION: '3.3.1', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html index e250c0387d6988e10e2be5816abbe0efd587ed46..9e41b3622e4984466e8c6a92a4039a38bc45f734 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 3.3.0 documentation</title> + <title>ProMod3 Actions — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -101,7 +102,7 @@ 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/2.3.1/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 +<a class="reference external" href="https://www.openstructure.org/docs/2.4/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>, <code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>. At least one structure must be given and you cannot mix file formats. Multiple structures can be given and each @@ -183,7 +184,7 @@ 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/2.3.1/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 +<a class="reference external" href="https://www.openstructure.org/docs/2.4/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>, <code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>.</p> <p>Several flags control the modelling behaviour:</p> diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html index c91acf1bae26aabd3aa6db5cd0a96a241f1178f1..c2fe078e002a4a1b68f57b3e68944fdd4dc8dc46 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 3.3.0 documentation</title> + <title>test_actions - Testing Actions — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -183,7 +184,7 @@ 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/2.3.1/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 +<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/2.4/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s <a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed as a script:</p> <div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13 diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html index 78cfa9bc845f3fa97dee73903c2fa83f616a231d..d43a812e52dd74d5d9a7d18e3ce91fc7e7342621 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 3.3.0 documentation</title> + <title>Building ProMod3 — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -36,7 +37,7 @@ <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 -2.4.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to +2.5.0. 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 @@ -45,7 +46,7 @@ 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> 2.4.0</li> +<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.5.0</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> diff --git a/doc/html/changelog.html b/doc/html/changelog.html index 4f246044f6a6a310bcb9755979772f35199e9251..4edb3657140d2706111b7ea2c40b460e91d956b7 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 3.3.0 documentation</title> + <title>Changelog — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -32,6 +33,13 @@ <div class="section" id="changelog"> <h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1> +<div class="section" id="release-3-3-1"> +<h2>Release 3.3.1<a class="headerlink" href="#release-3-3-1" title="Permalink to this headline">¶</a></h2> +<ul class="simple"> +<li>Bugfix release: Updates OpenStructure dependency to 2.5.0 and fixes issues +with Singularity container.</li> +</ul> +</div> <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"> diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html index 403551e94de69196008c9d1a10b20f9fff92efc3..445957fcca41c2b25cdb45f0fdb4292ae24bd4de 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 3.3.0 documentation</title> + <title>ProMod3’s Share Of CMake — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html index 70b21e457a6b9ca919f128539fbf7faad29c393a..268489f69c5d92237cc5b76c595700c6f59adf97 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 3.3.0 documentation</title> + <title>Docker — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -75,7 +76,7 @@ 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/2.3.1/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. +<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">CompoundLib</span></code></a> is generated. Compound libraries contain information on chemical compounds, such as their connectivity, chemical class and one-letter-code. The compound library has several uses, but the most important one is to provide the connectivy diff --git a/doc/html/container/index.html b/doc/html/container/index.html index 11a0a45b2354ae1755686ac1a1a41870a35825a0..f37f181a37a3d1e06f1387433069cae35abd0f8a 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 3.3.0 documentation</title> + <title>ProMod3 and Containers — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html index 79d7f49b1e7d3062d09d3c7938c42060d6d74c0f..85b7c9b344afbeeade4d2091b41f090f565eb9ff 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 3.3.0 documentation</title> + <title>Singularity — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/contributing.html b/doc/html/contributing.html index 1fdfbf12c0a454f631ecf3941e3ed35e522308d3..ef4e0f873baee4ab285bfd6b81f05b9daab63ee0 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 3.3.0 documentation</title> + <title>Contributing — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html index 7a551e0371800bbc8d785ddae9b5273b80918942..cfff0da976ba58a7e8130acce8b2e20abd860001 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 3.3.0 documentation</title> + <title>Geometry functions — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -45,14 +46,14 @@ <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/2.3.1/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> +<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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.3.1/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> +<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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p> </td> </tr> </tbody> @@ -68,16 +69,16 @@ <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/2.3.1/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> +<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.3.1/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> +<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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p> </td> </tr> </tbody> @@ -94,9 +95,9 @@ 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/2.3.1/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>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</li> <li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -106,7 +107,7 @@ 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/2.3.1/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> +<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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p> </td> </tr> </tbody> @@ -123,16 +124,16 @@ 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/2.3.1/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> +<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.3.1/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> +<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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p> </td> </tr> </tbody> @@ -149,8 +150,8 @@ 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/2.3.1/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>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li> <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -158,7 +159,7 @@ 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/2.3.1/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> +<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/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p> </td> </tr> </tbody> @@ -175,7 +176,7 @@ 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/2.3.1/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>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li> <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -183,7 +184,7 @@ 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/2.3.1/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> +<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/2.4/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p> </td> </tr> </tbody> @@ -200,7 +201,7 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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> <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> @@ -219,7 +220,7 @@ 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/2.3.1/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 class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td> </tr> </tbody> </table> diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html index 6c1b852d7a1cc9d8fcfd2d69506801b6125e8e84..0a28f4c28aedb0d7d79df5bc78a8b315c5fcc168 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 3.3.0 documentation</title> + <title>Graph Minimizer — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html index 02ce0b8a743df0d8fe0254150ab922cb55ddc4f1..3a603ac3d8a353319259d261e1cfe327438cb97d 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 3.3.0 documentation</title> + <title>helper - Shared Functionality For the Everything — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/core/index.html b/doc/html/core/index.html index 0a8d27bc7bf0adf0a92aa6f9d71e444b145f25f7..237aa85f2e4a108fab43cf4a5fac8e3ca256ecab 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 3.3.0 documentation</title> + <title>core - ProMod3 Core Functionality — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html index 7547ac6444e2cf93673a1a526152480460c6fba9..1f7549b4cafa8492cbf1dd213059ef47e7b72cf4 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 3.3.0 documentation</title> + <title>pm3argparse - Parsing Command Lines — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -255,7 +256,7 @@ 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/2.3.1/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>, +<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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>, ordered to match the target sequences.</li> </ul> <p>Exit codes related to profile input:</p> diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html index f22d0b777e665bcae8314cddf1a88860ff34e699..627e3ff595077a71b695bd03ba869f19e77ab44a 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 3.3.0 documentation</title> + <title>Runtime profiling — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html index 1af7258a0b77d5cb2c5cdfa467db86337f4f8d31..369e60e56b82d72a224983561042c9553231fbcd 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 3.3.0 documentation</title> + <title>SetCompoundsChemlib() — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html index 5a09c032e65f1f2b17e9d6a8e37176cabad99507..596af58a3aa25aa2c7fe0ccb39dcf8f8430978d6 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 3.3.0 documentation</title> + <title>ProMod3 Setup — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/developers.html b/doc/html/developers.html index 91607a8019c11b7066bc5a07ccef624aa6e6bffe..b838c706184c9dfd262ceacd7bc3fed4d6aeec0f 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 3.3.0 documentation</title> + <title>Documentation For Developers — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 5b605538c950d2db69e465bcd77b129727a40f3d..70abe79670087210a7cb258e2cadeebdebc4985b 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 3.3.0 documentation</title> + <title>Index — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -15,6 +15,7 @@ <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" /> diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html index e79788840098db2df078376db7ffd2831adbf510..a455d5e897e54d971fdc8d4a5a1d2d812b12c3f6 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 3.3.0 documentation</title> + <title>Getting Started — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -87,7 +88,7 @@ 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/2.3.1/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> +(using <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><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 diff --git a/doc/html/index.html b/doc/html/index.html index 94f13fec1f198235bb39ef5e18cb34ce67bbef7f..ebc11c4440487811a4ecf3de9ec53fbcb4b67911 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 3.3.0 documentation</title> + <title>ProMod3 — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/license.html b/doc/html/license.html index 04749084cd6ec9c8e570c832900220e9bf4f9e94..76c882cece963a333ef32cf56f0a5d504d8666a7 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 3.3.0 documentation</title> + <title>License — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html index 5affbe0d808be1eea3e7a49074249b8cca596901..50e1ea3a5beab8f8b74aefbf9e69c7e86fda63ef 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 3.3.0 documentation</title> + <title>Handling All Atom Positions — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -80,8 +81,8 @@ 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/2.3.1/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 +<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/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><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/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td> </tr> </tbody> @@ -103,7 +104,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains in <em>env_structure</em> are expected to be in the same order as the SEQRES items provided in constructor.</td> </tr> @@ -133,7 +134,7 @@ 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/2.3.1/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>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/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li> <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -210,7 +211,7 @@ 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/2.3.1/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 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/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td> </tr> </tbody> </table> @@ -344,7 +345,7 @@ 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/2.3.1/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> +<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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> @@ -390,7 +391,7 @@ 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/2.3.1/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> +<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -440,7 +441,7 @@ 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/2.3.1/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 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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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> @@ -544,7 +545,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> @@ -659,7 +660,7 @@ out of bounds.</p> if required atom positions (CA-C-N-CA) are not set. Here, we use CA-C of residue <em>res_index</em> - 1 and N-CA of residue <em>res_index</em> (consistent with OST’s -<code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle.GetOmegaTorsion" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</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/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p> @@ -823,9 +824,9 @@ 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/2.3.1/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> +Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td> </tr> -<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/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 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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td> </tr> </tbody> </table> @@ -845,8 +846,8 @@ 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/2.3.1/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> +<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -939,7 +940,7 @@ 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/2.3.1/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 +(<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>).</p> <dl class="staticmethod"> <dt id="promod3.loop.AminoAcidLookup.GetOLC"> @@ -952,7 +953,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td> </tr> </tbody> </table> @@ -974,7 +975,7 @@ 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/2.3.1/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>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li> <li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -1004,7 +1005,7 @@ 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/2.3.1/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>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li> <li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -1033,7 +1034,7 @@ 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/2.3.1/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>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li> <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -1061,7 +1062,7 @@ 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/2.3.1/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>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li> <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -1085,7 +1086,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td> </tr> </tbody> </table> @@ -1117,7 +1118,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td> </tr> </tbody> </table> @@ -1150,7 +1151,7 @@ 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/2.3.1/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> +<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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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"> @@ -1244,7 +1245,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> @@ -1268,7 +1269,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html index adc18a285338a31c95c7f84aa7671b3a9efa8ec7..b2a0e71c9af3026a42465bfb1e428ebcf4f2935f 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 3.3.0 documentation</title> + <title>Representing Loops — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -36,7 +37,7 @@ <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/2.3.1/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> +converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p> <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span> <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span> <span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span> @@ -86,7 +87,7 @@ residue has a CB position defined (i.e. even if it’s a glycine) and we only allow amino acid types belonging to the 20 default amino acids. Note that the omega torsion angle defined here for residue <em>i</em> is the dihedral between CA-C of residue <em>i</em> and N-CA of residue <em>i+1</em> (this is shifted by 1 residue -compared to OST’s <code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p> +compared to OST’s <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle.GetOmegaTorsion" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code></a>).</p> <dl class="method"> <dt id="promod3.loop.BackboneList.BackboneList"> <code class="descname">BackboneList</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.BackboneList" title="Permalink to this definition">¶</a></dt> @@ -148,7 +149,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from which the backbone positions and one letter codes are extracted.</td> </tr> @@ -172,7 +173,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from which the backbone positions are extracted.</li> </ul> </td> @@ -196,7 +197,7 @@ 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/2.3.1/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 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/2.4/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></td> </tr> </tbody> </table> @@ -206,7 +207,7 @@ 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/2.3.1/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>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </li> <li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -225,7 +226,7 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td> </tr> </tbody> </table> @@ -242,8 +243,8 @@ 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/2.3.1/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> +<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -259,7 +260,7 @@ 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/2.3.1/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>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li> <li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -278,7 +279,7 @@ 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/2.3.1/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 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/2.4/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.4.0)"><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> @@ -382,7 +383,7 @@ 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/2.3.1/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 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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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> @@ -407,7 +408,7 @@ 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/2.3.1/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 +<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon / oxygen atom to this.</li> </ul> </td> @@ -459,7 +460,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> @@ -476,7 +477,7 @@ 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/2.3.1/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> +<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -502,12 +503,12 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li> <li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li> </ul> </td> @@ -577,12 +578,12 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li> <li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li> </ul> </td> @@ -646,7 +647,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last element of this backbone list)</td> </tr> </tbody> @@ -663,7 +664,7 @@ 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/2.3.1/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> +<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li> </ul> </td> </tr> @@ -683,7 +684,7 @@ 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/2.3.1/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> +<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li> </ul> </td> </tr> @@ -699,7 +700,7 @@ 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/2.3.1/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 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/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td> </tr> </tbody> </table> @@ -719,12 +720,12 @@ 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/2.3.1/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> +<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/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li> <li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li> <li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -744,7 +745,7 @@ 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/2.3.1/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 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/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><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> diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html index 540e0f8c4d81fe33abbcddbfbe19838418f93433..d031b39d5221fdb45a4ee1d1e8fc2161eab8df44 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 3.3.0 documentation</title> + <title>loop - Loop Handling — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html index 51d3acd6a7d7f89955e4b4cdeec8cefbe4ea8376..a2d25fd6f34b570c9e97e65d9e7b1b1f6cc8647c 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 3.3.0 documentation</title> + <title>Loading Precomputed Objects — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html index 05816c62a4fd69fed419d722ae047bdb5719adcb..b1e50413487d64ba6adeddabb5329f3aecb9f064 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 3.3.0 documentation</title> + <title>Generate ost.mol.mm systems — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -32,8 +33,8 @@ <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/2.3.1/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 +<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><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/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) and a specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>).</p> <p>The example below showcases the creation and use of an MM system:</p> @@ -278,7 +279,7 @@ 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/2.3.1/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 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/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></td> </tr> </tbody> </table> @@ -425,7 +426,7 @@ 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/2.3.1/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> +<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p> <ul class="simple"> <li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where <em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a @@ -538,7 +539,7 @@ 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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> @@ -654,7 +655,7 @@ 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/2.3.1/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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.4.0)"><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> @@ -670,7 +671,7 @@ 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/2.3.1/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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.4.0)"><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> @@ -685,7 +686,7 @@ 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/2.3.1/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> +<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/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.4.0)"><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> @@ -709,7 +710,7 @@ 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/2.3.1/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> +<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/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.4.0)"><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> @@ -734,7 +735,7 @@ 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/2.3.1/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> +(see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.4.0)"><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> @@ -759,7 +760,7 @@ 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/2.3.1/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> +(see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.4.0)"><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> @@ -905,7 +906,7 @@ 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/2.3.1/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, +correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally, there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine (<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown types. The full list of values is:</p> @@ -922,7 +923,7 @@ 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/2.3.1/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>. +indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>. The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the @@ -1032,7 +1033,7 @@ 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/2.3.1/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> +<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p> <dl class="attribute"> <dt id="promod3.loop.ForcefieldBondInfo.index_one"> <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt> @@ -1094,7 +1095,7 @@ 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/2.3.1/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> +<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p> <dl class="attribute"> <dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one"> <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt> @@ -1171,7 +1172,7 @@ 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/2.3.1/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> +(see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p> <dl class="attribute"> <dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one"> <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt> @@ -1276,8 +1277,8 @@ 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/2.3.1/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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.4.0)"><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/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p> <dl class="attribute"> <dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one"> <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt> @@ -1381,7 +1382,7 @@ 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/2.3.1/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> +<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p> <dl class="attribute"> <dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one"> <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt> @@ -1471,7 +1472,7 @@ 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/2.3.1/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> +<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p> <dl class="attribute"> <dt id="promod3.loop.ForcefieldLJPairInfo.index_one"> <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt> diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html index f5413e9fd7c236b612a8b0182faa7369708076ec..e917888a0e6ee2c1fd02a4f295a1218bdd6a7524 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 3.3.0 documentation</title> + <title>Structural Data — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -115,7 +116,7 @@ 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/2.3.1/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> +structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p> </dd></dl> </dd></dl> @@ -257,7 +258,7 @@ 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/2.3.1/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 +<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs running in parallel</li> </ol> <dl class="class"> @@ -392,11 +393,11 @@ 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/2.3.1/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 +<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named as specified by <em>chain_name</em>.</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 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 +<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name <em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li> <li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest connected stretch of residues are all connected @@ -532,9 +533,9 @@ 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/2.3.1/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 +<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be superposed onto.</li> -<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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 +<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be superposed onto.</li> </ul> </td> @@ -688,7 +689,7 @@ 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/2.3.1/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 +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to the database.</p> </td> </tr> @@ -727,7 +728,7 @@ 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/2.3.1/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> +<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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><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"> @@ -761,7 +762,7 @@ 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/2.3.1/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> +<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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><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"> @@ -802,7 +803,7 @@ 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/2.3.1/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> +<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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><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 @@ -824,7 +825,7 @@ 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/2.3.1/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>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li> <li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -1127,8 +1128,8 @@ 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/2.3.1/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>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li> <li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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 @@ -1352,7 +1353,7 @@ 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/2.3.1/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> +<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -1370,7 +1371,7 @@ 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/2.3.1/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> +<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html index 0f280d3cb2606eb6b2556717c1f3451e6a2dc6de..04b213039aa44587e2d327407cb57c3d821d7acb 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 3.3.0 documentation</title> + <title>Sampling Dihedral Angles — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -128,7 +129,7 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><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> </tbody> </table> @@ -200,9 +201,9 @@ 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/2.3.1/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> +<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -242,9 +243,9 @@ 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/2.3.1/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> +<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -280,9 +281,9 @@ 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/2.3.1/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>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li> <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -324,9 +325,9 @@ 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/2.3.1/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>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li> <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -368,9 +369,9 @@ 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/2.3.1/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>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li> <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -414,9 +415,9 @@ 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/2.3.1/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>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li> <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -438,9 +439,9 @@ 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/2.3.1/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>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li> <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html index 20a4c6e471c12cc54588a0a1a01adab7b8d7f7a2..c4a6693b8cac004463b12f12fa57352eb9505fd5 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 3.3.0 documentation</title> + <title>Modelling Algorithms — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -84,7 +85,7 @@ 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/2.3.1/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 +<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to superpose the according positions in <strong>bb_list_one</strong> onto <strong>bb_list_two</strong></p> </td> @@ -102,7 +103,7 @@ 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/2.3.1/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> +<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> objects from which the positions are extracted</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> @@ -123,9 +124,9 @@ 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/2.3.1/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> +relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a> and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of -<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/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 +<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to superpose the according positions from the first sequence onto the second sequence.</p> </td> @@ -162,7 +163,7 @@ 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/2.3.1/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 +<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to superpose the according positions in <strong>pos_one</strong> onto <strong>pos_two</strong></p> </td> @@ -225,8 +226,8 @@ 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/2.3.1/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>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/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li> <li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li> <li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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 @@ -318,7 +319,7 @@ 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/2.3.1/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 +<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the fragment search performance.</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> @@ -580,7 +581,7 @@ only coordinates matter.</li> <dl class="method"> <dt id="promod3.modelling.FindMotifs"> -<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt> +<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em>, <em>swap_thresh=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt> <dd><p>Performs the detection and refinement stages of the geometric hashing algorithm.</p> <table class="docutils field-list" frame="void" rules="none"> @@ -597,6 +598,10 @@ algorithm.</p> constructor. If you didn’t provide anything there, this can be ignored. Only the actual coordinates matter in this case.</li> +<li><strong>swap_thresh</strong> – <em>hash_thresh</em> and <em>refine_thresh</em> refer to fraction of +covered positions in <em>query</em>. When setting this to +True, they refer to the fraction of covered positions +in <em>target_positions</em>.</li> </ul> </td> </tr> @@ -633,7 +638,7 @@ scripts and documentation are available in <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> +Step 2: Generate pairwise alignments with <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/alg/seqalg/#ost.seq.alg.LocalAlign" title="(in OpenStructure v2.4.0)"><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. @@ -645,7 +650,7 @@ Step 4: Return top <em>tpl_n</em> (or less)</p> <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>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><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#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 @@ -658,7 +663,7 @@ described scoring</li> </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 +the second element being a <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><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, @@ -684,7 +689,7 @@ idx refers to the raw idx of the template in <em>fs_server</em>.</p> <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>trg_seq</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><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#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. diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html index 367970a45918d669797c5add095557368852cf1c..231efce67e407fdfc2fd86ebb74f68f7608f9c00 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 3.3.0 documentation</title> + <title>Handling Gaps — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -50,8 +51,8 @@ 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/2.3.1/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>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></li> <li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -106,7 +107,7 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></td> </tr> </tbody> </table> @@ -257,13 +258,13 @@ 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/2.3.1/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><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p> </dd></dl> <dl class="attribute"> <dt id="promod3.modelling.StructuralGap.after"> <code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt> -<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.3.1/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><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p> </dd></dl> <dl class="attribute"> @@ -308,7 +309,7 @@ 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/2.3.1/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>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/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> @@ -349,7 +350,7 @@ 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/2.3.1/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>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/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li> <li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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 @@ -402,7 +403,7 @@ 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/2.3.1/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>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/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li> <li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html index 8329bb87acfa8d00d660ea8a1cafae5aaf4ad1fc..1dbcbd28e1679c4b77051ca4449bbc423b6ce96d 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 3.3.0 documentation</title> + <title>modelling - Protein Modelling — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html index 98a3289adb73745b06583b32dcc2bb6c1866b3df..b0a14aff4c63471baf5b4a6c1341050652abb1f9 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 3.3.0 documentation</title> + <title>Handling Loop Candidates — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -122,8 +123,8 @@ 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/2.3.1/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>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li> <li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -234,9 +235,9 @@ 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/2.3.1/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 +<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li> -<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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 +<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li> <li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.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 @@ -278,9 +279,9 @@ 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/2.3.1/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 +<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate should match</li> -<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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 +<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate should match</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> @@ -354,7 +355,7 @@ 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/2.3.1/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 +<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for details, <em>prof.null_model</em> is used for weighting).</p> <p>Note that for profile scores a higher “score” is better! So take care when combining this to other scores, where it is commonly the other way around.</p> @@ -370,7 +371,7 @@ 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/2.3.1/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>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li> <li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -402,8 +403,8 @@ 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/2.3.1/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>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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> </ul> </td> </tr> diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html index 7cd4dcf9b6eb59022a7d70f9071066107d3f0fd9..6a4c5a923e8e0704cf045bc6fe9fd7b850daaa33 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 3.3.0 documentation</title> + <title>Fitting Loops Into Gaps — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <script type="text/javascript" src="../_static/underscore.js"></script> <script type="text/javascript" src="../_static/doctools.js"></script> <script type="text/javascript" src="../_static/language_data.js"></script> + <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script> <link rel="index" title="Index" href="../genindex.html" /> <link rel="search" title="Search" href="../search.html" /> <link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" /> @@ -73,11 +74,11 @@ 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/2.3.1/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><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem. If the residue before <em>n_stem</em> doesn’t exist, the torsion sampler will use a default residue (ALA) and and phi angle (-1.0472) to evaluate the first angle.</li> -<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/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><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem. If the residue after <em>c_stem</em> doesn’t exist, the torsion sampler will use a default residue (ALA) and psi angle (-0.7854) to evaluate the last angle.</li> @@ -114,8 +115,8 @@ 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/2.3.1/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>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li> <li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -316,7 +317,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li> <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -338,7 +339,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li> <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -361,7 +362,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li> <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -383,7 +384,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li> <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -405,7 +406,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li> <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html index d39b5fe78f18d2c81779a3672c75647d30420458..1aa89625db4cab9f530968c7f17a7fbae8967f56 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 3.3.0 documentation</title> + <title>Model Checking — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -47,14 +48,14 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td> </tr> <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/2.3.1/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>), +center (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>), radius (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>), -residue (<a class="reference external" href="https://www.openstructure.org/docs/2.3.1/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> +residue (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</td> </tr> </tbody> </table> @@ -70,11 +71,11 @@ 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/2.3.1/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> +<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li> </ul> </td> </tr> -<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which have a punched ring.</p> </td> </tr> @@ -93,7 +94,7 @@ 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/2.3.1/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> +<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li> </ul> </td> </tr> @@ -118,7 +119,7 @@ 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/2.3.1/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>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li> <li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li> <li><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -161,15 +162,15 @@ within 0.065 (HIS), 0.075 (TRP), 0.057 (TYR), 0.060 (PHE).</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>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>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><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> +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.4.0)"><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> @@ -187,7 +188,7 @@ residue is considered non-planar.</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>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>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><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> @@ -251,7 +252,7 @@ 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/2.3.1/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.3.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity” +<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/2.4/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity” executable is not found.</p> </td> </tr> @@ -268,7 +269,7 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><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> </tbody> </table> diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html index e307c44dfc5ba42e349b2bac26a389f36de7ee99..6d1a98053f0329fd461aea8058aa1efc4d95577e 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 3.3.0 documentation</title> + <title>Generating Loops De Novo — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -495,9 +496,9 @@ 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/2.3.1/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 +<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li> -<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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 +<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li> <li><strong>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> @@ -545,9 +546,9 @@ 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/2.3.1/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 +<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt.</li> -<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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 +<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt.</li> </ul> </td> @@ -587,9 +588,9 @@ 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/2.3.1/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 +<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt.</li> -<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/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 +<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt.</li> <li><strong>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> @@ -628,7 +629,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt.</td> </tr> </tbody> @@ -666,7 +667,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should adapt.</td> </tr> </tbody> diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html index 5548082996d7a865a38f946ceb9ca0c9fdb77593..7eccbbe4c668b87581d2949f583aa907a9079fae 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 3.3.0 documentation</title> + <title>Modelling Pipeline — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -107,7 +108,7 @@ 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/2.3.1/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 class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></td> </tr> </tbody> </table> @@ -133,13 +134,13 @@ 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/2.3.1/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 +<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain of the target protein.</p> <table class="docutils field-list" frame="void" rules="none"> <col class="field-name" /> <col class="field-body" /> <tbody valign="top"> -<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.3.1/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 class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></td> </tr> </tbody> </table> @@ -148,7 +149,7 @@ 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/2.3.1/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 +<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please note, that this attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have to fill it manually or even better by the convenient function @@ -157,7 +158,7 @@ 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/2.3.1/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 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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></td> </tr> </tbody> </table> @@ -344,7 +345,7 @@ 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/2.3.1/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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p> <p>Before extracting the coordinates, the alignments are pre-processed according to <em>aln_preprocessing</em>.</p> <p>This is a basic protein core modelling algorithm that copies backbone @@ -374,7 +375,7 @@ 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/2.3.1/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 +<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or list of alignment handles for raw model with multiple chains.</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 @@ -387,7 +388,7 @@ 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/2.3.1/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>, +If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>, <em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>. If <em>aln</em> is of type <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentList</span></code>, <em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of @@ -413,7 +414,7 @@ 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/2.3.1/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 +<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the template sequence (but not for the target))</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> @@ -457,12 +458,12 @@ 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/2.3.1/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>). +CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.4.0)"><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/2.4/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>). Both do a similarly good job without ligands (CHARMM slightly better), but you will want to be consistent with the optional force fields in <cite>extra_force_fields</cite>.</li> -<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.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 +<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/2.4/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a (ligand) residue cannot be parametrized with the default force field. The force fields are tried in the order as given and ligands without an @@ -483,7 +484,7 @@ 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/2.3.1/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> +<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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p> </td> </tr> </tbody> @@ -658,7 +659,7 @@ 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/2.3.1/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 +<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when they’re copied over</li> </ul> </td> @@ -689,7 +690,7 @@ 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/2.3.1/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> +<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/2.4/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li> </ul> </td> </tr> @@ -846,7 +847,7 @@ 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/2.3.1/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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.4.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li> <li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/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 @@ -1216,7 +1217,7 @@ one is loaded if None.</li> <dt id="promod3.modelling.MinimizeModelEnergy"> <code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em>, <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/2.3.1/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. +<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization. It will iteratively (at most <em>max_iterations</em> times):</p> <ul class="simple"> <li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li> @@ -1243,12 +1244,12 @@ minimization is aborted. This issue is logged and added as a major issue to <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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.4.0)"><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/2.3.1/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 +<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/2.4/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</li> </ul> </td> @@ -1256,7 +1257,7 @@ 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/2.3.1/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> +<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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p> </td> </tr> </tbody> @@ -1345,8 +1346,8 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><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/2.4/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></td> </tr> </tbody> </table> @@ -1420,17 +1421,17 @@ 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/2.3.1/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 +and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><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/2.3.1/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 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/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><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/2.3.1/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 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/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td> </tr> </tbody> </table> @@ -1472,16 +1473,16 @@ 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/2.3.1/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> +attached <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.4.0)"><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/2.3.1/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 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/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><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/2.3.1/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 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/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td> </tr> </tbody> </table> diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html index 53ea062ed1d80e4c55f8f08c33b6d87de26fd2bd..6f940d4f2b9683b7243a8227dba538cb3b34452b 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 3.3.0 documentation</title> + <title>Sidechain Reconstruction — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -36,7 +37,7 @@ <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/2.3.1/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> +<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></li> <li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment and used to reconstruct sidechains of single loops</li> </ul> @@ -91,7 +92,7 @@ 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/2.3.1/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 +<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain reconstruction gets directly applied on the structure itself.</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 @@ -203,7 +204,7 @@ 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/2.3.1/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>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/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li> <li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html index fb4c10e0697802ef1fe597a5c97a168c14d95452..a6c32dc2b2b514df92920276cd8f0e9edc9ecd08 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 3.3.0 documentation</title> + <title>Using Binary Files In ProMod3 — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html index 400d92030f69ae9d638f76c183d330d2c8b79f40..6e2f5e7db7d0a12594e206a9cd1d2dc018c249b8 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 3.3.0 documentation</title> + <title>Python Module Index — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/references.html b/doc/html/references.html index a7cf963db411916dad7bf40f62986f3848c5c595..94e58f063eebaaeb2a754e2111048478bb764a6d 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 3.3.0 documentation</title> + <title>References — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html index de7b370f9fe6a9c4f54473f63f259f8aed3046f2..4259699ea7dace262ea01a8318a41b144683a411 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 3.3.0 documentation</title> + <title>All Atom Scorers — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html index 1c6e7ef03738a3a47531008b353601f329acef43..aaceae9f48df6c85dab28e76395c6fbf32a44335 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 3.3.0 documentation</title> + <title>Backbone Score Environment — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -58,8 +59,8 @@ 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/2.3.1/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 +<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/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><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/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td> </tr> </tbody> @@ -96,7 +97,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains in <em>env_structure</em> are expected to be in the same order as the SEQRES items provided in constructor.</td> </tr> @@ -120,7 +121,7 @@ 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/2.3.1/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>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/2.4/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li> <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -269,7 +270,7 @@ 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/2.3.1/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 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/2.4/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td> </tr> </tbody> </table> @@ -376,7 +377,7 @@ 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/2.3.1/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>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li> <li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA or CB atoms</li> </ul> @@ -391,7 +392,7 @@ 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/2.3.1/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 +<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/2.4/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial SEQRES and the second sequence the actual structural info. The second sequence must have a view attached.</td> </tr> diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html index 24f2cd2ef3a9ef6a800d41c8d459d3e848b4d5f9..4cfd63fa5509f898946b2503bf70f9e2d8a4a079 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 3.3.0 documentation</title> + <title>Backbone Scorers — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -370,7 +371,7 @@ 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/2.3.1/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>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li> <li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -504,8 +505,8 @@ 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/2.3.1/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>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li> <li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -684,8 +685,8 @@ 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/2.3.1/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>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li> <li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html index 606b2b56daee011aeca20c3498c8990756b6e429..070c044134c9af6ee0786c3debe00527e6e54c7f 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 3.3.0 documentation</title> + <title>scoring - Loop Scoring — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html index 2648f13f707bce27881de467b4c6be0e48baffe9..f9440a12361bd8b8a36a03957e004fe76d7eb989 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 3.3.0 documentation</title> + <title>Other Scoring Functions — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/search.html b/doc/html/search.html index 0e575bda06a6effc3c18a7919b846566d7248223..19e3491e8fbfe5a323d608623eb91895542be903 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 3.3.0 documentation</title> + <title>Search — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> @@ -15,6 +15,7 @@ <script type="text/javascript" src="_static/underscore.js"></script> <script type="text/javascript" src="_static/doctools.js"></script> <script type="text/javascript" src="_static/language_data.js"></script> + <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script> <script type="text/javascript" src="_static/searchtools.js"></script> <link rel="index" title="Index" href="genindex.html" /> <link rel="search" title="Search" href="#" /> diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 9c6db87e7c87d959cc9603e6561f22232d7fc947..dcab7f12ef364767ed2eee252bde6744f56332ee 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({docnames:["actions/index","actions/index_dev","buildsystem","changelog","cmake/index","container/docker","container/index","container/singularity","contributing","core/geometry","core/graph_minimizer","core/helper","core/index","core/pm3argparse","core/runtime_profiling","core/setcompoundschemlib","dev_setup","developers","gettingstarted","index","license","loop/all_atom","loop/backbone","loop/index","loop/load_loop_objects","loop/mm_system_creation","loop/structure_db","loop/torsion_sampler","modelling/algorithms","modelling/gap_handling","modelling/index","modelling/loop_candidates","modelling/loop_closing","modelling/model_checking","modelling/monte_carlo","modelling/pipeline","modelling/sidechain_reconstruction","portableIO","references","scoring/all_atom_scorers","scoring/backbone_score_env","scoring/backbone_scorers","scoring/index","scoring/other_scoring_functions","sidechain/disulfid","sidechain/frame","sidechain/graph","sidechain/index","sidechain/loading","sidechain/rotamer","sidechain/rotamer_constructor","sidechain/rotamer_lib","sidechain/subrotamer_optimizer","user_contributions","users"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":1,sphinx:55},filenames:["actions/index.rst","actions/index_dev.rst","buildsystem.rst","changelog.rst","cmake/index.rst","container/docker.rst","container/index.rst","container/singularity.rst","contributing.rst","core/geometry.rst","core/graph_minimizer.rst","core/helper.rst","core/index.rst","core/pm3argparse.rst","core/runtime_profiling.rst","core/setcompoundschemlib.rst","dev_setup.rst","developers.rst","gettingstarted.rst","index.rst","license.rst","loop/all_atom.rst","loop/backbone.rst","loop/index.rst","loop/load_loop_objects.rst","loop/mm_system_creation.rst","loop/structure_db.rst","loop/torsion_sampler.rst","modelling/algorithms.rst","modelling/gap_handling.rst","modelling/index.rst","modelling/loop_candidates.rst","modelling/loop_closing.rst","modelling/model_checking.rst","modelling/monte_carlo.rst","modelling/pipeline.rst","modelling/sidechain_reconstruction.rst","portableIO.rst","references.rst","scoring/all_atom_scorers.rst","scoring/backbone_score_env.rst","scoring/backbone_scorers.rst","scoring/index.rst","scoring/other_scoring_functions.rst","sidechain/disulfid.rst","sidechain/frame.rst","sidechain/graph.rst","sidechain/index.rst","sidechain/loading.rst","sidechain/rotamer.rst","sidechain/rotamer_constructor.rst","sidechain/rotamer_lib.rst","sidechain/subrotamer_optimizer.rst","user_contributions.rst","users.rst"],objects:{"":{"--backbone-independent":[0,7,1,"cmdoption-i"],"--energy_function":[0,7,1,"cmdoption-f"],"--keep-sidechains":[0,7,1,"cmdoption-k"],"--no-disulfids":[0,7,1,"cmdoption-n"],"--no-subrotamer-optimization":[0,7,1,"cmdoption-s"],"--rigid-rotamers":[0,7,1,"cmdoption-r"],"-f":[0,7,1,"cmdoption-f"],"-i":[0,7,1,"cmdoption-i"],"-k":[0,7,1,"cmdoption-k"],"-n":[0,7,1,"cmdoption-n"],"-r":[0,7,1,"cmdoption-r"],"-s":[0,7,1,"cmdoption-s"],"command:add_doc_dependency":[4,0,1,""],"command:add_doc_source":[4,0,1,""],"command:convert_module_data":[4,0,1,""],"command:module":[4,0,1,""],"command:pm_action":[4,0,1,""],"command:promod3_unittest":[4,0,1,""],"command:pymod":[4,0,1,""],test_actions:[1,2,0,"-"]},"promod3.core":{ConstructAtomPos:[9,1,1,""],ConstructCBetaPos:[9,1,1,""],ConstructCTerminalOxygens:[9,1,1,""],EvaluateGromacsPosRule:[9,1,1,""],GraphMinimizer:[10,3,1,""],RotationAroundLine:[9,1,1,""],StaticRuntimeProfiler:[14,3,1,""],StemCoords:[9,3,1,""],StemPairOrientation:[9,3,1,""],helper:[11,2,0,"-"],pm3argparse:[13,2,0,"-"]},"promod3.core.GraphMinimizer":{AStarSolve:[10,4,1,""],AddEdge:[10,4,1,""],AddNode:[10,4,1,""],ApplyDEE:[10,4,1,""],ApplyEdgeDecomposition:[10,4,1,""],MCSolve:[10,4,1,""],NaiveSolve:[10,4,1,""],Prune:[10,4,1,""],Reset:[10,4,1,""],TreeSolve:[10,4,1,""]},"promod3.core.StaticRuntimeProfiler":{Clear:[14,5,1,""],IsEnabled:[14,5,1,""],PrintSummary:[14,5,1,""],Start:[14,5,1,""],StartScoped:[14,5,1,""],Stop:[14,5,1,""]},"promod3.core.StemCoords":{c_coord:[9,6,1,""],ca_coord:[9,6,1,""],n_coord:[9,6,1,""]},"promod3.core.StemPairOrientation":{angle_four:[9,6,1,""],angle_one:[9,6,1,""],angle_three:[9,6,1,""],angle_two:[9,6,1,""],distance:[9,6,1,""]},"promod3.core.helper":{FileExists:[11,1,1,""],FileExtension:[11,1,1,""],FileGzip:[11,1,1,""],MsgErrorAndExit:[11,1,1,""]},"promod3.core.pm3argparse":{PM3ArgumentParser:[13,3,1,""]},"promod3.core.pm3argparse.PM3ArgumentParser":{AddAlignment:[13,4,1,""],AddFragments:[13,4,1,""],AddProfile:[13,4,1,""],AddStructure:[13,4,1,""],AssembleParser:[13,4,1,""],Parse:[13,4,1,""],__init__:[13,4,1,""],action:[13,6,1,""]},"promod3.loop":{AllAtomEnv:[21,3,1,""],AllAtomEnvPositions:[21,3,1,""],AllAtomPositions:[21,3,1,""],AminoAcidAtom:[21,3,1,""],AminoAcidHydrogen:[21,3,1,""],AminoAcidLookup:[21,3,1,""],BackboneList:[22,3,1,""],CoordInfo:[26,3,1,""],ForcefieldAminoAcid:[25,3,1,""],ForcefieldBondInfo:[25,3,1,""],ForcefieldConnectivity:[25,3,1,""],ForcefieldHarmonicAngleInfo:[25,3,1,""],ForcefieldHarmonicImproperInfo:[25,3,1,""],ForcefieldLJPairInfo:[25,3,1,""],ForcefieldLookup:[25,3,1,""],ForcefieldPeriodicDihedralInfo:[25,3,1,""],ForcefieldUreyBradleyAngleInfo:[25,3,1,""],FragDB:[26,3,1,""],Fragger:[26,3,1,""],FraggerMap:[26,3,1,""],FragmentInfo:[26,3,1,""],LoadFragDB:[24,4,1,""],LoadStructureDB:[24,4,1,""],LoadTorsionSampler:[24,4,1,""],LoadTorsionSamplerCoil:[24,4,1,""],LoadTorsionSamplerExtended:[24,4,1,""],LoadTorsionSamplerHelical:[24,4,1,""],MmSystemCreator:[25,3,1,""],PsipredPrediction:[26,3,1,""],StructureDB:[26,3,1,""],StructureDBDataType:[26,3,1,""],TorsionSampler:[27,3,1,""]},"promod3.loop.AllAtomEnv":{ClearEnvironment:[21,4,1,""],GetAllAtomPositions:[21,4,1,""],GetEnvironment:[21,4,1,""],GetSeqres:[21,4,1,""],SetEnvironment:[21,4,1,""],SetInitialEnvironment:[21,4,1,""]},"promod3.loop.AllAtomEnvPositions":{all_pos:[21,6,1,""],res_indices:[21,6,1,""]},"promod3.loop.AllAtomPositions":{AllAtomPositions:[21,4,1,""],ClearPos:[21,4,1,""],ClearResidue:[21,4,1,""],Copy:[21,4,1,""],Extract:[21,4,1,""],ExtractBackbone:[21,4,1,""],GetAA:[21,4,1,""],GetFirstIndex:[21,4,1,""],GetIndex:[21,4,1,""],GetLastIndex:[21,4,1,""],GetNumAtoms:[21,4,1,""],GetNumResidues:[21,4,1,""],GetOmegaTorsion:[21,4,1,""],GetPhiTorsion:[21,4,1,""],GetPos:[21,4,1,""],GetPsiTorsion:[21,4,1,""],GetSequence:[21,4,1,""],InsertInto:[21,4,1,""],IsAllSet:[21,4,1,""],IsAnySet:[21,4,1,""],IsSet:[21,4,1,""],SetPos:[21,4,1,""],SetResidue:[21,4,1,""],ToEntity:[21,4,1,""]},"promod3.loop.AminoAcidLookup":{GetAA:[21,5,1,""],GetAAA:[21,5,1,""],GetAAH:[21,5,1,""],GetAnchorAtomIndex:[21,5,1,""],GetAtomName:[21,5,1,""],GetAtomNameAmber:[21,5,1,""],GetAtomNameCharmm:[21,5,1,""],GetElement:[21,5,1,""],GetH1Index:[21,5,1,""],GetH2Index:[21,5,1,""],GetH3Index:[21,5,1,""],GetHNIndex:[21,5,1,""],GetHydrogenIndex:[21,5,1,""],GetIndex:[21,5,1,""],GetMaxNumAtoms:[21,5,1,""],GetMaxNumHydrogens:[21,5,1,""],GetNumAtoms:[21,5,1,""],GetNumHydrogens:[21,5,1,""],GetOLC:[21,5,1,""]},"promod3.loop.BackboneList":{ApplyTransform:[22,4,1,""],BackboneList:[22,4,1,""],CARMSD:[22,4,1,""],Copy:[22,4,1,""],Extract:[22,4,1,""],GetAA:[22,4,1,""],GetBounds:[22,4,1,""],GetC:[22,4,1,""],GetCA:[22,4,1,""],GetCB:[22,4,1,""],GetN:[22,4,1,""],GetO:[22,4,1,""],GetOLC:[22,4,1,""],GetOmegaTorsion:[22,4,1,""],GetPhiTorsion:[22,4,1,""],GetPsiTorsion:[22,4,1,""],GetSequence:[22,4,1,""],GetTransform:[22,4,1,""],InsertInto:[22,4,1,""],MinCADistance:[22,4,1,""],RMSD:[22,4,1,""],ReconstructCBetaPositions:[22,4,1,""],ReconstructCStemOxygen:[22,4,1,""],ReconstructOxygenPositions:[22,4,1,""],ReplaceFragment:[22,4,1,""],RotateAroundOmegaTorsion:[22,4,1,""],RotateAroundPhiPsiTorsion:[22,4,1,""],RotateAroundPhiTorsion:[22,4,1,""],RotateAroundPsiTorsion:[22,4,1,""],Set:[22,4,1,""],SetAA:[22,4,1,""],SetAroundOmegaTorsion:[22,4,1,""],SetAroundPhiPsiTorsion:[22,4,1,""],SetAroundPhiTorsion:[22,4,1,""],SetAroundPsiTorsion:[22,4,1,""],SetBackrub:[22,4,1,""],SetC:[22,4,1,""],SetCA:[22,4,1,""],SetCB:[22,4,1,""],SetN:[22,4,1,""],SetO:[22,4,1,""],SetOLC:[22,4,1,""],SetSequence:[22,4,1,""],SuperposeOnto:[22,4,1,""],ToDensity:[22,4,1,""],ToEntity:[22,4,1,""],TransOmegaTorsions:[22,4,1,""],__len__:[22,4,1,""],append:[22,4,1,""],clear:[22,4,1,""],empty:[22,4,1,""],resize:[22,4,1,""]},"promod3.loop.CoordInfo":{chain_name:[26,6,1,""],id:[26,6,1,""],offset:[26,6,1,""],shift:[26,6,1,""],size:[26,6,1,""],start_resnum:[26,6,1,""]},"promod3.loop.ForcefieldBondInfo":{bond_length:[25,6,1,""],force_constant:[25,6,1,""],index_one:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldConnectivity":{harmonic_angles:[25,6,1,""],harmonic_bonds:[25,6,1,""],harmonic_impropers:[25,6,1,""],lj_pairs:[25,6,1,""],periodic_dihedrals:[25,6,1,""],periodic_impropers:[25,6,1,""],urey_bradley_angles:[25,6,1,""]},"promod3.loop.ForcefieldHarmonicAngleInfo":{angle:[25,6,1,""],force_constant:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldHarmonicImproperInfo":{angle:[25,6,1,""],force_constant:[25,6,1,""],index_four:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldLJPairInfo":{epsilon:[25,6,1,""],index_one:[25,6,1,""],index_two:[25,6,1,""],sigma:[25,6,1,""]},"promod3.loop.ForcefieldLookup":{GetAA:[25,4,1,""],GetCharges:[25,4,1,""],GetDefault:[25,5,1,""],GetDisulfidConnectivity:[25,4,1,""],GetEpsilons:[25,4,1,""],GetFudgeLJ:[25,4,1,""],GetFudgeQQ:[25,4,1,""],GetHeavyIndex:[25,4,1,""],GetHydrogenIndex:[25,4,1,""],GetInternalConnectivity:[25,4,1,""],GetMasses:[25,4,1,""],GetNumAtoms:[25,4,1,""],GetOXTIndex:[25,4,1,""],GetPeptideBoundConnectivity:[25,4,1,""],GetSigmas:[25,4,1,""],Load:[25,5,1,""],LoadCHARMM:[25,5,1,""],LoadPortable:[25,5,1,""],Save:[25,4,1,""],SavePortable:[25,4,1,""],SetCharges:[25,4,1,""],SetDefault:[25,5,1,""],SetDisulfidConnectivity:[25,4,1,""],SetEpsilons:[25,4,1,""],SetFudgeLJ:[25,4,1,""],SetFudgeQQ:[25,4,1,""],SetInternalConnectivity:[25,4,1,""],SetMasses:[25,4,1,""],SetPeptideBoundConnectivity:[25,4,1,""],SetSigmas:[25,4,1,""]},"promod3.loop.ForcefieldPeriodicDihedralInfo":{force_constant:[25,6,1,""],index_four:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""],multiplicity:[25,6,1,""],phase:[25,6,1,""]},"promod3.loop.ForcefieldUreyBradleyAngleInfo":{angle:[25,6,1,""],angle_force_constant:[25,6,1,""],bond_force_constant:[25,6,1,""],bond_length:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.FragDB":{AddFragments:[26,4,1,""],GetAngularBinSize:[26,4,1,""],GetDistBinSize:[26,4,1,""],GetNumFragments:[26,4,1,""],GetNumStemPairs:[26,4,1,""],HasFragLength:[26,4,1,""],Load:[26,5,1,""],LoadPortable:[26,5,1,""],MaxFragLength:[26,4,1,""],PrintStatistics:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SearchDB:[26,4,1,""]},"promod3.loop.Fragger":{AddSSAgreeParameters:[26,4,1,""],AddSeqIDParameters:[26,4,1,""],AddSeqSimParameters:[26,4,1,""],AddSequenceProfileParameters:[26,4,1,""],AddStructureProfileParameters:[26,4,1,""],AddTorsionProbabilityParameters:[26,4,1,""],Fill:[26,4,1,""],GetFragmentInfo:[26,4,1,""],GetScore:[26,4,1,""],__getitem__:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.FraggerMap":{Contains:[26,4,1,""],Load:[26,4,1,""],LoadBB:[26,4,1,""],Save:[26,4,1,""],SaveBB:[26,4,1,""],__getitem__:[26,4,1,""],__setitem__:[26,4,1,""]},"promod3.loop.FragmentInfo":{chain_index:[26,6,1,""],length:[26,6,1,""],offset:[26,6,1,""]},"promod3.loop.MmSystemCreator":{ExtractLoopPositions:[25,4,1,""],GetCpuPlatformSupport:[25,4,1,""],GetDisulfidBridges:[25,4,1,""],GetForcefieldAminoAcids:[25,4,1,""],GetIndexing:[25,4,1,""],GetLoopLengths:[25,4,1,""],GetLoopStartIndices:[25,4,1,""],GetNumLoopResidues:[25,4,1,""],GetNumResidues:[25,4,1,""],GetSimulation:[25,4,1,""],SetCpuPlatformSupport:[25,4,1,""],SetupSystem:[25,4,1,""],UpdatePositions:[25,4,1,""]},"promod3.loop.PsipredPrediction":{Add:[26,4,1,""],Extract:[26,4,1,""],FromHHM:[26,4,1,""],FromHoriz:[26,4,1,""],GetConfidence:[26,4,1,""],GetConfidences:[26,4,1,""],GetPrediction:[26,4,1,""],GetPredictions:[26,4,1,""],PsipredPrediction:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.StructureDB":{AddCoordinates:[26,4,1,""],GenerateStructureProfile:[26,4,1,""],GetBackboneList:[26,4,1,""],GetCoordIdx:[26,4,1,""],GetCoordInfo:[26,4,1,""],GetDSSPStates:[26,4,1,""],GetDihedralAngles:[26,4,1,""],GetNumCoords:[26,4,1,""],GetResidueDepths:[26,4,1,""],GetSequence:[26,4,1,""],GetSequenceProfile:[26,4,1,""],GetSolventAccessibilitites:[26,4,1,""],GetStructureProfile:[26,4,1,""],GetSubDB:[26,4,1,""],HasData:[26,4,1,""],Load:[26,5,1,""],LoadPortable:[26,5,1,""],PrintStatistics:[26,4,1,""],RemoveCoordinates:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SetStructureProfile:[26,4,1,""]},"promod3.loop.TorsionSampler":{Draw:[27,4,1,""],DrawPhiGivenPsi:[27,4,1,""],DrawPsiGivenPhi:[27,4,1,""],ExtractStatistics:[27,4,1,""],GetBinSize:[27,4,1,""],GetBinsPerDimension:[27,4,1,""],GetHistogramIndex:[27,4,1,""],GetHistogramIndices:[27,4,1,""],GetPhiProbabilityGivenPsi:[27,4,1,""],GetProbability:[27,4,1,""],GetPsiProbabilityGivenPhi:[27,4,1,""],Load:[27,5,1,""],LoadPortable:[27,5,1,""],Save:[27,4,1,""],SavePortable:[27,4,1,""],UpdateDistributions:[27,4,1,""]},"promod3.modelling":{AFDBModel:[28,1,1,""],AFDBTPLSearch:[28,1,1,""],AddModellingIssue:[35,1,1,""],AllAtomRelaxer:[32,3,1,""],BackboneRelaxer:[32,3,1,""],BuildFromRawModel:[35,1,1,""],BuildRawModel:[35,1,1,""],BuildSidechains:[35,1,1,""],CCD:[32,3,1,""],CCDCloser:[34,3,1,""],CTerminalCloser:[34,3,1,""],CheckFinalModel:[35,1,1,""],ClearGaps:[29,1,1,""],CloseGaps:[35,1,1,""],CloseLargeDeletions:[35,1,1,""],CloseSmallDeletions:[35,1,1,""],CloserBase:[34,3,1,""],CoolerBase:[34,3,1,""],CountEnclosedGaps:[29,1,1,""],CountEnclosedInsertions:[29,1,1,""],DeNovoCloser:[34,3,1,""],DeleteGapCols:[35,1,1,""],DirtyCCDCloser:[34,3,1,""],ExponentialCooler:[34,3,1,""],FSStructureServer:[28,3,1,""],FillLoopsByDatabase:[35,1,1,""],FillLoopsByMonteCarlo:[35,1,1,""],FilterCandidates:[33,1,1,""],FilterCandidatesWithSC:[33,1,1,""],FindMotifs:[28,4,1,""],FraggerHandle:[28,3,1,""],FragmentSampler:[34,3,1,""],FullGapExtender:[29,3,1,""],GapExtender:[29,3,1,""],GenerateDeNovoTrajectories:[28,1,1,""],GetNonPlanarRings:[33,1,1,""],GetRingPunches:[33,1,1,""],GetRings:[33,1,1,""],HasNonPlanarRings:[33,1,1,""],HasRingPunches:[33,1,1,""],InsertLoop:[35,1,1,""],InsertLoopClearGaps:[29,1,1,""],IsAllAtomScoringSetUp:[35,1,1,""],IsBackboneScoringSetUp:[35,1,1,""],KIC:[32,3,1,""],KICCloser:[34,3,1,""],LinearScorer:[34,3,1,""],LoopCandidates:[31,3,1,""],MergeGaps:[29,1,1,""],MergeGapsByDistance:[35,1,1,""],MergeMHandle:[35,1,1,""],MinimizeModelEnergy:[35,1,1,""],ModelTermini:[35,1,1,""],ModellingHandle:[35,3,1,""],ModellingIssue:[35,3,1,""],MotifMatch:[28,3,1,""],MotifQuery:[28,3,1,""],NTerminalCloser:[34,3,1,""],PentaMatch:[28,3,1,""],PhiPsiSampler:[34,3,1,""],PullTerminalDeletions:[35,1,1,""],ReconstructSidechains:[36,1,1,""],RemoveTerminalGaps:[35,1,1,""],ReorderGaps:[35,1,1,""],ReportMolProbityScores:[33,1,1,""],RigidBlocks:[28,4,1,""],RunMolProbity:[33,1,1,""],RunMolProbityEntity:[33,1,1,""],SampleMonteCarlo:[34,1,1,""],SamplerBase:[34,3,1,""],ScoreContainer:[31,3,1,""],ScorerBase:[34,3,1,""],ScoringGapExtender:[29,3,1,""],ScoringWeights:[31,3,1,""],SetFraggerHandles:[35,1,1,""],SetPsipredPredictions:[35,1,1,""],SetSequenceProfiles:[35,1,1,""],SetupDefaultAllAtomScoring:[35,1,1,""],SetupDefaultBackboneScoring:[35,1,1,""],ShiftExtension:[29,3,1,""],SidechainReconstructionData:[36,3,1,""],SidechainReconstructor:[36,3,1,""],SoftSampler:[34,3,1,""],StructuralGap:[29,3,1,""],StructuralGapList:[29,3,1,""]},"promod3.modelling.AllAtomRelaxer":{GetSystemCreator:[32,4,1,""],Run:[32,4,1,""],UpdatePositions:[32,4,1,""]},"promod3.modelling.BackboneRelaxer":{AddCARestraint:[32,4,1,""],AddCBRestraint:[32,4,1,""],AddCRestraint:[32,4,1,""],AddNRestraint:[32,4,1,""],AddORestraint:[32,4,1,""],GetNonBondedCutoff:[32,4,1,""],Run:[32,4,1,""],SetNonBondedCutoff:[32,4,1,""]},"promod3.modelling.CCD":{CCD:[32,4,1,""],Close:[32,4,1,""]},"promod3.modelling.CCDCloser":{Close:[34,4,1,""]},"promod3.modelling.CTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.CloserBase":{Close:[34,4,1,""]},"promod3.modelling.CoolerBase":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.DeNovoCloser":{Close:[34,4,1,""]},"promod3.modelling.DirtyCCDCloser":{Close:[34,4,1,""]},"promod3.modelling.ExponentialCooler":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.FSStructureServer":{FromDataChunks:[28,5,1,""],GetIdx:[28,4,1,""],GetOMF:[28,4,1,""],GetOMFByIdx:[28,4,1,""],chunk:[28,6,1,""],data:[28,6,1,""],indexer:[28,6,1,""],length:[28,6,1,""],n_entries:[28,6,1,""],pos:[28,6,1,""],search_keys:[28,6,1,""]},"promod3.modelling.FraggerHandle":{Get:[28,4,1,""],GetList:[28,4,1,""],LoadCached:[28,4,1,""],SaveCached:[28,4,1,""]},"promod3.modelling.FragmentSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.FullGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.GapExtender":{Extend:[29,4,1,""]},"promod3.modelling.KIC":{Close:[32,4,1,""],KIC:[32,4,1,""]},"promod3.modelling.KICCloser":{Close:[34,4,1,""]},"promod3.modelling.LinearScorer":{GetScore:[34,4,1,""]},"promod3.modelling.LoopCandidates":{Add:[31,4,1,""],AddFragmentInfo:[31,4,1,""],ApplyCCD:[31,4,1,""],ApplyKIC:[31,4,1,""],CalculateAllAtomScores:[31,4,1,""],CalculateBackboneScores:[31,4,1,""],CalculateSequenceProfileScores:[31,4,1,""],CalculateStemRMSDs:[31,4,1,""],CalculateStructureProfileScores:[31,4,1,""],Extract:[31,4,1,""],FillFromDatabase:[31,5,1,""],FillFromMonteCarloSampler:[31,5,1,""],GetClusteredCandidates:[31,4,1,""],GetClusters:[31,4,1,""],GetFragmentInfo:[31,4,1,""],GetLargestCluster:[31,4,1,""],GetSequence:[31,4,1,""],HasFragmentInfos:[31,4,1,""],Remove:[31,4,1,""]},"promod3.modelling.ModellingHandle":{Copy:[35,4,1,""],all_atom_scorer:[35,6,1,""],all_atom_scorer_env:[35,6,1,""],all_atom_sidechain_env:[35,6,1,""],backbone_scorer:[35,6,1,""],backbone_scorer_env:[35,6,1,""],fragger_handles:[35,6,1,""],gaps:[35,6,1,""],model:[35,6,1,""],modelling_issues:[35,6,1,""],profiles:[35,6,1,""],psipred_predictions:[35,6,1,""],seqres:[35,6,1,""],sidechain_reconstructor:[35,6,1,""]},"promod3.modelling.ModellingIssue":{Severity:[35,3,1,""],is_major:[35,4,1,""],residue_list:[35,6,1,""],severity:[35,6,1,""],text:[35,6,1,""]},"promod3.modelling.ModellingIssue.Severity":{MAJOR:[35,6,1,""],MINOR:[35,6,1,""]},"promod3.modelling.MotifMatch":{alignment:[28,6,1,""],mat:[28,6,1,""],query_idx:[28,6,1,""]},"promod3.modelling.MotifQuery":{GetIdentifiers:[28,4,1,""],GetN:[28,4,1,""],GetPositions:[28,4,1,""],Load:[28,5,1,""],Save:[28,4,1,""]},"promod3.modelling.NTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.PentaMatch":{FromSeqList:[28,5,1,""],N:[28,6,1,""],TopN:[28,4,1,""],indexer:[28,6,1,""],length:[28,6,1,""],pos:[28,6,1,""]},"promod3.modelling.PhiPsiSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.SamplerBase":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.ScoreContainer":{Contains:[31,4,1,""],Copy:[31,4,1,""],Extend:[31,4,1,""],Extract:[31,4,1,""],Get:[31,4,1,""],GetNumCandidates:[31,4,1,""],IsEmpty:[31,4,1,""],LinearCombine:[31,4,1,""],Set:[31,4,1,""]},"promod3.modelling.ScorerBase":{GetScore:[34,4,1,""]},"promod3.modelling.ScoringGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.ScoringWeights":{GetAllAtomScoringKeys:[31,5,1,""],GetAllAtomWeights:[31,5,1,""],GetBackboneScoringKeys:[31,5,1,""],GetBackboneWeights:[31,5,1,""],GetSequenceProfileScoresKey:[31,5,1,""],GetStemRMSDsKey:[31,5,1,""],GetStructureProfileScoresKey:[31,5,1,""],GetWeights:[31,5,1,""],SetAllAtomScoringKeys:[31,5,1,""],SetBackboneScoringKeys:[31,5,1,""],SetSequenceProfileScoresKey:[31,5,1,""],SetStemRMSDsKey:[31,5,1,""],SetStructureProfileScoresKey:[31,5,1,""],SetWeights:[31,5,1,""]},"promod3.modelling.ShiftExtension":{Extend:[29,4,1,""]},"promod3.modelling.SidechainReconstructionData":{disulfid_bridges:[36,6,1,""],env_pos:[36,6,1,""],is_c_ter:[36,6,1,""],is_n_ter:[36,6,1,""],loop_lengths:[36,6,1,""],loop_start_indices:[36,6,1,""],rotamer_res_indices:[36,6,1,""]},"promod3.modelling.SidechainReconstructor":{AttachEnvironment:[36,4,1,""],Reconstruct:[36,4,1,""]},"promod3.modelling.SoftSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.StructuralGap":{Copy:[29,4,1,""],ExtendAtCTerm:[29,4,1,""],ExtendAtNTerm:[29,4,1,""],GetChain:[29,4,1,""],GetChainIndex:[29,4,1,""],GetChainName:[29,4,1,""],GetLength:[29,4,1,""],IsCTerminal:[29,4,1,""],IsNTerminal:[29,4,1,""],IsTerminal:[29,4,1,""],ShiftCTerminal:[29,4,1,""],after:[29,6,1,""],before:[29,6,1,""],full_seq:[29,6,1,""],length:[29,6,1,""],seq:[29,6,1,""]},"promod3.scoring":{AllAtomClashScorer:[39,3,1,""],AllAtomInteractionScorer:[39,3,1,""],AllAtomOverallScorer:[39,3,1,""],AllAtomPackingScorer:[39,3,1,""],AllAtomScorer:[39,3,1,""],BackboneOverallScorer:[41,3,1,""],BackboneScoreEnv:[40,3,1,""],BackboneScorer:[41,3,1,""],CBPackingScorer:[41,3,1,""],CBetaScorer:[41,3,1,""],ClashScorer:[41,3,1,""],ConstraintFunction:[40,3,1,""],ContactFunction:[40,3,1,""],DiscoContainer:[40,3,1,""],HBondScorer:[41,3,1,""],LoadAllAtomInteractionScorer:[39,1,1,""],LoadAllAtomPackingScorer:[39,1,1,""],LoadCBPackingScorer:[41,1,1,""],LoadCBetaScorer:[41,1,1,""],LoadDefaultAllAtomOverallScorer:[39,1,1,""],LoadDefaultBackboneOverallScorer:[41,1,1,""],LoadHBondScorer:[41,1,1,""],LoadReducedScorer:[41,1,1,""],LoadSSAgreementScorer:[41,1,1,""],LoadTorsionScorer:[41,1,1,""],PairwiseFunction:[40,3,1,""],PairwiseFunctionType:[40,3,1,""],PairwiseScorer:[41,3,1,""],ReducedScorer:[41,3,1,""],SCWRL3DisulfidScore:[43,4,1,""],SCWRL3PairwiseScore:[43,4,1,""],SSAgreementScorer:[41,3,1,""],TorsionScorer:[41,3,1,""]},"promod3.scoring.AllAtomClashScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""]},"promod3.scoring.AllAtomInteractionScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""],Load:[39,5,1,""],LoadPortable:[39,5,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomOverallScorer":{AttachEnvironment:[39,4,1,""],CalculateLinearCombination:[39,4,1,""],Contains:[39,4,1,""],Get:[39,4,1,""],__getitem__:[39,4,1,""],__setitem__:[39,4,1,""]},"promod3.scoring.AllAtomPackingScorer":{DoNormalize:[39,4,1,""],Load:[39,5,1,""],LoadPortable:[39,5,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomScorer":{AttachEnvironment:[39,4,1,""],CalculateScore:[39,4,1,""],CalculateScoreProfile:[39,4,1,""]},"promod3.scoring.BackboneOverallScorer":{AttachEnvironment:[41,4,1,""],Calculate:[41,4,1,""],CalculateLinearCombination:[41,4,1,""],Contains:[41,4,1,""],Get:[41,4,1,""],__getitem__:[41,4,1,""],__setitem__:[41,4,1,""]},"promod3.scoring.BackboneScoreEnv":{AddPairwiseFunction:[40,4,1,""],ApplyPairwiseFunction:[40,4,1,""],ClearEnvironment:[40,4,1,""],Copy:[40,4,1,""],GetSeqres:[40,4,1,""],Pop:[40,4,1,""],SetEnvironment:[40,4,1,""],SetInitialEnvironment:[40,4,1,""],SetPsipredPrediction:[40,4,1,""],Stash:[40,4,1,""]},"promod3.scoring.BackboneScorer":{AttachEnvironment:[41,4,1,""],CalculateScore:[41,4,1,""],CalculateScoreProfile:[41,4,1,""]},"promod3.scoring.CBPackingScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.CBetaScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.ClashScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.DiscoContainer":{AddStructuralInfo:[40,1,1,""],AttachConstraints:[40,1,1,""]},"promod3.scoring.HBondScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.PairwiseFunction":{Score:[40,4,1,""]},"promod3.scoring.PairwiseScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.ReducedScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.SSAgreementScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetScore:[41,4,1,""]},"promod3.scoring.TorsionScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.sidechain":{AAToRotID:[49,4,1,""],BBDepRotamerLib:[51,3,1,""],CreateSCWRL3Particle:[49,4,1,""],CreateSCWRL4Particle:[49,4,1,""],CreateVINAParticle:[49,4,1,""],DihedralConfiguration:[51,3,1,""],DisulfidScore:[44,4,1,""],FRMRotamer:[49,3,1,""],FRMRotamerGroup:[49,3,1,""],Frame:[45,3,1,""],FrameResidue:[45,3,1,""],GetDihedralConfiguration:[51,4,1,""],GetRotamericConfiguration:[51,4,1,""],GetVINAWeightGaussian1:[49,4,1,""],GetVINAWeightGaussian2:[49,4,1,""],GetVINAWeightHBond:[49,4,1,""],GetVINAWeightHydrophobic:[49,4,1,""],GetVINAWeightRepulsion:[49,4,1,""],LoadBBDepLib:[48,4,1,""],LoadLib:[48,4,1,""],PScoringFunction:[49,3,1,""],Particle:[49,3,1,""],RRMRotamer:[49,3,1,""],RRMRotamerGroup:[49,3,1,""],ReadDunbrackFile:[48,4,1,""],ResolveCysteins:[44,4,1,""],RotamerConstructor:[50,3,1,""],RotamerGraph:[46,3,1,""],RotamerID:[49,3,1,""],RotamerLib:[51,3,1,""],RotamerLibEntry:[51,3,1,""],SCWRL3RotamerConstructor:[50,3,1,""],SCWRL4ParticleType:[49,3,1,""],SCWRL4RotamerConstructor:[50,3,1,""],SetVINAWeightGaussian1:[49,4,1,""],SetVINAWeightGaussian2:[49,4,1,""],SetVINAWeightHBond:[49,4,1,""],SetVINAWeightHydrophobic:[49,4,1,""],SetVINAWeightRepulsion:[49,4,1,""],SubrotamerOptimizer:[52,4,1,""],TLCToRotID:[49,4,1,""],VINAParticleType:[49,3,1,""],VINARotamerConstructor:[50,3,1,""]},"promod3.sidechain.BBDepRotamerLib":{AddRotamer:[51,4,1,""],Load:[51,5,1,""],LoadPortable:[51,5,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""],SetInterpolate:[51,4,1,""]},"promod3.sidechain.FRMRotamer":{AddFrameEnergy:[49,4,1,""],AddSubrotamerDefinition:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetActiveSubrotamer:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetNumSubrotamers:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],GetSubrotamerDefinition:[49,4,1,""],GetTemperature:[49,4,1,""],SetActiveSubrotamer:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],SetTemperature:[49,4,1,""],ToFrameResidue:[49,4,1,""],ToRRMRotamer:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FrameResidue":{__getitem__:[45,4,1,""],__len__:[45,4,1,""]},"promod3.sidechain.Particle":{GetCollisionDistance:[49,4,1,""],GetName:[49,4,1,""],GetPos:[49,4,1,""],GetScoringFunction:[49,4,1,""],PairwiseScore:[49,4,1,""]},"promod3.sidechain.RRMRotamer":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],ToFrameResidue:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructBackboneFrameResidue:[50,4,1,""],ConstructRRMRotamerGroup:[50,4,1,""],ConstructSidechainFrameResidue:[50,4,1,""]},"promod3.sidechain.RotamerGraph":{CreateFromFRMList:[46,5,1,""],CreateFromRRMList:[46,5,1,""]},"promod3.sidechain.RotamerLib":{AddRotamer:[51,4,1,""],Load:[51,5,1,""],LoadPortable:[51,5,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""]},"promod3.sidechain.RotamerLibEntry":{FromResidue:[51,5,1,""],IsSimilar:[51,4,1,""],SimilarDihedral:[51,4,1,""],chi1:[51,6,1,""],chi2:[51,6,1,""],chi3:[51,6,1,""],chi4:[51,6,1,""],probability:[51,6,1,""],sig1:[51,6,1,""],sig2:[51,6,1,""],sig3:[51,6,1,""],sig4:[51,6,1,""]},"promod3.sidechain.SCWRL3RotamerConstructor":{AssignInternalEnergies:[50,4,1,""]},"promod3.sidechain.SCWRL4RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFrameResidue:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""]},"promod3.sidechain.VINARotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFRMRotamerHeuristic:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""],ConstructRRMRotamerHeuristic:[50,4,1,""]},"test_actions.ActionTestCase":{RunAction:[1,4,1,""],RunExitStatusTest:[1,4,1,""],pm_action:[1,6,1,""],pm_bin:[1,6,1,""],testPMExists:[1,4,1,""]},promod3:{SetCompoundsChemlib:[15,1,1,""],core:[12,2,0,"-"],loop:[23,2,0,"-"],modelling:[30,2,0,"-"],scoring:[42,2,0,"-"],sidechain:[47,2,0,"-"]},test_actions:{ActionTestCase:[1,3,1,""]}},objnames:{"0":["cmake","command","CMake command"],"1":["py","function","Python function"],"2":["py","module","Python module"],"3":["py","class","Python class"],"4":["py","method","Python method"],"5":["py","staticmethod","Python static method"],"6":["py","attribute","Python attribute"],"7":["std","cmdoption","program option"]},objtypes:{"0":"cmake:command","1":"py:function","2":"py:module","3":"py:class","4":"py:method","5":"py:staticmethod","6":"py:attribute","7":"std:cmdoption"},terms:{"0288eced23a9a541a88005a7ed30b8f019e06226":3,"10a":36,"1ake":28,"1aki":26,"1crn":[21,23,25,26,30,31,32,34,35,36,42,47],"1crn_cut":[30,31,35],"1crna":[26,31],"1e2q":28,"1ey":8,"1eye_rec":8,"1ko5":28,"20a":36,"214e6":3,"2e6":28,"2iyw":28,"2jlp":0,"30a":36,"3x3":9,"4tb":3,"655a":26,"abstract":[34,50],"boolean":[11,13,35],"break":[3,4,8,16],"byte":[10,28,37],"case":[0,1,5,8,13,16,22,26,27,28,29,32,34,35,36,37,41,44,47,49,50,51],"catch":26,"char":[22,37],"class":[0,1,3,5,8,9,10,12,13,14,17,20,23,25,28,30,32,34,35,37,42,45,46,49,50,51],"const":37,"default":[0,1,2,3,4,5,8,10,13,14,15,18,21,22,25,26,27,28,30,31,32,33,34,36,39,41,47,49,50],"enum":[26,49],"export":[8,21],"final":[8,18,26,28,30,31,35,40,42,44,46,47,49],"float":[9,10,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,49,50,51,52],"function":[0,1,3,8,10,13,14,15,16,17,19,21,22,25,26,28,30,31,32,33,34,35,37,38,39,41,42,44,46,47,51,54],"import":[0,1,5,7,8,11,13,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,42,47,49,50],"int":[1,9,10,11,14,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,45,49,50,51,52],"long":35,"new":[1,3,7,8,13,16,17,21,22,25,26,28,29,31,32,34,35,36,37,38,47,49],"null":26,"public":[8,37,49],"return":[1,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,45,48,49,50,51],"s\u00f6ding":38,"short":[8,16,35,37],"static":[8,14,21,25,26,27,28,31,36,37,39,41,46,48,51],"super":47,"switch":[8,16,40],"throw":[1,37,47,48],"true":[1,11,13,14,21,22,23,25,26,28,29,31,32,33,34,35,36,37,39,41,44,47,50],"try":[1,8,18,29,35,37,51],"void":37,"while":[1,4,8,14,20,21,25,35,37,49],AND:[20,39,41,50],Added:3,Adding:[3,4],And:26,But:[1,4,8,16,28,35,50],CYS:[25,36,49,51],FOR:20,For:[1,2,5,8,12,13,16,18,20,21,25,26,28,31,34,35,36,37,40,41,44,49,50,51],HIS:[21,25,33,49,51],Has:4,IDs:49,ILE:[27,49],Into:[30,54],Its:[4,16,19],LYS:49,NOT:5,Not:20,One:[16,21,22,26,28,35,40,44,49,52],RMS:33,Res:[21,31,34,35,39,40,41],That:[0,1,4,8,11,13,16,26,28,41],Thats:52,The:[0,2,3,4,8,10,11,13,14,17,18,19,20,23,24,25,28,29,30,32,33,34,37,38,39,40,41,42,43,44,46,47,48,52,54],Then:[4,8,11,35],There:[1,4,5,8,10,13,16,25,26,27,34,39,41,48,49],These:[1,2,4,26,28,29,34,35],USE:20,Use:[0,4,25,26,27,35,39,41,51],Used:[31,35],Useful:[21,25,36],Uses:[31,35],Using:[4,17,25,54],Will:35,With:[8,30,35,51],__doc__:[11,13],__getitem__:[26,39,41,45,49],__init__:[1,8,13,16],__len__:[22,26,45,49],__main__:[1,8],__name__:[1,8],__setitem__:[26,39,41],_data:37,_name:4,_run:[1,4],_xml:4,a3m:[0,13],a3mtoprofil:[0,13],aa1:41,aa2:41,aa_aft:26,aa_befor:26,aa_clash:[35,39],aa_interact:[35,39],aa_pack:[35,39],aa_packing_scor:37,aa_relax_test:32,aa_res_idx:50,aa_scor:37,aa_with_rotam:47,aaa1:39,aaa2:39,aaa:[21,39],aaaaaaaa:22,aaaaggggggggggggggggggggaaaaaa:35,aafrequ:26,aafrequenciesstruct:26,aah:21,aatorotid:49,abcd:35,abcdef:35,abcdefghi:35,abcdefghij:35,abcdefghijklmnopqrstuvwxyz0123456789abcdefghijklmnopqrstuvwxyz:35,abil:16,abl:[2,8,35],abort:[8,10,32,35],about:[1,4,8,10,26,28,35],abov:[0,1,5,8,13,16,20,22,29,31,33,35,37,49,51],absolut:[4,5,34],academ:8,accept:[10,13,20,31,32,34,35,36,37],acceptor:[41,49,50],access:[4,5,8,21,22,26,27,28,31,35,39,40,41,49],accessor:26,accord:[0,5,10,16,21,22,25,26,27,28,29,31,34,35,36,39,44,47,49,50,51],accordingli:[26,40],account:[8,53],accumul:28,accur:28,accuraci:[0,28,35,38],achiev:[10,16],acid:[22,23,24,26,28,32,35,36,41,43,46,47,49,51],acknowledg:8,across:[1,51],act:[20,32],acta:38,action:[3,7,13,16,17,18,19,32,54],action_nam:16,action_unit_test:1,actiontest:1,actiontestcas:8,activ:[13,14,16,35,44,49,52],active_internal_energi:52,actual:[3,8,13,16,22,26,28,34,35,36,40,41,42,50,51],actual_posit:34,actual_step:34,adapt:[3,8,25,26,32,34,35,38],add:[1,2,4,6,8,10,13,18,20,21,26,27,28,31,32,35,36,39,40,41,44,47,49,50,53],add_argu:11,add_custom_target:8,add_doc_depend:4,add_doc_sourc:[4,8],add_flag:28,add_subdirectori:8,addalign:13,addcarestraint:32,addcbrestraint:32,addcoordin:26,addcrestraint:32,added:[0,4,8,10,13,21,22,26,28,29,31,33,35,36,39,40,41,49,50,51],addedg:10,addendum:20,addfrag:[13,26],addfragmentinfo:31,addframeenergi:49,addharmonicangl:25,addharmonicbond:25,addharmonicimprop:25,adding:[0,2,4,8,13,14,16,26,45],addit:[3,4,11,13,14,16,20,22,23,25,26,28,33,35,37],addition:[1,4,16,21,25,26,28],addljpair:25,addmodellingissu:35,addnod:10,addnrestraint:32,addorestraint:32,addpairwisefunct:40,addperiodicdihedr:25,addperiodicimprop:25,addprofil:13,addresidu:28,address:37,addrotam:51,addseqidparamet:26,addseqsimparamet:[23,26],addsequenceprofileparamet:26,addssagreeparamet:26,addstructur:13,addstructuralinfo:40,addstructureprofileparamet:26,addsubrotamerdefinit:49,addtorsionprobabilityparamet:26,addureybradleyangl:25,admir:8,advanc:28,advantag:25,advic:[8,16],advis:20,afdb:[3,30],afdb_frag:28,afdb_model:28,afdb_vers:28,afdbmodel:28,afdbtplsearch:28,afdptplsearch:[],affect:[8,22,35,49,50],after:[1,2,4,5,8,10,13,16,21,22,25,26,27,29,31,32,34,35,37,40,51],after_c_stem:22,afterward:[8,26,35],again:[2,3,8,26,28,50],against:[20,28,39],agg:27,agglom:31,ago:1,agre:20,agreement:[13,20,26,28,41],agress:[2,10],aim:19,ala:[22,27,32,47,49,50,51],ala_cb:21,ala_h1:21,ala_h:21,alanin:[3,49],alg:[23,26,28,35],algorithm:[3,10,19,22,23,26,30,31,32,33,34,35,38,42,43,46,47,49,54],alia:29,align:[0,3,13,18,26,28,30,38,40],alignedcuboid:22,alignmenthandl:[28,35,40],alignmentlist:[0,13,35],all:[0,1,2,3,4,7,8,10,13,14,16,18,19,20,22,23,25,26,27,28,29,30,31,33,34,35,36,37,40,41,42,44,45,47,48,49,50,51,52,54],all_atom:[21,22,25,49],all_atom_env:21,all_atom_po:[21,50],all_atom_scor:35,all_atom_scorer_env:35,all_atom_sidechain_env:35,all_po:[21,25,32],all_scor:31,allatom:[32,35,36],allatomclashscor:[35,42],allatomenv:[23,32,35,36,39],allatomenvposit:[23,36],allatominteractionscor:[35,37,42],allatomoverallscor:[31,35,42],allatompackingscor:[35,37,42],allatomposit:[23,25,49,50],allatomrelax:[25,32],allatomscor:42,alleg:20,alloc:26,allow:[0,2,3,5,8,11,16,22,26,27,28,31,34,35,37,39,41,46,51],allow_multitempl:13,allow_prepro_ci:22,almost:[4,32,35],aln:[0,28,30,31,35,40],aln_preprocess:35,aln_sourc:13,alon:[11,20],along:[1,8,20],alongsid:20,alot:8,alpha:[9,22,41,47],alpha_bin:41,alreadi:[1,4,8,10,16,22,25,26,28,31,35,36,39,40,41,49,50,51,52],also:[1,2,3,4,8,11,16,20,26,27,28,31,32,33,34,35,36,44,45,46,50,51],alter:[31,34],altern:[4,5,8,31,34,35,48,50],alwai:[0,1,8,16,29,34,35,37],amber:[21,35],ambig:51,ambigu:[0,13,51],amino:[22,23,24,26,28,32,35,36,41,43,46,47,49,51],aminoacid:[21,22,25,27,41,49,51],aminoacidatom:[21,39],aminoacidhydrogen:21,aminoacidlookup:[21,25],among:31,amount:[3,18,28,51],analog:28,analysi:[32,33,38],analyt:[31,51],anchor:[9,21,35],ancient:[3,15],angl:[0,9,21,22,23,25,26,31,32,33,34,35,41,47,50,51,54],angle_bin:41,angle_bin_s:26,angle_force_const:25,angle_four:9,angle_on:9,angle_thre:9,angle_two:9,angstrom:[26,32],ani:[0,1,4,5,8,10,13,14,15,18,20,21,22,25,26,27,28,29,31,33,34,35,36,37,39,40,41,45,47,49,50],anneal:[10,31,34],annot:20,announc:[1,8],anoth:[4,14,22,29,32,35,36,44],anymor:[3,10,28,35],anyon:[8,16],anyth:[0,2,5,8,13,14,15,28,31,32,36,39,41],anywai:8,anywher:16,apach:[3,20],apart:[1,31,35,36,39,41],api:[8,17],appear:20,append:[0,13,22,26,27,28,35,47],appendix:20,appli:[3,7,10,11,15,16,20,22,26,28,29,31,32,34,35,36,38,40,44,47,49,51],applic:[1,20,32,50],applyccd:31,applyde:10,applyedgedecomposit:10,applyk:31,applylbfg:35,applyonresidu:[47,49],applypairwisefunct:[40,41],applysd:[25,35],applyselfenergythresh:[47,49],applytransform:[22,28],approach:[0,2,10,26,28,35,37,44,47,50],appropri:[10,20,27,28,35,37,50],approx:35,approxim:25,arbitrari:[3,7,21,26,44],arbitrarili:34,archiv:20,arendal:38,arg:[1,4,13,49],arg_ca:21,arg_hd3:21,arg_sorted_scor:31,arginin:49,argpars:13,argument:[0,1,2,4,11,12,34,40],argumentpars:13,argv:13,aris:20,around:[1,4,8,9,16,22,31,32,35,39,40,41,51],arrai:[0,8,37],arrang:28,artifici:26,ascend:29,ask:8,asn:[49,51],asn_c:21,asn_hb2:21,asp:[21,49,51],asp_ha:21,asp_o:21,asparagin:49,aspart:[49,51],ass:34,assembl:13,assemblepars:13,assert:20,assertequ:8,assess:[39,40],assign:[3,10,22,26,31,34,39,41,50,52],assigninternalenergi:50,assignsecstruct:35,associ:[20,26,29,45],assum:[1,4,5,8,20,25,26,32,35,37,40,41,44,50],assur:44,astar:3,astarsolv:10,atom:[3,8,9,22,23,25,26,28,30,31,33,35,36,40,41,42,44,45,49,50,51,54],atom_idx:[21,25],atom_nam:[21,25],atomhandl:50,atomseq:35,atp:28,atp_at:28,atp_idx:28,atp_list:28,atp_r:28,atp_sel:28,atp_view:28,attach:[0,4,8,13,20,21,25,28,29,31,35,36,39,40,41,42],attach_view:13,attachconstraint:40,attachenviron:[31,32,34,36,39,41,42],attachview:[30,31,35],attent:[1,16],attribut:[8,13,20,26,35,36,51],aug2022:3,author:20,authorship:20,autodock:[38,49],autom:[2,4],automat:[1,8,10,11,14,16,26,30,31,37,50,51],automatis:8,avaibl:50,avail:[1,2,3,5,8,15,16,18,20,25,26,28,31,34,35,40,47,49],availab:20,availabl:8,averag:[31,40,44],avg:26,avg_sampling_per_posit:28,avoid:[0,3,6,11,13,15,26,28,32,34],awai:[16,28,36],awar:[0,3,8,35,50],awesom:[1,8],axi:[9,22],back:[1,16,25,34],backbon:[0,3,7,9,18,21,22,26,27,28,29,30,31,34,35,36,38,42,45,47,48,49,50,54],backbone_scor:35,backbone_scorer_env:35,backbonelist:[7,18,21,23,26,28,29,31,32,34,35,40],backboneoverallscor:[28,31,34,35,42],backbonerelax:[32,35],backbonescor:[8,42],backbonescoreenv:[8,28,31,34,35,41,42],backbonescoreenvlisten:8,background:[2,36],backrub:[22,38],backward:[2,3,37],bad:[25,35],bare:26,base:[0,3,4,5,9,11,13,19,20,22,23,27,28,31,32,34,35,37,38,40,42,47,49,50,51],base_target:4,baseclass:47,basel:[8,53],bashrc:8,basi:[4,8,16,20,28,32,33,34,48],basic:[1,2,8,11,16,27,28,34,35,47,51],bb_dep_lib:37,bb_list:[7,18,21,22,23,26,29,31,32,34,35,40],bb_list_on:28,bb_list_two:28,bb_score:31,bbdeprotamerlib:[35,36,37,48,50,51],bcde:35,becaus:[8,16,21,28,35,40],becom:[10,35,51],been:[2,3,10,16,20,24,26,28,31,32,35,39,41,44,51],befor:[0,1,4,7,8,13,16,22,25,26,27,29,31,32,34,35,36,37,50],begin:[1,8,21,22,28,34,40],behalf:20,behav:[1,51],behaviour:[0,13,39,40,49,50,51],behind:8,being:[3,5,8,10,21,26,28,31,34,35,44,51],believ:53,bell:8,belong:[3,4,16,21,22,26,29,31,34,35,36,39,40,41,45,49,50],belov:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,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],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:[1,3,4,8,11,13,28,35,36,42,46,51],command:[0,1,7,8,11,12,16,18,54],commandlin:13,comment:[16,20],commerci:[8,20],commit:[3,8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib:50,compar:[3,8,22,23,26,31,32,51],comparison:[35,38,51],compat:[2,3,16,25,37],compensatori:22,compil:[1,2,3,4,8,14,16,18,20,37,54],complain:1,complaint:16,complet:[14,16,22,25,32,34,35,36,51],complex:[8,16,36,44,49,52],compli:20,complianc:20,complib_dir_contain:[5,7],complib_dir_localhost:[5,7],compon:[5,7,10,15,26,33,41,50],compound:[3,15,50],compoundlib:[5,50],compress:[3,11,26,28],comput:[3,8,19,20,28,31,33,38,39,41],concaten:21,concept:8,concern:8,condit:[8,20,27],conf:[2,8],confid:[26,41],config:[4,8],config_head:4,configur:[2,3,8,10,16,20,31,47],conflict:16,conform:[26,32,34,38,46,51],connect:[4,5,7,10,16,21,25,26,31],connectivi:5,conop:[5,21,22,25,27,41,49,50],conquer:8,consecut:[26,27,35,41],consequenti:20,conserv:[18,29],consid:[0,4,8,10,13,14,16,21,22,26,27,28,31,32,33,34,35,36,39,40,41,44,47,49,50,51,53],consider_all_nod:10,consider_hydrogen:49,consider_ligand:36,consist:[3,8,20,21,25,28,29,31,32,34,35,36,37,40,44,49,51],conspicu:20,constant:[3,25,32,39,41,52],constitut:20,constraint:[13,26,32,34,40],constraintfunct:40,constru:20,construct:[0,3,9,21,22,26,28,29,33,34,35,37,42,43,45,49,50,51],constructatompo:9,constructbackboneframeresidu:[47,50],constructcbetapo:9,constructcterminaloxygen:9,constructetd:10,constructframeresidu:50,constructframeresidueheurist:50,constructfrmrotamergroup:[47,50],constructfrmrotamerheurist:50,constructor:[21,25,28,29,32,34,37,40,41,47,49,54],constructrrmrotamergroup:50,constructrrmrotamerheurist:50,constructsidechainframeresidu:50,contact:[40,53],contactfunct:40,contain:[0,1,2,3,4,5,7,8,9,11,13,16,18,19,20,21,22,24,25,26,27,28,31,33,34,35,36,39,40,41,42,44,45,47,49,50,51,54],content:[8,12,17,20,23,26,42,47,54],contigu:[25,36,37],continu:[1,21,29,32,47],contract:20,contrast:45,contribut:[4,10,16,17,19,20,54],contributor:20,contributori:20,control:[0,3,8,10,20,31,34,36,40,49,50,51,52],conveni:[1,8,18,28,31,34,35,42,49,50,51],convent:[1,49],converg:[28,31,32,34],convers:[20,37],convert:[4,5,22,25,26,27,35,37,39,41,51,52],convert_module_data:4,convertbasetyp:37,cooler:[3,30,31],coolerbas:34,cooling_factor:[10,34],coord:[26,31],coord_idx:26,coordin:[3,9,26,28,31,32,34,35,38,39,47],coordinfo:26,cope:16,copi:[2,3,4,8,16,18,20,21,22,28,29,31,34,35,40],copyright:20,copyright_cmak:20,core:[0,8,9,10,11,13,14,19,35,37,46,53,54],correct:[5,25,50],correctli:35,correspond:[0,10,16,21,22,25,26,27,28,31,37,49,50,51],corrupt:[21,40],could:[1,4,5,8,13,16,25,26,35],couldn:35,count:[14,28,29,34,35,39,41],countenclosedgap:29,countenclosedinsert:29,counter:[28,34],counterclaim:20,counterpart:[31,41,50],coupl:[1,8,16,35],cours:8,coutsia:38,coutsias2005:[32,38],coval:49,cover:[0,1,8,12,13,14,21,25,28,30,34,35],coverag:[0,3,35],cparticl:49,cpp:4,cpr:[49,51],cpu:[18,25,35],cpu_platform_support:25,crambin:[26,31,34],crash:47,creat:[2,4,5,7,8,9,10,13,16,17,21,22,23,26,27,28,30,34,35,39,41,47,48,49,50,51],createalign:[31,35],createemptyview:28,createentityfromview:[28,36,47],createfromfrmlist:[46,47],createfromrrmlist:46,createfullview:[30,31,35],createscwrl3particl:49,createscwrl4particl:49,createsequ:[26,31,35],createvinaparticl:49,creation:[25,28,32,49],creator:[25,28,32],criteria:36,criterion:[10,34],criterium:31,croak:16,cross:[20,28],crucial:8,crude:[0,35],cryst:38,cterminalclos:34,cumul:50,current:[2,4,5,8,10,14,16,21,22,25,26,31,34,35,37,40,41,42,49,50,52],custom:[8,26,34,35,36,37,48,49],customari:20,cutoff:[24,25,31,32,36,39,41],cycl:29,cyclic:[31,32,38],cyd:[49,51],cyh:[49,51],cys_hb3:21,cys_sg:21,cystein:[25,36,44,47,49],d_bin:41,dai:11,damag:20,dampen:25,danc:38,dare:4,dat:[26,28,37],data1:4,data2:4,data:[0,1,3,4,8,16,17,21,23,24,25,28,29,30,31,32,34,35,36,40,42,47,49,54],data_:37,data_gener:[3,28,37,48],data_to_stor:26,data_typ:26,databas:[0,3,9,23,24,28,31,35],databs:26,datatyp:26,date:[5,7,16,20],davi:38,davis2006:[22,38],db_dir:28,dbg:8,dcmake_install_prefix:2,deactiv:10,dead:[10,38],deal:[35,36],debug:[8,10,21],decent:15,decid:[3,8,32,50],decis:27,declar:[4,8,16],decod:13,decompos:[3,10],decomposit:[10,28,33,46],decreas:[28,34],dedic:[4,8,16],dee:10,deep:[22,35],def:[1,8,21,35],def_angl:21,defend:20,defin:[1,4,8,9,13,14,15,20,21,22,23,24,25,28,29,31,32,33,34,35,36,37,39,40,41,44,49,50,51],definem:8,definit:[8,20,26,27,31,41,49],degre:[22,26,27],deleg:28,delet:[0,2,8,22,35,49],deletegapcol:35,deliber:20,deliv:[1,26,34,35],delta_scor:34,demand:35,demonstr:26,denovoclos:34,densiti:[22,32,38],dep1:4,dep2:4,dep:4,depend:[0,3,4,8,10,13,18,22,25,26,27,28,31,35,36,37,38,39,40,41,47,48,49,54],dependency1:4,dependency2:4,depends_on:4,depth:[26,38],deriv:[1,20,26,28,33,38,43,44],descend:35,descent:[31,32,38],describ:[0,4,7,8,10,11,17,20,21,22,26,28,29,30,32,33,37,39,41,44,47,48,49,50,51,54],descript:[0,5,13,16,20,34,35,51],descriptor:[26,28],descsrib:10,design:[1,3,19,20],desir:[9,18,25,26,31,32,34,35,39,40,41],despit:3,detail:[0,3,9,13,16,20,25,26,27,28,31,33,34,35,39,41,48,49,51],detect:[0,3,11,28,30,38,44],determin:[8,11,20,25,26,31,34,40,41],determinist:28,deuterium:[35,50],develop:[1,3,8,16,19,53],deviat:[22,33,34,51],devot:12,dict:[4,28,31,33,34,39,41],dictionari:[4,5,13,15,33,38],did:[8,26,31,35],didn:[7,28],didnt:5,diff:10,differ:[1,2,4,7,8,10,15,16,20,21,26,28,29,31,35,39,41,47,49,51],differenti:49,dihedr:[7,9,18,22,23,25,26,32,34,35,41,50,51,54],dihedral_angl:22,dihedral_bin:41,dihedral_idx:51,dihedral_pair:27,dihedralconfigur:51,dill:38,dimens:27,dimension:38,dir:[4,8,18],direct:[8,20,22,24,26,33,41,49,50],directli:[8,10,18,26,31,35,36,40,44,49,51,53],directori:[1,2,4,5,7,8,17,26,28,48],dirti:1,dirtyccdclos:34,disabl:[1,16,35],disable_doctest:2,disable_document:2,disable_linkcheck:2,discard:26,disclaim:20,discocontain:40,disconnect:3,discret:[28,39,41],discuss:[20,26],disk:[8,25,28,39,41,51],displai:[7,11,13,14,20],displaystyl:10,dissimilar:28,dist:41,dist_bin:41,dist_bin_s:26,distanc:[7,9,22,26,28,31,33,35,36,39,40,41,43,49],distance_thresh:28,distant:40,distinct:[21,28,36,51],distinguish:[3,23,25,37,39,41,51],distribut:[1,8,20,25,26,27,34,37,39,41,48,51],disulfid:[0,25,32,36,43,47,49,51,54],disulfid_bridg:[25,36],disulfid_score_thresh:36,disulfidscor:[36,44],dive:[16,35],diverg:8,divers:[26,28],divid:28,dng:18,do_it:[39,41],doc:[2,4,8,16,20,28],dock:38,docker:[3,6,7,54],dockerfil:[5,7],docstr:13,doctest:[2,8,16],document:[1,2,7,16,20,26,28,53],doe:[1,3,4,8,9,10,11,13,15,16,20,22,26,30,31,34,35,37,40,48],doesn:[8,16,29,32,34,35,51],doesnt:51,doexternalscor:[39,41],doing:[1,5,16,28],dointernalscor:[39,41],domain:28,domin:10,don:[2,10,20,31,35,50],done:[1,8,11,13,16,23,25,27,28,31,33,34,35,37],donor:[41,49,50],donorm:[39,41],dont:[0,34],dont_write_bytecod:1,dost_root:2,doubl:28,doubt:13,down:[13,22,26,28,34],download:5,dpm3_runtime_profiling_level:14,draw:[22,27,34],drawback:8,drawn:[27,34],drawphigivenpsi:27,drawpsigivenphi:27,drop:[3,8],dssp:[3,26,41],dssp_state:41,dtype:28,due:[0,26,31,32,35,44],dump:[28,51],dunbrack:[3,38,48],duplic:[6,28],dure:[1,3,21,32,35,37,45,51],dynam:51,dynamicspatialorgan:3,e_cut:10,e_thresh:[10,35],e_tresh:10,each:[0,7,8,10,13,14,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,41],earli:3,earlier:2,easi:8,easier:[1,8,20],easili:[4,16,35],echo:8,edg:[10,28],edge_idx:10,editor:1,editori:20,editxc:28,edu:3,educ:8,effect:[4,8,10,25,36,44],effici:[21,28,34,38,42],egg:26,eigen3_include_dir:2,eigen:[2,3],either:[0,7,8,13,16,18,20,21,22,27,29,31,32,34,35,36,37,39,40,41,45,49,51],elabor:[8,20],electron:20,electrostat:[25,32],element:[1,10,21,22,26,28,31,33,37,40,44,50],elimin:[10,38],els:[8,16,36,37],emerg:1,empir:[43,44],emploi:16,empti:[8,11,13,22,26,28,31,35,49],enabl:[1,2,3,11,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,52],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,28,33,35,42,47],entityhandl:[13,21,22,26,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,28,31,32,33,36,41,47,50],entries_from_seqnam:28,entrypoint:5,enumer:[8,10,21,25,26,28,31,35,40,47,49,50,51],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39,41,42,54],epsilon:[10,25,36,52],equal:[28,34,39,41,44,50],equidist:51,equip:5,equival:[28,35,39,41],error:[0,11,13,14,26,28,32,35,37],especi:28,estim:[10,28,33,34,35,38,41,44,49,50,51],etc:[1,3,8,16,22,26,31,40],evalu:[4,8,32,35,39,40,41,46,47,49,51,54],evaluategromacsposrul:9,even:[2,8,10,20,22,25,29,35],event:[20,28],eventu:13,ever:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,51,52],everyth:[1,2,3,7,8,12,13,16,28,32,35,36,37,39,54],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,49],exampl:[0,1,2,3,8,11,13,16,17,18,20,21,23,25,26,27,28,30,32,34,35,36,42,47,48,49],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35],exclud:[8,20,26],exclus:[1,8,20,25],execut:[0,2,3,4,7,8,16,18,20,26,33,35],exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,28,31,32,33,34,35,37,39,40,41,48,49,51],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:[10,34],expect:[1,3,7,21,25,26,33,35,36,40,44,50,52],expens:26,experiment:[33,35],explain:[1,8],explan:8,explicit:2,explicitli:20,explor:[5,38],exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28,30,31,35,41,46],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,28,29,35],extension_penalti:29,extent:26,extern:[3,4,5,8,28,34],external_script:[3,8],extra:[2,3,8,16,22,28,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,49,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:[3,22,28],eye:1,f_i:26,f_idx:40,f_vinaparticl:49,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,35,51],fall:32,fallback:51,fals:[1,8,10,11,13,22,25,26,28,29,31,34,35,36,44,47,49,50],fantast:8,far:[31,35],fast:[0,9,18,19,21,25,26,27,28,37,39,40,41,51],fasta:[0,13,28,30,35],fasta_fil:28,faster:[10,25,26,28,32,33,40],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,filesystem:28,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:[0,3,5,13,20,26,28,48],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],fromdatachunk:28,fromhhm:26,fromhoriz:26,fromresidu:51,fromseqlist:28,front:[1,11,16],fs_data_:28,fs_server:28,fsstructureserv:[3,28],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:[0,3,9,18,24,25,28,30,31,33,35,36,54],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:[3,9,23,28,31,33,38,44],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,getattachedview:28,getaveragescor:31,getbackbonelist:[23,26],getbackbonescoringkei:31,getbackboneweight:31,getbins:27,getbinsperdimens:27,getbound:22,getc:22,getca:22,getcb:22,getchain:29,getchainindex:29,getchainnam:29,getchains:8,getcharg:25,getclust:31,getclusteredcandid:31,getcollisiondist:49,getconfid:26,getcoordidx:26,getcoordinfo:26,getcpuplatformsupport:25,getcreationd:5,getdefault:[25,32,35],getdefaultlib:5,getdihedralangl:26,getdihedralconfigur:51,getdistbins:26,getdisulfidbridg:25,getdisulfidconnect:25,getdsspstat:26,getel:21,getenviron:21,getenvsetdata:8,getepsilon:25,getfirstindex:21,getforcefieldaminoacid:25,getfragmentinfo:[26,31],getframeenergi:49,getfudgelj:25,getfudgeqq:25,geth1index:21,geth2index:21,geth3index:21,getheavyindex:25,gethistogramindex:[22,27],gethistogramindic:27,gethnindex:21,gethydrogenindex:[21,25],getidentifi:28,getidx:28,getindex:[21,25],getinternalconnect:25,getinternalenergi:49,getinternalenergyprefactor:49,getlargestclust:31,getlastindex:21,getlength:29,getlist:28,getlooplength:25,getloopstartindic:25,getmass:25,getmaxnumatom:21,getmaxnumhydrogen:21,getn:[22,28],getnam:[28,47,49],getnonbondedcutoff:32,getnonplanar:33,getnum:31,getnumatom:[21,25],getnumb:31,getnumcandid:31,getnumchain:8,getnumcoord:26,getnumfrag:26,getnumhydrogen:21,getnumloopresidu:25,getnumresidu:[8,21,25],getnumstempair:26,getnumsubrotam:49,geto:22,getolc:[21,22],getomegators:[21,22],getomf:28,getomfbyidx:28,getoxtindex:25,getpeptideboundconnect:25,getphiprobabilitygivenpsi:27,getphitors:[21,22,47],getpo:[21,28,49],getposit:28,getpotentialenergi:25,getpredict:26,getprob:[27,49],getpsiprobabilitygivenphi:27,getpsitors:[21,22,47],getr:33,getresidu:28,getresiduedepth:26,getringpunch:33,getrotamericconfigur:51,getscor:[26,34],getscoringfunct:49,getselfenergi:49,getseqr:[21,40],getsequ:[21,22,26,28,31],getsequenceprofil:26,getsequenceprofilescoreskei:31,getsigma:25,getsimul:25,getsolventaccessibilitit:26,getstemrmsdskei:31,getstructureprofil:26,getstructureprofilescoreskei:31,getsubdb:26,getsubrotamerdefinit:49,getsystemcr:32,gettemperatur:[34,49],gettransform:22,getversionnumb:37,getvinaweightgaussian1:49,getvinaweightgaussian2:49,getvinaweighthbond:49,getvinaweighthydrophob:49,getvinaweightrepuls:49,getweight:[28,31],gggg:35,ggggagggg:35,gggggggggggggggggggg:35,git:[1,4,8,17,18,19,53],git_root:28,gitignor:8,gitlab:[5,53],give:[4,8,16,20,23,28,31,34,35,49],given:[0,1,3,4,8,9,10,11,13,14,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51],glass:38,gln:[49,51],gln_ne2:21,global:[15,26,31,35,37,49],glu:[21,49,51],glu_oe1:21,glutam:49,glutamin:49,gly:[35,36,47,49,50],gly_n:21,glycin:[3,22,26,32,36,49],goal:[1,10,28,30],goe:[2,8,14,16,35,51],going:[8,9],goldfarb:35,goldstein1994:[10,38],goldstein:[10,38],good:[4,8,18,25,26,35],goodwil:20,got:2,govern:20,grain:8,grant:20,graph:[3,12,38,47,54],graph_initial_epsilon:36,graph_intial_epsilon:36,graph_max_complex:36,graphminim:[10,46],greatest:5,grep:2,grid:26,gromac:9,grossli:20,group:[4,14,24,26,27,28,41,44,45,46,47,50,52],group_definit:[27,41],group_idx:41,guarante:[26,28,31,34,36,37],gui:[8,27],guid:32,guidelin:[8,37],gzip:[0,5,11,13,28],haa:38,hand:[0,2,4,13],handl:[3,8,9,13,19,22,28,30,36,40,44,54],handler:28,happen:[1,8,25,28,29,34,35,49],hard:[43,49],hardwar:18,harmless:20,harmon:[25,32],harmonic_angl:25,harmonic_bond:25,harmonic_improp:25,has:[0,1,2,3,4,5,8,10,11,13,16,20,21,22,23,24,25,26,28,29,31,32,34,35,36,39,40,41,44,46,49,50,52],hasattr:35,hasdata:26,hasfraglength:26,hasfragmentinfo:31,hash:[3,26,28],hash_thresh:28,hash_tresh:28,hasnonplanar:33,hasringpunch:33,have:[0,2,3,4,5,7,8,10,13,14,16,18,20,21,22,25,26,28,29,31,33,34,35,36,37,39,40,41,44,46,47,50,51,52],hbond:[28,35,41,49,50],hbond_scor:37,hbondscor:[35,37,42],headach:8,header1:4,header2:4,header3:4,header4:4,header:[0,2,4,16,17],header_output_dir:4,headlin:8,heavi:[21,25,36,39,49,50],heavili:[26,47],helic:[22,24,25,28,35,41],helix:[7,18,22,34,47],hell:28,hello:37,hello_world:8,hellyeah:[7,18],help:[0,1,2,3,4,7,8,13,16,18,25,41],helpactiontest:1,helper:[4,12,16,17,21,25,31,36,37,54],hen:26,henc:[8,14,21,26,37],here:[0,1,2,3,4,8,11,13,14,16,18,19,21,22,25,26,27,28,30,31,32,33,34,35,37,39,41,44,48,51],herebi:20,herein:20,het:35,heurist:[3,28,35,50],heuristicprocessor:21,hg_po:49,hgfhvhefgdntngcmssgphfnpygkehgapvdenrhlg:0,hhblit:[0,13],hhm:[0,13,26,31],hhsearch:26,hide:[8,16],hierarch:[31,40],hierarchi:15,high:[3,8,16,28,30,35],high_resolut:22,higher:[31,40,41],highest:[15,33],highli:[2,8],hint:13,histidin:[25,49],histogram:[27,34],histori:16,hit:[1,10,16,27,28,32],hmm:38,hold:[20,28],home:[4,5],homo:[0,13],homolog:[0,12,18,19,35,38],homologu:26,honor:35,honour:35,hook:[8,17],horiz:26,horribl:50,host:[4,7,8,16],hotfix:16,how:[1,16,17,20,26,31,34,35,38,40,48,54],howev:[5,20,26],hparticl:49,hpp:37,hsd:[49,51],hse:[49,51],html:[2,3,8,16],http:[3,8,18,19,20,53],huge:28,hybrid:51,hydrogen:[3,21,22,25,35,38,41,49,50],hydrophob:49,hyphen:1,i_loop:[25,36],i_vinaparticl:49,id_:37,idea:[1,8,21,23,25,26,35,40,49,52],ideal:[22,32,52],ident:[3,26,27,28,41,51],identif:20,identifi:[0,3,13,14,20,26,28,31,35,36,39,41,49,50,51],ids:47,idx:[10,21,22,25,26,28,32,40,49],idx_ca_res_37:21,idxhandl:8,iff:[26,29,33],ifstream:37,ignor:[0,25,28,32,35],iii:20,illustr:26,imag:7,image_nam:5,imagehandl:22,imagin:8,imaginari:1,img:[7,22],immedi:[1,8,15,16],impact:[0,25,26],implement:[3,16,19,26,28,29,32,34,35,37,43,44,46,47,49,50,53],impli:20,implicit:2,improp:25,improv:[3,20,25,35,38,44],in_dir:4,in_fil:8,in_path:4,in_stream:37,in_stream_:37,inabl:20,inaccur:25,inaccurate_pot_energi:25,inact:52,inactive_internal_energi:52,incident:20,incl:[25,26,35],includ:[2,3,7,8,11,16,18,20,21,25,26,28,29,31,33,35,37,39,41,47],include_atom:28,include_ligand:35,inclus:[20,35],incompat:[31,32],incomplet:[35,48],inconsist:[10,13,21,22,25,26,29,31,32,36,40,49],inconveni:16,incorpor:[3,20],increas:[0,3,10,28,31,32,35,50],increment:28,incur:20,indemn:20,indemnifi:20,independ:[0,3,25,36,48],index:[8,10,21,22,25,26,27,28,29,31,32,33,34,35,39,40,41,45,49,50,51],index_four:25,index_on:25,index_thre:25,index_two:25,indic:[8,10,11,13,20,21,22,25,26,27,28,29,31,32,35,36,40,44,47,49],indirect:20,individu:[7,20,39,41],inf:[10,32,35],infin:32,infinit:32,influenc:[13,28,40,50],info:[26,28,31,35,40],inform:[0,5,7,8,13,16,20,22,23,26,28,29,31,34,35,38,40,41,42,53],infring:20,inherit:[1,39,40,41,46],init:16,init_bb_list:34,init_frag:34,initi:[3,10,21,22,26,28,31,32,34,35,36,39,40,41,46,49,50,51],initial_bb:31,initial_epsilon:[10,52],initialis:1,inlin:37,inner:14,input:[0,1,3,13,16,18,25,26,27,28,32,34,35,36,39,40,41,44,48,52],insert:[21,22,29,31,34,35,52],insertinto:[21,22,31],insertloop:[29,35],insertloopcleargap:[29,31,35],insid:[1,4],insight:16,instal:[8,16,37,54],instanc:[3,8,13,24,25,37,53],instead:[0,1,2,3,4,8,11,26,28,29,31,34,35,50],institut:20,instruct:2,int16:28,int16_t:37,int32:28,int32_t:37,int64:28,int_32_t:37,integ:[8,13,21,28,40],integr:[4,8,38],intend:[1,8,34,49],intent:26,intention:20,interact:[3,8,25,32,39,40,41,43,44,45,49],intercept:[39,41],interest:[1,10,25,26,34,37,49,51],interfac:[0,3,4,8,20,50],intermedi:8,intern:[0,1,3,4,5,8,16,21,24,25,26,27,28,31,32,33,34,35,36,37,38,39,40,41,46,49,50,52],internal_e_prefac:50,internal_e_prefactor:49,internal_energi:49,internet:8,interpl:51,interpol:[40,51],interpret:[8,11],intervent:8,intrins:2,introduc:[1,3,4,8,16,32,35],introduct:[12,17],invalid:[8,21,25,26,28,29,32,35,36,39,40,41,45,49,51],invalid_vinaparticl:49,invok:[2,4,8,15,16],involv:[16,30,44,49],iodin:49,ios:37,iostream:37,ipython:7,irrevoc:20,is_c_ter:[25,36],is_cter:25,is_hbond_acceptor:50,is_hbond_donor:50,is_major:35,is_n_ter:[25,36],is_nter:25,isallatomscoringsetup:[31,35],isallset:21,isanyset:21,isbackbonescoringsetup:35,isctermin:29,isempti:31,isen:14,isntermin:29,isoleucin:49,isset:21,issimilar:51,issourc:37,issu:[3,12,16,17,20,32,35,37],istermin:29,isvalid:47,item:[1,8,16,21,22,25,26,35,40],iter:[10,26,27,28,31,32,34,35,49],its:[0,1,2,4,5,8,11,16,20,25,26,30,31,33,34,35,41,48,49,50,51],itself:[3,4,8,16,26,28,34,36,37,39,41],januari:20,job:[8,26,34,35],johner:38,join:[8,21,23,26,31,32,34,36],jone:[38,49],jones1999:[26,38],journal:38,json:[0,13],jupyt:7,just:[1,2,8,13,15,16,23,25,26,28,29,31,35,50],kabsch1983:[26,38],kabsch:38,keep:[0,1,2,4,5,8,13,16,28,30,35,47],keep_non_converg:31,keep_sidechain:[8,36],kei:[0,13,26,28,31,34,35,39,40,41],kept:[8,16,25,31,32,36,45,49],kernel:[7,38],keyword:27,kic:[30,31,34],kicclos:34,kick:13,kill_electrostat:25,kind:[1,8,20],kinemat:32,kmer:3,kmer_search:3,know:[2,51],knowledg:51,known:[4,11,21,40,50],krivov2009:[10,38,47,49],krivov:38,kwarg:1,l_e:49,lab:48,label:[16,25],lack:35,languag:[4,20],larg:[3,5,27,32,35],larger:[10,14,22,26,28,35,50],largest:[28,31,44],last:[1,2,3,4,21,22,25,29,31,32,34,35,40,41,48],last_psi:22,later:[1,8,10,21,28,47],latest:[2,3,5,8],latter:[0,5,16,28,35],launcher:[4,8],law:20,lawsuit:20,layer:44,layout:[26,28,37],lbfg:35,lbfgs_toler:[],lddt:7,leach1998:[10,38],leach:38,lead:[0,8,9,11,22,25,31,32,36,39,41,48],learn:28,least:[0,2,4,8,10,16,20,22,25,26,35,39,41,44],leav:1,left:[10,11,32],legal:[8,20],lemon:38,len:[22,23,25,26,28,31,35,36,41,47],length:[0,9,10,21,24,25,26,27,28,29,31,32,34,35,36,37,39,40,44],length_dep_weight:35,length_depend:31,lennard:49,less:[0,10,16,22,25,26,27,28,31,35,39,41,50,51],let:[1,8,22,26,28,31,47],letter:[3,5,21,22,26,27,34,49],leu:49,leu_h:21,leucin:49,level:[2,3,8,14,15,16,30,35],lexicograph:35,liabil:20,liabl:20,lib64:8,lib:[5,7,37],libexec:[4,8],libpromod3_nam:4,librari:[0,3,4,8,15,28,33,36,38,47,50,54],library1:4,library2:4,licenc:48,licens:[3,17,19],licensor:20,lies:26,life:16,ligand:[3,35,36,49,50],like:[0,1,4,8,16,35,37,48],limit:[0,3,20,26,28,32,35],line:[0,1,7,8,9,12,16,27,41,54],linear:[26,28,31,34,39,40,41],linear_weight:[31,34,39,41],linearcombin:31,linearli:[28,49],linearscor:34,link:[0,2,4,8,16,20,21,25,26,28,34,36,39,40,41,42],link_cmd:4,linkcheck:[2,8,16],linker:[4,35],linker_length:35,list:[0,1,2,3,4,7,8,9,10,11,13,20,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,45,46,47,49,50,51,52],listen:8,literalinclud:8,litig:20,littl:[4,8,16,37],live:[4,8],lj_pair:25,load:[1,8,13,15,21,23,25,26,27,28,31,32,35,36,37,39,41,42,47,51,54],loadalign:[30,35],loadallatominteractionscor:39,loadallatompackingscor:39,loadamberforcefield:35,loadbb:26,loadbbdeplib:[0,36,47,48],loadcach:28,loadcbetascor:[31,34,41,42],loadcbpackingscor:41,loadcharmm:25,loadcharmmforcefield:35,loaddefaultallatomoverallscor:39,loaddefaultbackboneoverallscor:41,loadent:[0,13],loadfragdb:[23,24,31,35],loadhbondscor:41,loadlib:[0,36,48],loadpdb:[8,21,23,25,26,28,30,31,32,34,35,36,42,47],loadport:[25,26,27,37,39,41,51],loadreducedscor:41,loadsequenceprofil:[13,26,31],loadssagreementscor:41,loadstructuredb:[23,24,26,31,35],loadtorsionsampl:[22,24,27,34],loadtorsionsamplercoil:[24,31,35],loadtorsionsamplerextend:24,loadtorsionsamplerhel:24,loadtorsionscor:41,local:[2,5,7,25,26,27,39,41,51],localalign:28,localhost:7,locat:[2,3,4,5,10,22,24,26,28,29,37,39,41,49],log:[11,16,33,35,49,50],logic:0,loginfo:33,lone:49,lone_pair:49,longest:26,look:[5,8,11,16,22,26,36,40,50],lookup:[9,21,23,28,42],looooooong:10,loop:[0,3,7,8,13,18,19,21,24,26,27,28,29,30,33,35,36,37,38,39,40,41,50,54],loop_candid:31,loop_length:[25,26,31,36],loop_main:8,loop_po:25,loop_seq:31,loop_start_indic:[25,36],loopcandid:[28,30,33],loss:[16,20],lossi:26,lost:[1,16],lot:[1,8,13,16],low:[1,3,8,10,28,50],lower:[31,34,35,39,41],lowest:[31,33,34,49],lowest_energy_conform:34,lying:40,lysin:49,m_idx:28,m_vinaparticl:[49,50],mac:3,machin:[25,26,27,37,39,41,51],macro:[4,8],macromolecul:38,made:[4,5,20,51],magic:[8,37],mai:[0,1,2,4,8,11,13,16,20,21,25,29,32,35],mail:20,main:[8,35,37,51],mainli:[21,34,49],maintain:[8,16],mainten:17,maintin:34,major:[16,35],make:[3,4,7,8,11,13,16,18,20,21,22,26,37,40,48,54],makefil:[2,8],makestat:51,malfunct:20,malici:16,man:[2,8],manag:[4,8,20,42],mani:[11,13,26,28,32,33,35,50],manipul:22,manner:[8,10,34],manual:[1,2,5,8,9,16,26,31,34,35,37,49],map:[0,13,21,22,26,28,33,36],mariani:38,mark:[4,20,50],mass:25,massiv:28,master:[8,16],mat3:9,mat4:[9,22,28,35],mat:28,match:[0,4,13,22,25,26,27,28,31,32,34,35,40,41],materi:[1,8],math:33,mathemat:[31,32],matplotlib:27,matric:38,matrix:[9,26,28],matter:[4,7,28,53],max:[9,10,21,29,33,35,36,41,51,52],max_alpha:41,max_beta:41,max_complex:[10,52],max_count:[39,41],max_d:41,max_dev:34,max_dist:[31,40],max_dist_thresh:33,max_extens:35,max_gamma:41,max_iter:[28,31,35],max_iter_lbfg:35,max_iter_sd:35,max_length:29,max_loops_to_search:35,max_n:10,max_num_all_atom:35,max_p:50,max_prob:49,max_res_extens:35,max_step:32,max_to_show:14,max_triangle_edge_length:28,max_visited_nod:10,maxfraglength:26,maxim:[10,26,28,31,32,34,35,38,40,41],maximum:[10,26,31,32,33,34,49,50],mc_closer:34,mc_cooler:34,mc_num_loop:35,mc_sampler:34,mc_scorer:34,mc_step:[10,35],mcsolv:10,mean:[4,8,13,16,20,21,25,28,32,35,36],meaning:[26,31],meant:[18,21,26,33,35,50],measur:28,mechan:[18,20,28,31,32,34,35,40],meddl:[7,35],media:20,medium:20,meet:20,member:[8,13,31,35],memori:[10,26,28,35,37],mention:[1,2],mer:3,merchant:20,mere:20,merg:[16,25,28,29,31,35,36,40,49],merge_dist:35,mergegap:29,mergegapsbydist:35,mergemhandl:35,mess:[8,16,40],messag:[12,13,37],messi:16,met:49,meta:28,metal:49,methionin:[35,49],method:[0,1,10,13,21,25,26,27,28,32,35,36,37,50],metric:40,metropoli:[10,31,34],mhandl:[29,30,31,35],middl:16,might:[3,10,25,26,28,31,32,34,40,50,52],min:[28,31,41],min_alpha:41,min_beta:41,min_candid:31,min_d:41,min_dist:40,min_gamma:41,min_loops_requir:35,min_scor:31,min_terminal_anchor_s:35,min_triangle_edge_length:28,mincadist:22,mind:[1,8],minim:[3,12,18,22,25,26,31,32,35,39,40,41,46,47,54],minimizemodelenergi:35,minimum:[22,26,28,44],minor:[3,25,35],mirror:37,miser:14,mismatch:[21,35,40],miss:[0,11,13,25,28,35],mix:[0,4],mkdir:[2,8],mm_sy:[25,32],mm_sys_output:25,mm_system_cr:32,mmap:28,mmcif:[5,11],mmsystemcr:[25,32],mod:8,mode:[1,51],model:[1,3,7,8,12,13,14,19,21,25,26,29,32,34,36,40,41,42,45,46,49,50,52,53,54],model_termini:35,modelling_issu:35,modellinghandl:[3,29,31,35],modellingissu:35,modeltermini:35,modif:[20,35],modifi:[8,16,20,22,31,35],modified_crambin:31,modul:[1,3,11,12,15,16,17,18,23,24,28,30,37,44,47,49],modular:19,module_data:4,mol:[8,9,18,21,22,23,26,27,28,29,31,32,34,35,36,38,40,47,49,50,51,54],molck:7,molecular:[7,18,32,35],molprob:30,molprobity_bin:33,molprobity_execut:33,moment:8,monitor:1,monolith:8,mont:[0,3,10,28,31,34,35,46],montecarlo:3,mood:8,more:[1,2,4,7,8,10,13,14,16,20,28,35,44,49,53],most:[0,3,4,5,8,22,25,26,27,28,31,32,35,39,41,48,50],mostli:[4,16],motif:[3,30,38],motiffind:28,motifmatch:28,motifqueri:28,motion:[22,38],mount:[5,7],movabl:25,move:[2,3,8,16,25,31,32,34,35,37],movement:28,mpscore:33,msg:11,msgerrorandexit:11,msm:3,msse4:2,much:[10,26,28,35],multi:18,multipl:[0,2,3,4,8,13,14,18,25,28,31,35,36,39,41],multipli:[10,34],multitempl:13,multithread:38,must:[0,2,4,8,10,13,14,16,20,22,25,26,28,29,31,32,33,34,35,36,37,39,40,41,44,51],mutlipl:13,my_db_on:26,my_db_two:26,my_script:7,myclass:37,myclassptr:37,mytrg:0,n_a_vinaparticl:49,n_ad_vinaparticl:49,n_coord:9,n_d_vinaparticl:49,n_entri:28,n_i:10,n_j:10,n_num:29,n_po:[9,22,41],n_stem:[9,23,26,29,31,32,34],n_stem_phi:34,n_stem_plddt:28,n_ter:[32,50],n_vinaparticl:49,naivesolv:10,name:[0,1,3,4,5,7,8,11,13,14,20,21,25,26,27,28,29,31,33,35,44,48,49,51],name_pymod:4,namespac:[13,37],nan:[32,35,51],nativ:37,ndarrai:28,necessari:[8,22,34,40],necessarili:[20,52],need:[1,2,3,4,5,8,11,13,15,16,22,25,26,27,28,31,32,35,36,37,39,40,41,47,50],need_config_head:4,neg:[1,10,25,32,40],negelect:[0,35],neglect:[28,32,45,49,50],neglect_size_on:31,neglig:20,neighbor:[8,21,35],neighbour:[28,35,51],network:[22,44],never:[13,16,26,31,35,36,37,39,41],nevertheless:8,new_default:25,new_env_po:21,new_po:21,new_res_nam:49,new_siz:22,newli:[5,21,34],next:[1,8,16,22,27,28,29,37],next_aa:34,nglview:7,nice:8,nitrogen:[9,22,32,43,49,50],nobodi:1,node:10,node_idx:10,node_idx_on:10,node_idx_two:10,non:[0,3,4,10,13,16,20,24,25,27,28,29,30,31,32,35,37,47,48,50],non_rotamer:51,nonbonded_cutoff:[25,32],none:[13,26,28,33,34,35,36,49],nonredund:26,nonzero:51,norm:[28,41],normal:[20,33,39,41],normalis:40,notabl:26,note:[0,2,8,13,14,21,22,25,26,28,31,32,34,35,36,37,39,40,41,47,49,50],notebook:7,noth:[0,4,8,13,14,20,28,34,49],notic:[1,4,16,20],notwithstand:20,novel:[19,38],novo:[3,30,54],now:[3,8,14,16,18,22,26],nparticl:49,nterminalclos:34,null_model:31,num:[23,28,31,32,36],num_frag:[26,35],num_gap_extens:29,num_loop:31,num_residu:[21,25,34,36,39,40,41],num_residues_list:36,num_trajectori:28,number:[0,1,3,8,9,10,13,14,18,21,22,24,25,26,27,28,29,31,32,34,35,36,37,39,40,41,42,44,45,49,51],numer:35,numpi:[27,34],nussinov1991:[28,38],nussinov:[28,38],o_a_vinaparticl:[49,50],o_ad_vinaparticl:49,o_d_vinaparticl:49,o_po:22,o_vinaparticl:49,object:[0,3,8,13,14,20,21,22,23,25,26,27,28,30,31,32,35,36,37,39,41,44,46,47,49,50,54],oblig:20,observ:[10,26,28,32,50,52],obtain:[10,18,20,23,28,35],obviou:16,occupi:[45,50],occur:[21,28,35,40,41],ocparticl:49,odd:26,off:[1,8,14,35],offend:33,offer:[6,20,24,30,49,51],offset:[0,3,13,26,31,35],ofstream:37,often:[8,11,13,32],og_po:49,olc:22,old:[33,35],oligom:[0,13,30],oligomer:3,olson:38,omega:[21,22],omf:[3,28],omit:35,onc:[1,3,8,16,25,28,31,32,34,46,51,52],one:[0,1,2,4,5,6,8,9,10,13,14,15,16,20,21,22,25,26,28,29,31,32,34,35,36,39,40,41,44,49,50,51,52],one_letter_cod:[21,23,26,31,32,33,34,36],ones:[22,28,31,34,50,51],onli:[0,1,2,3,4,8,10,11,13,14,15,16,20,21,22,25,26,28,29,31,33,34,35,36,37,39,41,44,47,48,49,50],only_longest_stretch:26,onto:[1,22,26,28],oparticl:49,open:[13,25,26,27,37,39,41,51,53],openmm:[2,18,25,32],openstructur:[2,3,5,7,19,38],oper:[3,10,16,18,21,26,28,40],opt:[11,13,16],optim:[0,2,3,10,13,25,26,27,31,33,35,38,39,41,44,47,48,51,54],optimis:8,optimize_subrotam:[36,44],option:[0,2,3,5,7,13,26,31,32,35,51],order:[0,5,13,21,25,26,29,31,35,37,40],org:[3,20],organ:[8,26,51],orient:[9,32,41],orig_indic:[31,33],origin:[5,7,9,13,16,20,22,26,31,34,35,40,52],orthogon:[28,33],ost:[0,1,2,3,4,5,7,8,9,11,13,15,18,21,22,23,26,27,28,29,30,31,32,33,34,35,36,37,40,41,42,43,44,47,49,50,51,54],ost_double_precis:2,ost_ent:33,ost_librari:4,ost_root:[2,8],other:[0,1,2,3,4,8,10,14,16,20,21,22,31,32,35,36,39,41,42,49,50,51,52,53,54],other_index:22,other_particl:49,other_res_index:21,otherwis:[1,4,8,10,14,16,20,21,22,25,26,28,29,31,32,34,35,39,40,41,49,51],our:[3,4,5,8,16,26,28,31],out:[0,1,2,4,8,14,16,20,21,25,26,27,28,29,31,34,47,51],out_path:4,out_po:25,out_stream:37,out_stream_:37,outdat:[3,5,7],outer:[14,26],outlier:33,output:[0,5,8,11,13,25,27,28,32],output_dir:4,outsid:[8,40],outstand:20,over:[2,4,13,16,26,28,32,34,35,49],overal:[10,34,40,46],overhead:25,overlap:[25,34,35,36],overli:16,overload:37,overrid:[2,5,25,35,50],overridden:4,overriden:5,overview:[8,16],overwrit:[31,49],overwritten:25,own:[1,3,4,16,17,20,25,26,35,48,49,50],owner:20,ownership:20,oxt:[9,21,25],oxygen:[22,35,43,49,50],p_vinaparticl:49,pack:21,packag:[4,8,16],pad:[22,37],page:[2,8,20],pai:1,pair:[9,10,25,26,27,28,32,34,36,37,39,40,41,44,49,51],pairwis:[3,8,10,22,28,31,35,39,41,42,43,44,46,47,49,50,52],pairwise_energi:10,pairwisefunct:[40,41],pairwisefunctiontyp:40,pairwisescor:[8,35,42,49],paper:[43,44,47,49],paragraph:[1,8],parallel:26,paramet:[1,4,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,43,44,45,46,48,49,50,51,52],parameter_index:26,parametr:[3,32,35,36,49,50],parent:35,pars:[0,11,12,25,26,27,28,39,41,51,54],parser:12,part:[0,1,8,16,18,20,21,26,34,35,40,44,46,47,49,54],parti:[16,17,20],partial:29,particip:[36,44],particl:[3,25,26,32,41,43,44,45,47,50],particle_typ:49,particular:[8,10,20,26,31,32,34,49,51],partner:[39,40,41],pass:[13,16,21,25,26,28,29,32,34,35,44,45,49,50],past:[8,16,22,29],patent:20,path:[1,2,4,5,7,8,11,16,18,25,26,27,28,33,39,41,51],path_to_chemlib:15,path_to_dockerfile_dir:5,path_to_promod3_checkout:6,pattern:[28,38],paus:14,pdb:[0,5,7,8,11,13,18,21,22,23,24,25,26,28,30,31,32,33,34,35,36,42,47],penal:[29,35],penalti:[29,35],pentam:28,pentamatch:[3,28],pentamatch_n:28,pentamermatch:[],penultim:3,peopl:16,pep:[1,16],peptid:[3,21,23,25,26,28,35,36,47],peptide_sel:28,per:[4,8,10,12,16,21,27,31,34,35,39,40,41,44],percent:20,percentag:33,perfect:8,perfectli:8,perform:[0,10,16,18,19,20,25,28,31,32,33,34,35,37,40,44],period:25,periodic_dihedr:25,periodic_improp:25,permiss:[8,20],permut:10,perpetu:20,perspect:33,pertain:20,phase:25,phe:[33,49,51],phenix:33,phenylalanin:49,phi:[21,22,26,27,32,34,41,47,50,51],phi_bin:[41,51],phi_handl:47,philippsen:38,phipsisampl:34,phosphoru:49,phosphoserin:35,phrase:8,pick:[31,34],pickl:28,pictur:8,piec:[8,28],pipelin:[0,3,14,19,26,28,29,30,33,34,47,53,54],pivot:[31,32,34],pivot_on:[31,32],pivot_thre:[31,32],pivot_two:[31,32],place:[1,2,4,8,11,13,16,20,26],plain:[0,13],plan:16,planar:[3,30,35],plane:33,platform:[18,25],playground:7,plddt:28,pleas:[2,8,16,28,31,32,35,53],plot:27,plt:27,plu:[8,13,15,26,44,49],pluribu:28,pm3_csc:16,pm3_openmm_cpu_thread:[18,25,35],pm3_runtime_profiling_level:14,pm3argpars:[0,11,12,54],pm3argumentpars:[0,11,13],pm_action:[1,4,8],pm_action_init:8,pm_bin:1,pna:38,png:27,pocket:28,pocket_view:28,point:[2,8,13,15,21,26,28,33,34,35,40,49,51],pointer:[2,8,37],polar:[49,50],polar_direct:49,polici:8,pop:[16,31,34,40],popul:[2,16],port_str_db:26,portabl:[4,17,25,26,27,39,41,51],portable_binary_seri:37,portable_fil:4,portablebinarydatasink:37,portablebinarydatasourc:37,pos:[21,22,26,28,32,49],pos_end:28,pos_on:28,pos_start:28,pos_two:28,posit:[3,8,9,22,23,25,26,27,28,29,31,32,34,35,36,38,39,40,41,43,44,45,46,49,50,54],possibl:[0,3,8,10,13,16,20,22,25,26,27,28,29,31,32,34,35,36,37,39,40,41,44,46,49,51],post:13,postprocess:36,pot:25,pot_:32,potenti:[3,10,23,25,26,28,31,32,35,36,37,38,41,49],power:[7,20],pqhpg:0,practic:[4,8,25,26],pre:[8,16,35],pre_commit:[8,16],preceed:36,precis:[2,31,35],precomput:[23,54],pred:40,predefin:[4,18,25,35,39,41],predict:[13,26,28,35,38,40,41],prefactor:49,prefer:[2,4,20,26,51,52],prefilt:35,prefix:[1,4,8,11],prepar:[8,20,35],preprocess:28,present:[3,22,28,32,36,49,50,51],prev_aa:34,prevent:[1,8],previous:[25,26,31,36,40],primary_rot_angl:22,principl:[3,34,40],print:[1,2,5,20,22,23,25,26,31,32,33,35,42],printstatist:26,printsummari:14,prior:35,privat:[1,37],pro:[21,27,49,51],probabilist:[26,50],probability_cutoff:50,probabl:[4,8,10,13,16,26,27,28,31,32,34,49,50,51],problem:[3,7,10,13,16,26,28,31,32,34,35,40,42,44,46,48,52],problemat:[3,5,28],proce:42,procedur:[10,28,34,36,50],process:[1,3,13,16,21,25,28,32,34,35,37,40,45,49,51],processor:5,produc:[0,1,2,4,8,10,26,29,33,35],product:[1,3,16,20],prof:[0,26,31],prof_dir:26,prof_path:26,profil:[0,3,12,13,26,28,31,35,38,54],profiledb:26,profilehandl:[13,26,28,31,35],prog:13,program:[4,5,8,12],project:[3,4,5,8,16],prolin:[22,33,49],promin:[0,20],promod3:[1,3,7,9,10,11,13,14,15,17,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],promod3_checkout:7,promod3_mod:4,promod3_nam:4,promod3_name_head:4,promod3_path:8,promod3_root:8,promod3_shared_data_path:[8,37],promod3_unittest:[1,4,8],promod:[5,7],promot:8,propag:[8,22],proper:[16,26,50],properli:[1,35,39,41,50],properti:[21,22,35,50,51],propos:[29,31,32,34,44],proposed_posit:34,proposestep:34,prot:[8,23,26,28,32,34,36,47],prot_rec:8,protein:[0,18,19,24,25,28,33,34,35,36,38,45,47,49,54],proteinogen:26,proton:[21,25,49,51],prototyp:19,provid:[0,1,2,3,4,5,7,8,13,16,20,21,22,23,25,26,28,29,31,32,33,34,35,36,37,40,48,49,50,51],prune:[10,52],pscoringfunct:49,pseudo:[34,35,39,41],psi:[21,22,26,27,32,34,41,47,50,51],psi_bin:[41,51],psi_handl:47,psipr:[13,26,28,40,41],psipred_confid:41,psipred_pr:28,psipred_predict:[26,28,35],psipred_st:41,psipredpredict:[23,28,35,40],pssm:[0,13],publicli:20,pull:[5,8,16,18],pullterminaldelet:35,punch:[1,3,30,35],pure:0,purpos:[8,10,20,35,51],push:16,pushverbositylevel:13,put:[1,4,8,11,13,33,35],pwd:5,py_run:[1,4,8],pyc:1,pylint:16,pylintrc:16,pymod:[4,8,16],pyplot:27,pytest:8,python3:8,python:[1,2,3,4,5,7,8,11,14,15,16,18,21,22,25,28,32,37,49,50],python_root_dir:2,pythonpath:8,qmeandisco:40,qualiti:35,quantum:38,queri:[26,28,51],query_idx:28,query_list:28,querylib:51,question:[3,27],quick:17,quickli:[5,8,32],quit:[8,13],rackovski:38,radian:[9,22,25,27],radii:[33,43],radiu:[8,33,39,41,49],raihvhqfgdlsqgcestgphynplavph:0,rais:[0,9,10,13,21,22,25,26,27,28,29,31,32,33,34,35,36,39,40,41,44,45,49,50,51],rama_iffi:33,ramachandran:33,random:[10,22,24,27,31,32,34],random_se:31,randomized_frag:22,randomli:[27,34],rang:[8,9,21,22,23,25,26,27,28,29,32,34,35,39,40,41,51],rank:31,rapid:38,rare:8,rather:[5,7,8,11,16,34,51],raw:[7,18,25,26,27,28,30,31,37,39,41,44,51],rawmodel:[3,8],rbvi:3,reach:[0,28,29,32],read:[0,8,11,13,16,25,26,27,28,29,36,37,39,41,48,51],readabl:[0,8,13,20,51],readdunbrackfil:48,reader:[16,18],readi:[2,5,51],readm:[2,8,48],real:[8,13,37],realli:[1,2,8,11,16],reappear:16,reason:[8,16,20,32,34,52],rebas:16,rebuild:[2,8],recalcul:27,receiv:20,recent:[3,16],recip:[3,6],recipi:20,recoginz:49,recogn:[0,13],recognis:[1,8,16],recognit:38,recommend:[2,5,8,20,25,35],reconstruct:[0,3,8,18,21,22,25,30,32,35,44,47,49,52,54],reconstructcbetaposit:22,reconstructcstemoxygen:22,reconstructor:[32,35,36],reconstructoxygenposit:22,reconstructsidechain:[0,3,8,35,36],reconstructtest:8,record:[1,35],recreat:16,redistribut:20,redo:28,reduc:[3,25,28,35,41],reduced_scor:37,reducedscor:[35,37,42],redund:[24,31,33],ref_backbon:[23,26],ref_fil:8,refactor:3,refer:[1,4,8,18,19,21,22,23,25,26,28,34],referenc:8,refin:28,refine_thresh:28,refresh:31,regard:[20,32,44],region:[0,25,28,29,32,34,35,45,50],regist:[4,8],regress:38,regularli:5,reinterpret_cast:37,reintroduc:3,reject:[31,32,34],rel:[4,5,9,10,26,28,32,41],relat:[4,8,13,26,28,37,38,49],relax:[30,35],releas:[2,5,8,16],relev:[2,3,4,7,25,28,36,49],reli:5,remain:[20,30,34,35],rememb:[1,8,34],remodel:[28,31,36],remodel_cutoff:36,remov:[2,3,10,22,25,26,29,31,33,35,36,40,47,49],removecoordin:26,removeterminalgap:35,renumb:[26,35],reorder:35,reordergap:35,repeat:28,replac:[3,20,21,22,34,35],replacefrag:22,report:[1,3,8,35],reportmolprobityscor:33,repositori:[1,4,8,16,53],repres:[10,20,21,23,26,27,28,29,40,41,44,45,46,47,50,52,54],represent:[22,23,25,26,27,37,39,41,49,51],reproduc:[3,20,35],reproduct:20,repuls:49,request:[26,28,48,51],requir:[0,2,3,5,8,13,16,19,20,21,22,26,27,28,31,32,35,36,37,42,49,50,51],reread:26,res:[9,21,22,25,28,31,32,33,36,40,49,50,51],res_depth:26,res_idx:[49,50],res_index:21,res_indic:[21,25,36],res_list:[21,25,32,36],res_num:21,resembl:[16,28],reserv:11,reset:[10,21,25,32,34,40,49],resid:5,residu:[0,3,8,9,21,22,23,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,42,44,45,47,49,50,51],residue_depth:26,residue_index:[45,49,50],residue_list:35,residuedepth:26,residuehandl:[9,21,22,26,29,31,32,33,34,35,49,50,51],residuehandlelist:21,residueview:[33,35],resiz:[22,37],resnum:[21,22,29,31,35,36,40],resnum_on:40,resnum_rang:35,resnum_two:40,resolut:[22,32],resolv:[16,21,32,35],resolvecystein:44,resort:35,respect:[9,25,28,35],respons:[8,16,20],rest:[1,8,16,36],restor:[22,31,34,40],restraint:[26,32],restrict:[8,16,29],restructuredtext:[4,8],result:[0,2,3,8,10,20,25,27,28,31,32,33,34,35,36,38,44,51],resum:14,retain:[20,28,35],retriev:28,return_count:28,reus:[35,36],review:[16,53],revis:20,reviv:16,rewrit:1,richardson:38,ridig:36,right:[1,2,8,10,13,20],rigid:[0,3,30,32,34,36,46,47,49,51,52,54],rigid_frame_cutoff:36,rigidblock:28,rij:43,ring:[3,30,35],ring_punch_detect:35,risk:20,rmsd:[22,23,26,28,31,32],rmsd_cutoff:[26,31,32],rmsd_thresh:[26,28],rname:28,rnum:40,robot:38,role:13,root:[2,4,8,16],rosetta:41,rot:36,rot_constructor:47,rot_group:[47,50],rot_lib:50,rot_lib_entri:50,rota_out:33,rotam:[0,3,33,36,38,44,45,47,52,54],rotamer:[48,51],rotamer_group:[44,46,47],rotamer_id:47,rotamer_librari:[3,35,36,48],rotamer_model:36,rotamer_on:44,rotamer_res_indic:36,rotamer_two:44,rotamerconstructor:[3,47,49],rotamergraph:[36,46,47,52],rotamergroup:49,rotamerid:[47,50,51],rotamerlib:[35,36,37,48,50,51],rotamerlibentri:[50,51],rotat:[9,22],rotatearoundomegators:22,rotatearoundphipsitors:22,rotatearoundphitors:22,rotatearoundpsitors:22,rotationaroundlin:9,roughli:24,round:51,routin:[1,18,31],royalti:20,rrm:36,rrmrotam:[44,49,50],rrmrotamergroup:[44,46,49,50],rst1:4,rst2:4,rst:[4,8,16],rsync:8,rule:[5,8,9,16],run:[0,4,7,8,10,13,14,15,16,25,26,31,32,33,35,54],runact:1,runexitstatustest:1,runmolprob:33,runmolprobityent:33,runnabl:8,runner:1,runtest:[1,8],runtim:[0,3,10,12,35,50,54],runtimeerror:[9,10,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,44,45,48,49,50,51],runtimeexcept:27,s_id:26,s_vinaparticl:49,safe:[2,8],said:4,same:[0,1,2,4,7,8,10,13,14,20,21,25,26,28,31,32,33,34,35,36,37,39,40,41,42,45,48,49,50,51],samiti:35,sampl:[0,3,8,22,23,28,31,34,35,54],sampled_frag:34,samplemontecarlo:[3,34],sampler:[3,23,24,26,28,30,31,32,35],samplerbas:34,sampling_start_index:34,sander:38,saniti:2,sanity_check:2,satisfi:49,save:[16,22,25,26,27,28,31,34,37,39,40,41,51],savebb:26,savecach:28,savefig:27,savepdb:[7,18,21,22,25,26,28,30,31,32,34,35,36,47],saveport:[25,26,27,37,39,41,51],sc_data:32,sc_rec:[32,36],sc_rec_test:36,sc_result:32,scale:22,scatter:27,scheme:[1,8,13,21,26,29,34],schenk:38,schmidt:38,schwede:[5,8,18,19,38,53],sci:38,scicor:[5,8,18,19,53],scondari:35,scope:14,score:[0,3,8,13,19,23,26,28,29,30,33,34,35,36,37,38,39,41,44,47,54],score_contain:31,score_env:[31,34,42],score_threshold:44,score_vari:35,scorecontain:31,scorer:[3,17,28,30,31,35,40,42,54],scorer_env:[28,31,34],scorerbas:34,scoring_weight:28,scoringgapextend:[29,35],scoringweight:[28,31,35],scratch:[26,34],script:[2,3,4,7,11,13,16,17,18,26,28,37,48,54],scriptnam:11,scriptpath:8,scwrl3:[36,42,50],scwrl3disulfidscor:[43,44],scwrl3pairwisescor:43,scwrl3rotamerconstructor:50,scwrl4:[0,36,38,44,47,50],scwrl4particletyp:49,scwrl4rotamerconstructor:[3,47,50],scwrlrotamerconstructor:3,seamlessli:16,search:[0,2,3,8,21,26,28,31,33,35,36,41,44,49,50],search_kei:28,searchdb:[23,26],second:[8,10,22,25,26,28,31,32,35,39,40,41,43,44],secondari:[3,13,26,28,38,41],secondli:8,section:[1,4,7,17,20,53,54],see:[0,1,3,7,8,9,10,11,13,16,18,20,21,25,26,27,28,29,31,33,34,35,37,39,40,41,51],seed:[10,24,27,31,32,34],seem:16,segment:22,select:[3,10,26,28,34,35,36,47],selenium:35,self:[1,8,10,44,47,49],self_energi:[10,49],sell:20,send:11,sensibl:35,sensit:[3,28],sent:20,seok:38,separ:[1,3,8,10,20,25,27,35,39,41,44],seq:[13,21,23,26,28,29,31,35,40,42],seq_idx_on:28,seq_idx_two:28,seq_one_idx:28,seq_sep:[39,41],seq_tpl:[31,35],seq_trg:[31,35],seq_two_idx:28,seqid:[24,26,28],seqid_thresh:28,seqprof:13,seqr:[0,21,23,26,28,29,31,34,35,36,39,40,41],seqres_str:[21,32,36],seqsim:26,sequenc:[0,3,7,8,13,18,21,22,23,27,28,29,30,31,32,34,35,38,39,40,41],sequencefromchain:42,sequencehandl:[21,26,28,29,35,40],sequencelist:[21,35,40],sequenceprofil:26,sequenti:[22,35],ser:49,serial:[26,37],serializ:37,serin:49,serv:[1,13,26,28,31,34],server:28,servic:[16,20],set:[1,2,4,8,10,11,13,15,16,18,21,22,25,26,28,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51,52],setaa:22,setactivesubrotam:49,setallatomscoringkei:31,setaroundomegators:22,setaroundphipsitors:22,setaroundphitors:22,setaroundpsitors:22,setbackbonescoringkei:31,setbackrub:22,setboolprop:50,setc:22,setca:22,setcb:22,setcharg:25,setcompoundschemlib:[19,54],setcpuplatformsupport:25,setdefault:25,setdisulfidconnect:25,setenergi:[39,41],setenviron:[21,32,36,40],setepsilon:25,setfraggerhandl:35,setframeenergi:[47,49],setfudgelj:25,setfudgeqq:25,setinitialenviron:[21,31,32,34,36,40,42],setinternalconnect:25,setinternalenergi:49,setinternalenergyprefactor:49,setinterpol:51,setmass:25,setn:22,setnonbondedcutoff:32,seto:22,setolc:22,setpeptideboundconnect:25,setphitors:22,setpo:21,setprob:49,setpsipredpredict:[35,40,41],setpsitors:22,setresidu:21,setscor:41,setsequ:22,setsequenceoffset:35,setsequenceprofil:35,setsequenceprofilescoreskei:31,setsigma:25,setstemrmsdskei:31,setstructureprofil:26,setstructureprofilescoreskei:31,settemperatur:49,setup:[0,2,5,8,13,17,25,28,31,32,34,35,37,39,40,41,42],setupdefaultallatomscor:[31,35],setupdefaultbackbonescor:[31,35],setupsystem:25,setvinaweightgaussian1:49,setvinaweightgaussian2:49,setvinaweighthbond:49,setvinaweighthydrophob:49,setvinaweightrepuls:49,setweight:31,sever:[0,2,3,5,8,10,13,24,26,27,28,31,32,35,36,40,41,42,44,48,49,51,52],sg_pos_on:43,sg_pos_two:43,shake:34,shall:20,shanno:35,shapovalov2011:[38,48],shapovalov:38,share:[5,7,12,17,20,25,37,53,54],shared_ptr:37,shebang:8,sheet:35,shelenkov:38,shell:[1,2,7,8,11],shift:[22,26,29,35],shiftctermin:29,shiftextens:29,ship:[5,48],shorten:35,shorter:[28,35],shortest:31,shortli:8,should:[1,2,4,5,7,8,10,11,13,16,18,20,22,23,26,27,28,31,32,34,35,36,37,40,45,47,49],show:[1,8,13,14,31,34,47,50],show_fil:7,showcas:[1,21,25,27],shown:[8,14,35],shrink:22,shrug:38,side:[8,35,38],sidechain:[3,8,18,19,25,30,32,33,35,37,38,43,44,45,46,48,50,51,52,54],sidechain_pymod:8,sidechain_reconstructor:35,sidechain_rst:8,sidechain_test_data:8,sidechain_test_orig:36,sidechain_test_rec:36,sidechain_unit_test:8,sidechainparticl:50,sidechainreconstructiondata:[30,32],sidechainreconstructor:[25,30,32,35],sidenot:[26,36],sig1:51,sig2:51,sig3:51,sig4:51,sigma:25,silent:1,sim:25,similar:[1,2,3,13,16,23,26,28,40,41,51],similardihedr:51,similarli:[2,25,35],simpl:[0,9,22,26,28,34,35,39,40,41,49,51],simpler:[25,35],simplest:[5,8,30],simpli:[5,21,22,28,31,32,34,35,49,50,51],simplic:[23,26],simplif:13,simplifi:[3,22,25,26],simul:[10,25,31,32,34,35],sinc:[1,2,4,8,10,11,16,18,22,25,26,27,28,49],singl:[2,4,8,10,21,22,25,26,28,31,32,34,35,36,40,41,45,48,49,50,52],singleton:25,singular:[3,6,28,33,54],sink:37,sit:8,site:[3,5,8,28],size:[8,21,22,26,27,28,32,34,35,37,39,40,41],sizeof:37,skip:[0,1,8,16,26,28,35,50],slide:28,slight:35,slightli:35,slope:28,slow:37,slower:[18,25,26,27,35,39,41,51],small:[8,26,32,35,36],smaller:[22,26,28,32,35,41],smallest:47,smallish:[2,8],smart:16,smng:3,smooth:38,smtl:35,snippet:7,soding2005:[26,38],softsampl:34,softwar:[8,20,38,49],sol:47,sole:[1,16,20,28],soli:38,solis2006:[24,38],solut:[8,10,28,31,32,34,35,36,46,47],solv:[10,16,47,52],solvent:26,solventaccess:26,solver:3,some:[1,2,4,5,6,7,8,13,16,21,23,26,30,33,34,35,36,37,40,42,47,50,51],somedata:37,someth:[1,8,11,16,26],sometim:16,somewher:4,soon:[10,32,41,47,51],sort:[1,4,10,14,31,34,51],sound:[16,50],sourc:[1,2,4,8,13,16,18,19,20,26,28,31,32,33,35,37,51],source1:[4,16],source2:[4,16],source3:4,source4:4,source_chain_idx:35,source_mhandl:35,sp3:51,space:[3,10,28,34,38],span:35,sparticl:49,spatial:[8,28,42],spawn:[1,8],spdbv:35,spdbv_style:35,special:[1,2,4,8,20,25,34,49,50,51],specif:[1,3,8,20,25,26,27,28,31,34,38,40,47,48,49,51],specifi:[0,2,3,4,5,9,10,22,26,27,28,31,32,35,36,40,49,51],specimen:11,speed:[3,25,35,38],spent:[14,18],sphere:[43,49],sphinx:[2,8],spin:38,spit:[29,34],split:[28,42],sport:8,squar:26,src:[8,16],ss_agreement:41,ss_agreement_scor:37,ssagre:26,ssagreementscor:[37,42],sse:2,sstream:37,stabil:38,stabl:[5,16],stack:16,stage:[1,2,4,8,17,18,28,37,40,51],stai:[1,8,10,16,34],standalon:7,standard:[2,8,12,13,16,21,27,37,41,51],start:[0,1,2,4,7,10,14,16,17,19,21,22,25,26,28,29,31,32,34,35,36,40,41,42,54],start_idx:31,start_resnum:[21,22,26,31,34,35,36,39,40,41],start_resnum_list:36,start_rnum:40,start_temperatur:[10,34],starter:1,startscop:14,stash:[16,31,34,40],state:[1,2,8,20,21,26,31,34,40,41,44,49,51],statement:20,staticruntimeprofil:14,statist:[14,26,38],statu:[1,8],std:37,stderr:1,stdout:1,steadili:[10,34],steepest:[32,35],stem:[9,22,25,26,28,29,31,32,34,35,36],stemcoord:9,stempairorient:9,step:[3,8,10,14,16,18,19,28,29,30,31,32,34,40,44],stereo:35,stereo_chemical_problem_backbon:35,stereochem:[3,35],steric:51,still:[8,14,25,26,35,37],stop:[1,8,14,28,29,32],stop_criterion:32,stoppag:20,storabl:26,storag:[3,8,21,25,28,39,41],store:[0,1,3,7,8,9,16,18,21,22,25,26,27,28,29,31,32,34,35,36,37,47],stori:8,str:[1,11,13,14,15,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,51],str_len:37,straight:16,strategi:51,stream:37,stretch:[21,26,28,31,34,35,40,41],strict:16,strictli:3,string:[0,3,11,13,26,27,29,37],stringstream:37,strip:[0,35],struc:5,struct:[5,26,37],struct_db:23,structral:[21,40],structur:[0,3,8,13,17,18,19,21,22,23,24,25,27,28,29,30,31,33,34,35,36,37,38,40,41,42,47,49,50,52,54],structural_db:31,structuralgap:[29,33],structuralgaplist:[29,35],structure_db:[26,28,31,35,37],structure_db_on:26,structure_db_two:26,structure_dir:26,structure_id:26,structure_path:26,structure_sourc:13,structuredb:[3,13,24,26,28,31,35,37],structuredbdatatyp:26,structureprofil:26,studer:38,stuff:[26,39],style:[35,40,41,49],sub:[8,26],sub_frag:22,sub_res_list:26,subclass:[8,13],subdir:8,subfold:8,subject:[8,20],sublicens:20,submiss:20,submit:20,submodul:8,submodule1:16,subpart:28,subrotam:[0,3,44,47,49,50,54],subrotameroptim:[36,52],subsequ:[10,20,22,35,49],subset:[0,13,25,26,28,31,32,35,36],subst:26,subst_matrix:26,substitut:26,substweightmatrix:26,subtre:[4,8],succeed:29,success:[10,11,34],successfulli:5,sudo:7,suffici:26,suffix:11,sugar:6,suggest:[5,8,43],suit:[1,8,26],sulfur:[43,44,49,50],sum:[14,28,29,35,36,43,44,49],sum_:10,sum_i:10,sum_ie_:10,summari:[14,26],superpos:[22,26,28,31,32,34],superpose_stem:22,superposed_rmsd:[22,31],superposeonto:22,superposit:[3,28,31,34],superpost:28,supersed:20,supervis:1,support:[0,1,2,3,8,11,13,18,20,25,32,35],suppos:[16,34],sure:[2,7,8,13,16,26],surfac:26,surotam:49,surprisingli:50,surround:[25,26,32,36,39,41],swap_thresh:[],symmetr:[26,40,51],symmetri:[39,41],sync:8,syntax:20,sys:[1,13,32],system:[1,2,4,8,16,20,23,26,32,42,54],t_sampler:27,tabl:26,tag:5,tail:22,tailor:[21,35],take:[8,10,21,26,27,28,31,32,34,35,37,41,44,50,52],taken:[0,21,25,32,34,50],talk:1,target:[0,1,2,4,8,13,18,26,28,30,31,32,34,35,40,49],target_chain_idx:35,target_mhandl:35,target_pdb:33,target_posit:28,target_sequ:26,task:[8,16,32,35,37,40],techniqu:[10,38],tell:[1,8,11,13,16,26],temperatur:[10,31,34,49],templat:[0,1,3,13,18,28,30,35,37,40],temporari:[26,35],temporarili:16,term:[8,20,26,49,51,52],termin:[0,1,9,11,18,20,21,22,25,29,31,32,34,35,36,50],terminal_len:34,terminal_seqr:34,termini:[0,3,29,34,35],terminu:[26,34,35],test:[2,7,12,16,17,18,25,26,33,37],test_:8,test_act:[8,17],test_action_:1,test_action_do_awesom:1,test_action_help:1,test_awesome_featur:8,test_check_io:37,test_cod:8,test_doctest:8,test_foo:4,test_portable_binari:37,test_reconstruct_sidechain:8,test_sidechain_reconstruct:8,test_submodule1:16,test_suite_:4,test_suite_your_module_run:8,test_your_modul:16,testcas:[1,8],testcasenam:8,testexit0:1,testpmexist:1,testreconstruct:8,testutil:[1,8],text:[1,13,20,35],than:[4,8,13,14,16,21,22,26,28,31,32,33,35,36,41,44,50],thats:[26,41],thei:[2,5,8,16,21,22,25,26,27,28,31,32,33,34,35,44,49,50,51,53],them:[4,8,16,22,25,26,27,28,29,31,35,36,40,45],themselv:25,theoret:34,theori:[20,38],therefor:[5,8,22,24,26,28,32,34,35,51],thereof:[20,25],thi:[0,1,2,3,4,5,7,8,10,11,12,13,14,15,16,17,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,42,44,47,49,50,51,52,54],thing:[1,2,8,16,26,28,35,51],think:10,third:[16,17,20,31,32],thoroughli:16,those:[0,1,2,4,8,10,13,16,20,25,28,31,35,36,37,39,41,47,50,51],though:[25,35,37],thr:49,thread:[18,25,35,38],three:[1,4,16,21,22,27,28,31,33,34,38,41,49,51],threonin:49,thresh:[22,49,51],threshold:[10,26,28,32,33,35,36,40,51],through:[1,8,9,20,22,26,29,35,39,41],throughout:[13,16,24,25],thrown:26,thu:[5,11,33,49],tidi:16,tightli:16,time:[1,5,8,13,14,16,18,28,35],timer:14,tini:[16,35],titl:[20,27],tlc:[21,49],tlc_an:21,tlctorotid:[47,49],tmp_buf:37,todens:22,toentiti:[7,18,21,22,25,26,32,34,36],toframeresidu:49,togeth:[8,16,26,44],toler:35,tolerance_lbfg:35,tolerance_sd:35,too:[13,16,31,32,35,37],tool:[3,4,23,35,37,42,47],toolbox:16,top:[2,6,8,14,15,16,28,32,35],topic:[1,8,16],topn:28,topolog:[25,32],torrmrotam:49,torsion:[0,13,21,22,23,24,26,28,31,32,34,35,41,47],torsion_angl:47,torsion_bin:41,torsion_plot:27,torsion_sampl:[22,26,31,32,34,35,37],torsion_sampler_coil:[28,37],torsion_sampler_extend:[28,37],torsion_sampler_hel:37,torsion_sampler_helix:28,torsion_sampler_list:26,torsion_scor:37,torsionprob:26,torsionsampl:[22,24,26,27,28,31,32,34,35,37,41],torsionscor:[35,37,42],tort:20,total:[10,14,26,28],touch:[1,8,25,32],toward:[0,3,8,13,26,28,29,32,35,39,41,47,49,50,52],tpl:[0,28,30,31,35],tpl_n:28,tpr:[49,51],trace:35,track:[3,11,20,30,35,47],trade:20,trademark:20,tradition:11,trail:0,train:[24,31,35],trajectori:[28,34],tran:[22,49,51],transfer:[20,28],transfer_bfactor:28,transform:[9,20,22,28,34,35,51],translat:[4,8,20,26,49,51],transomegators:22,treat:[3,8,25,28,35,36,37,51],treatment:50,tree:[1,4,8,10,16,46,47],treepack:3,treesolv:[10,36,47],trg:[0,13,31,35],trg_seq:28,tri:[10,28,29,35,44,51],triangl:28,trick:[1,7,16],trigger:[1,4,8,48],tripeptid:27,tripl:11,triplet:[23,28,34,41],trott2010:[38,49],trott:38,trp:[33,49,51],trustworthi:16,tryptophan:49,ttccpsivarsnfnvcrlpgtpea:[31,35],ttccpsivarsnfnvcrlpgtpeaicatgytciiipgatcpgdyan:35,ttccpsivarsnfnvcrlpgtpeaicatytgciiipgatcpgdyan:[31,35],tupl:[9,10,11,22,25,26,28,29,33,35,36,44],turn:[0,1,11,14,16,35],tutori:8,tweak:35,twice:[14,40],two:[1,7,8,10,16,21,22,25,26,28,29,31,32,35,36,37,39,40,41,43,44,47,49,51],txt:[1,2,4,8,16,20],type:[0,1,8,9,10,11,13,14,20,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,47,48,49,50,52],typedef:37,typenam:37,typic:[22,28,34,35,47,51],tyr:[33,49,51],tyrosin:49,ucsf:3,uint32_t:37,uint:37,ultra:26,uncertain:8,uncharg:50,unclos:35,undefin:25,under:[4,8,20],undergo:[28,32,34,36],underli:[28,29,31,49],underscor:1,understand:16,understood:0,undo:10,unexpect:2,unfavor:[22,32],unfavour:[32,34,44],unfortun:16,unhandl:[0,13],uniba:[5,8,18,19,53],uniform:32,union:20,uniprot:28,uniprot_ac:28,uniprotac:28,uniqu:[0,13,28,31,34,51],unique_pentam:28,unit:[2,16,17,37],unittest:[1,8,16],univers:[8,53],unix:16,unknown:25,unless:[13,20,21,22,25,31,39,41],unlik:47,unrecognis:11,unset:[21,25,36],unsupport:[13,37],until:[8,10,28,32,35,40,50],untouch:22,untrack:1,unum:28,unus:16,upat:5,updat:[3,5,7,8,16,21,25,28,29,31,32,35,36,40,42],updatedistribut:27,updateposit:[25,32],upon:[26,32,34],upper:28,ups:3,urei:25,urey_bradley_angl:25,usabl:16,usag:[0,3,10,13,24,26,31,32,36],use:[0,2,3,4,5,8,10,13,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,37,47,48,49,50],use_amber_ff:35,use_bbdep_lib:36,use_frm:36,use_full_extend:35,use_scoring_extend:35,used:[0,2,3,4,8,9,10,11,13,14,15,16,18,21,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,42,45,47,48,49,50],useful:[1,3,8,10,11,22,26,28,30,31,32,35,50],user:[1,5,8,19,28,53],userlevel:1,uses:[5,8,10,22,25,27,28],using:[1,2,3,4,7,8,10,18,20,21,22,25,26,28,31,33,34,35,37,38,39,41,44,45,46,47,49,50,51,54],usr:[2,5,7,8],usual:[1,2,4,8,13,14,16,22,31,35,39],util:18,utilis:[8,16],v_size:37,val:[27,49],valid:[0,10,16,22,26,29,34,35,36,48,51],valin:49,valu:[2,10,11,13,21,22,25,26,28,31,33,34,35,37,39,40,41,44,47,49,50,51,52],valueerror:[28,35],vanish:40,varadarajan:38,vari:[4,37],variabl:[1,2,3,8,14,18,25,33,35,37,49],varianc:33,variant:[25,31],variou:[1,2,4,16,30],vec3:[9,21,22,26,32,33,43,44,49],vec3list:[28,49],vector:[25,27,28,31,37,49],verbal:20,verbos:1,veri:[1,8,11,16,25,28,35,37],verif:13,verifi:[1,11,16],version:[2,3,5,8,16,20,26,28,35,37,48,49],vertic:28,via:[1,5,8,13,15,25],view:[7,13,16,27,35,40],vina:[3,36,38,50],vinaparticletyp:[49,50],vinarotamerconstructor:50,virtual:8,visibl:36,vision:38,visual:18,volum:5,wai:[1,2,4,5,8,16,22,23,25,28,31,41,47,49],wait:8,walk:[1,8],want:[1,2,3,8,15,16,22,26,28,31,32,35,40,49,50,51,52,53],warn:[3,8,16,35],warranti:20,watch:8,web:[2,8],weight:[3,26,28,31,34,35,39,41,49],weird:[28,32,47],well:[0,4,16,21,27,28,29,31,35,37,41,47,50,51],went:[0,8],were:[16,26,31,35],wester:38,wether:10,what:[1,8,11,13,16,23,26,36,40],when:[1,3,4,5,8,10,13,14,21,22,25,26,27,28,29,31,34,35,36,37,38,40,41,44,47,48,49,50,51],whenev:[8,21,31,40],where:[0,1,3,4,5,8,10,11,13,14,16,20,21,22,25,26,27,28,31,35,37,39,40,41,48,49,50,51],wherea:26,wherev:20,whether:[3,5,8,10,11,13,20,22,25,26,31,32,34,35,36,39,40,41,49,50,51],which:[0,1,2,4,8,9,11,12,13,16,18,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,50,51],whistl:8,whitespac:0,who:[10,47],whole:[1,2,8,16,20,22,26,28,35,49],whom:20,why:[1,16],width:[10,37,47],wild:4,window:28,window_length:28,wise:4,wish:[2,17,27,35],with_aa:31,with_db:31,within:[2,3,4,8,14,16,20,21,25,28,29,33,35,36,39,41,51],without:[0,1,3,4,8,11,13,20,25,29,32,35,40,51],wolfson:[28,38],won:[0,35,36,50],word:4,work:[1,2,4,5,7,8,14,16,18,20,25,29,35,37,50],worldwid:20,worst:16,worth:53,would:[1,2,8,11,22,26,27,35,44,49],wrap:26,wrapper:[1,4,8,15,35],write:[0,17,20,26,27,32,37,39,41,51],writebasetyp:37,writemagicnumb:37,writetypes:37,writeversionnumb:37,written:[8,20,28,37],wrong:[2,13],wwpdb:5,www:[3,20],x_1:10,x_2:10,x_i:10,x_j:10,x_n:10,xlabel:27,xlim:27,xml:8,xxx:[22,49],xxx_num_atom:21,xxx_num_hydrogen:21,year:1,yet:[26,31,35],ylabel:27,ylim:27,you:[0,1,2,3,4,5,7,8,10,11,13,14,15,16,18,20,21,22,23,25,26,27,28,30,31,32,33,34,35,36,37,39,40,41,47,48,49,50,51,52,53],your:[1,2,4,5,13,14,16,17,18,20,22,26,28,35,37,48],your_modul:[8,16],yourself:[2,8,10,16,35,50],yyyi:20,zero:[0,26,28,35,51],zhou2005:[26,38],zhou:38,zip:[26,47]},titles:["ProMod3 Actions","<code class=\"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 Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal notranslate\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal notranslate\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"docutils literal notranslate\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],For:[4,11,17,54],Into:32,The:[1,5,7,16,21,22,26,27,31,35,36,45,49,50,51],Using:[2,37],With:33,acid:[21,25,27],action:[0,1,4,5,8],actiontestcas:1,afdb:28,algorithm:28,align:35,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,app:7,argument:13,atom:[21,32,39],avail:7,backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:[1,5],exisit:37,extend:29,featur:[8,26],fiddl:35,file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:5,instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:[33,51],novo:[28,34],object:[24,34,45],optim:52,ost:25,other:43,output:1,own:[5,8],pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],planar:33,pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,5,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,registri:5,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}}) \ No newline at end of file +Search.setIndex({docnames:["actions/index","actions/index_dev","buildsystem","changelog","cmake/index","container/docker","container/index","container/singularity","contributing","core/geometry","core/graph_minimizer","core/helper","core/index","core/pm3argparse","core/runtime_profiling","core/setcompoundschemlib","dev_setup","developers","gettingstarted","index","license","loop/all_atom","loop/backbone","loop/index","loop/load_loop_objects","loop/mm_system_creation","loop/structure_db","loop/torsion_sampler","modelling/algorithms","modelling/gap_handling","modelling/index","modelling/loop_candidates","modelling/loop_closing","modelling/model_checking","modelling/monte_carlo","modelling/pipeline","modelling/sidechain_reconstruction","portableIO","references","scoring/all_atom_scorers","scoring/backbone_score_env","scoring/backbone_scorers","scoring/index","scoring/other_scoring_functions","sidechain/disulfid","sidechain/frame","sidechain/graph","sidechain/index","sidechain/loading","sidechain/rotamer","sidechain/rotamer_constructor","sidechain/rotamer_lib","sidechain/subrotamer_optimizer","user_contributions","users"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":1,sphinx:55},filenames:["actions/index.rst","actions/index_dev.rst","buildsystem.rst","changelog.rst","cmake/index.rst","container/docker.rst","container/index.rst","container/singularity.rst","contributing.rst","core/geometry.rst","core/graph_minimizer.rst","core/helper.rst","core/index.rst","core/pm3argparse.rst","core/runtime_profiling.rst","core/setcompoundschemlib.rst","dev_setup.rst","developers.rst","gettingstarted.rst","index.rst","license.rst","loop/all_atom.rst","loop/backbone.rst","loop/index.rst","loop/load_loop_objects.rst","loop/mm_system_creation.rst","loop/structure_db.rst","loop/torsion_sampler.rst","modelling/algorithms.rst","modelling/gap_handling.rst","modelling/index.rst","modelling/loop_candidates.rst","modelling/loop_closing.rst","modelling/model_checking.rst","modelling/monte_carlo.rst","modelling/pipeline.rst","modelling/sidechain_reconstruction.rst","portableIO.rst","references.rst","scoring/all_atom_scorers.rst","scoring/backbone_score_env.rst","scoring/backbone_scorers.rst","scoring/index.rst","scoring/other_scoring_functions.rst","sidechain/disulfid.rst","sidechain/frame.rst","sidechain/graph.rst","sidechain/index.rst","sidechain/loading.rst","sidechain/rotamer.rst","sidechain/rotamer_constructor.rst","sidechain/rotamer_lib.rst","sidechain/subrotamer_optimizer.rst","user_contributions.rst","users.rst"],objects:{"":{"--backbone-independent":[0,7,1,"cmdoption-i"],"--energy_function":[0,7,1,"cmdoption-f"],"--keep-sidechains":[0,7,1,"cmdoption-k"],"--no-disulfids":[0,7,1,"cmdoption-n"],"--no-subrotamer-optimization":[0,7,1,"cmdoption-s"],"--rigid-rotamers":[0,7,1,"cmdoption-r"],"-f":[0,7,1,"cmdoption-f"],"-i":[0,7,1,"cmdoption-i"],"-k":[0,7,1,"cmdoption-k"],"-n":[0,7,1,"cmdoption-n"],"-r":[0,7,1,"cmdoption-r"],"-s":[0,7,1,"cmdoption-s"],"command:add_doc_dependency":[4,0,1,""],"command:add_doc_source":[4,0,1,""],"command:convert_module_data":[4,0,1,""],"command:module":[4,0,1,""],"command:pm_action":[4,0,1,""],"command:promod3_unittest":[4,0,1,""],"command:pymod":[4,0,1,""],test_actions:[1,2,0,"-"]},"promod3.core":{ConstructAtomPos:[9,1,1,""],ConstructCBetaPos:[9,1,1,""],ConstructCTerminalOxygens:[9,1,1,""],EvaluateGromacsPosRule:[9,1,1,""],GraphMinimizer:[10,3,1,""],RotationAroundLine:[9,1,1,""],StaticRuntimeProfiler:[14,3,1,""],StemCoords:[9,3,1,""],StemPairOrientation:[9,3,1,""],helper:[11,2,0,"-"],pm3argparse:[13,2,0,"-"]},"promod3.core.GraphMinimizer":{AStarSolve:[10,4,1,""],AddEdge:[10,4,1,""],AddNode:[10,4,1,""],ApplyDEE:[10,4,1,""],ApplyEdgeDecomposition:[10,4,1,""],MCSolve:[10,4,1,""],NaiveSolve:[10,4,1,""],Prune:[10,4,1,""],Reset:[10,4,1,""],TreeSolve:[10,4,1,""]},"promod3.core.StaticRuntimeProfiler":{Clear:[14,5,1,""],IsEnabled:[14,5,1,""],PrintSummary:[14,5,1,""],Start:[14,5,1,""],StartScoped:[14,5,1,""],Stop:[14,5,1,""]},"promod3.core.StemCoords":{c_coord:[9,6,1,""],ca_coord:[9,6,1,""],n_coord:[9,6,1,""]},"promod3.core.StemPairOrientation":{angle_four:[9,6,1,""],angle_one:[9,6,1,""],angle_three:[9,6,1,""],angle_two:[9,6,1,""],distance:[9,6,1,""]},"promod3.core.helper":{FileExists:[11,1,1,""],FileExtension:[11,1,1,""],FileGzip:[11,1,1,""],MsgErrorAndExit:[11,1,1,""]},"promod3.core.pm3argparse":{PM3ArgumentParser:[13,3,1,""]},"promod3.core.pm3argparse.PM3ArgumentParser":{AddAlignment:[13,4,1,""],AddFragments:[13,4,1,""],AddProfile:[13,4,1,""],AddStructure:[13,4,1,""],AssembleParser:[13,4,1,""],Parse:[13,4,1,""],__init__:[13,4,1,""],action:[13,6,1,""]},"promod3.loop":{AllAtomEnv:[21,3,1,""],AllAtomEnvPositions:[21,3,1,""],AllAtomPositions:[21,3,1,""],AminoAcidAtom:[21,3,1,""],AminoAcidHydrogen:[21,3,1,""],AminoAcidLookup:[21,3,1,""],BackboneList:[22,3,1,""],CoordInfo:[26,3,1,""],ForcefieldAminoAcid:[25,3,1,""],ForcefieldBondInfo:[25,3,1,""],ForcefieldConnectivity:[25,3,1,""],ForcefieldHarmonicAngleInfo:[25,3,1,""],ForcefieldHarmonicImproperInfo:[25,3,1,""],ForcefieldLJPairInfo:[25,3,1,""],ForcefieldLookup:[25,3,1,""],ForcefieldPeriodicDihedralInfo:[25,3,1,""],ForcefieldUreyBradleyAngleInfo:[25,3,1,""],FragDB:[26,3,1,""],Fragger:[26,3,1,""],FraggerMap:[26,3,1,""],FragmentInfo:[26,3,1,""],LoadFragDB:[24,4,1,""],LoadStructureDB:[24,4,1,""],LoadTorsionSampler:[24,4,1,""],LoadTorsionSamplerCoil:[24,4,1,""],LoadTorsionSamplerExtended:[24,4,1,""],LoadTorsionSamplerHelical:[24,4,1,""],MmSystemCreator:[25,3,1,""],PsipredPrediction:[26,3,1,""],StructureDB:[26,3,1,""],StructureDBDataType:[26,3,1,""],TorsionSampler:[27,3,1,""]},"promod3.loop.AllAtomEnv":{ClearEnvironment:[21,4,1,""],GetAllAtomPositions:[21,4,1,""],GetEnvironment:[21,4,1,""],GetSeqres:[21,4,1,""],SetEnvironment:[21,4,1,""],SetInitialEnvironment:[21,4,1,""]},"promod3.loop.AllAtomEnvPositions":{all_pos:[21,6,1,""],res_indices:[21,6,1,""]},"promod3.loop.AllAtomPositions":{AllAtomPositions:[21,4,1,""],ClearPos:[21,4,1,""],ClearResidue:[21,4,1,""],Copy:[21,4,1,""],Extract:[21,4,1,""],ExtractBackbone:[21,4,1,""],GetAA:[21,4,1,""],GetFirstIndex:[21,4,1,""],GetIndex:[21,4,1,""],GetLastIndex:[21,4,1,""],GetNumAtoms:[21,4,1,""],GetNumResidues:[21,4,1,""],GetOmegaTorsion:[21,4,1,""],GetPhiTorsion:[21,4,1,""],GetPos:[21,4,1,""],GetPsiTorsion:[21,4,1,""],GetSequence:[21,4,1,""],InsertInto:[21,4,1,""],IsAllSet:[21,4,1,""],IsAnySet:[21,4,1,""],IsSet:[21,4,1,""],SetPos:[21,4,1,""],SetResidue:[21,4,1,""],ToEntity:[21,4,1,""]},"promod3.loop.AminoAcidLookup":{GetAA:[21,5,1,""],GetAAA:[21,5,1,""],GetAAH:[21,5,1,""],GetAnchorAtomIndex:[21,5,1,""],GetAtomName:[21,5,1,""],GetAtomNameAmber:[21,5,1,""],GetAtomNameCharmm:[21,5,1,""],GetElement:[21,5,1,""],GetH1Index:[21,5,1,""],GetH2Index:[21,5,1,""],GetH3Index:[21,5,1,""],GetHNIndex:[21,5,1,""],GetHydrogenIndex:[21,5,1,""],GetIndex:[21,5,1,""],GetMaxNumAtoms:[21,5,1,""],GetMaxNumHydrogens:[21,5,1,""],GetNumAtoms:[21,5,1,""],GetNumHydrogens:[21,5,1,""],GetOLC:[21,5,1,""]},"promod3.loop.BackboneList":{ApplyTransform:[22,4,1,""],BackboneList:[22,4,1,""],CARMSD:[22,4,1,""],Copy:[22,4,1,""],Extract:[22,4,1,""],GetAA:[22,4,1,""],GetBounds:[22,4,1,""],GetC:[22,4,1,""],GetCA:[22,4,1,""],GetCB:[22,4,1,""],GetN:[22,4,1,""],GetO:[22,4,1,""],GetOLC:[22,4,1,""],GetOmegaTorsion:[22,4,1,""],GetPhiTorsion:[22,4,1,""],GetPsiTorsion:[22,4,1,""],GetSequence:[22,4,1,""],GetTransform:[22,4,1,""],InsertInto:[22,4,1,""],MinCADistance:[22,4,1,""],RMSD:[22,4,1,""],ReconstructCBetaPositions:[22,4,1,""],ReconstructCStemOxygen:[22,4,1,""],ReconstructOxygenPositions:[22,4,1,""],ReplaceFragment:[22,4,1,""],RotateAroundOmegaTorsion:[22,4,1,""],RotateAroundPhiPsiTorsion:[22,4,1,""],RotateAroundPhiTorsion:[22,4,1,""],RotateAroundPsiTorsion:[22,4,1,""],Set:[22,4,1,""],SetAA:[22,4,1,""],SetAroundOmegaTorsion:[22,4,1,""],SetAroundPhiPsiTorsion:[22,4,1,""],SetAroundPhiTorsion:[22,4,1,""],SetAroundPsiTorsion:[22,4,1,""],SetBackrub:[22,4,1,""],SetC:[22,4,1,""],SetCA:[22,4,1,""],SetCB:[22,4,1,""],SetN:[22,4,1,""],SetO:[22,4,1,""],SetOLC:[22,4,1,""],SetSequence:[22,4,1,""],SuperposeOnto:[22,4,1,""],ToDensity:[22,4,1,""],ToEntity:[22,4,1,""],TransOmegaTorsions:[22,4,1,""],__len__:[22,4,1,""],append:[22,4,1,""],clear:[22,4,1,""],empty:[22,4,1,""],resize:[22,4,1,""]},"promod3.loop.CoordInfo":{chain_name:[26,6,1,""],id:[26,6,1,""],offset:[26,6,1,""],shift:[26,6,1,""],size:[26,6,1,""],start_resnum:[26,6,1,""]},"promod3.loop.ForcefieldBondInfo":{bond_length:[25,6,1,""],force_constant:[25,6,1,""],index_one:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldConnectivity":{harmonic_angles:[25,6,1,""],harmonic_bonds:[25,6,1,""],harmonic_impropers:[25,6,1,""],lj_pairs:[25,6,1,""],periodic_dihedrals:[25,6,1,""],periodic_impropers:[25,6,1,""],urey_bradley_angles:[25,6,1,""]},"promod3.loop.ForcefieldHarmonicAngleInfo":{angle:[25,6,1,""],force_constant:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldHarmonicImproperInfo":{angle:[25,6,1,""],force_constant:[25,6,1,""],index_four:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.ForcefieldLJPairInfo":{epsilon:[25,6,1,""],index_one:[25,6,1,""],index_two:[25,6,1,""],sigma:[25,6,1,""]},"promod3.loop.ForcefieldLookup":{GetAA:[25,4,1,""],GetCharges:[25,4,1,""],GetDefault:[25,5,1,""],GetDisulfidConnectivity:[25,4,1,""],GetEpsilons:[25,4,1,""],GetFudgeLJ:[25,4,1,""],GetFudgeQQ:[25,4,1,""],GetHeavyIndex:[25,4,1,""],GetHydrogenIndex:[25,4,1,""],GetInternalConnectivity:[25,4,1,""],GetMasses:[25,4,1,""],GetNumAtoms:[25,4,1,""],GetOXTIndex:[25,4,1,""],GetPeptideBoundConnectivity:[25,4,1,""],GetSigmas:[25,4,1,""],Load:[25,5,1,""],LoadCHARMM:[25,5,1,""],LoadPortable:[25,5,1,""],Save:[25,4,1,""],SavePortable:[25,4,1,""],SetCharges:[25,4,1,""],SetDefault:[25,5,1,""],SetDisulfidConnectivity:[25,4,1,""],SetEpsilons:[25,4,1,""],SetFudgeLJ:[25,4,1,""],SetFudgeQQ:[25,4,1,""],SetInternalConnectivity:[25,4,1,""],SetMasses:[25,4,1,""],SetPeptideBoundConnectivity:[25,4,1,""],SetSigmas:[25,4,1,""]},"promod3.loop.ForcefieldPeriodicDihedralInfo":{force_constant:[25,6,1,""],index_four:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""],multiplicity:[25,6,1,""],phase:[25,6,1,""]},"promod3.loop.ForcefieldUreyBradleyAngleInfo":{angle:[25,6,1,""],angle_force_constant:[25,6,1,""],bond_force_constant:[25,6,1,""],bond_length:[25,6,1,""],index_one:[25,6,1,""],index_three:[25,6,1,""],index_two:[25,6,1,""]},"promod3.loop.FragDB":{AddFragments:[26,4,1,""],GetAngularBinSize:[26,4,1,""],GetDistBinSize:[26,4,1,""],GetNumFragments:[26,4,1,""],GetNumStemPairs:[26,4,1,""],HasFragLength:[26,4,1,""],Load:[26,5,1,""],LoadPortable:[26,5,1,""],MaxFragLength:[26,4,1,""],PrintStatistics:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SearchDB:[26,4,1,""]},"promod3.loop.Fragger":{AddSSAgreeParameters:[26,4,1,""],AddSeqIDParameters:[26,4,1,""],AddSeqSimParameters:[26,4,1,""],AddSequenceProfileParameters:[26,4,1,""],AddStructureProfileParameters:[26,4,1,""],AddTorsionProbabilityParameters:[26,4,1,""],Fill:[26,4,1,""],GetFragmentInfo:[26,4,1,""],GetScore:[26,4,1,""],__getitem__:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.FraggerMap":{Contains:[26,4,1,""],Load:[26,4,1,""],LoadBB:[26,4,1,""],Save:[26,4,1,""],SaveBB:[26,4,1,""],__getitem__:[26,4,1,""],__setitem__:[26,4,1,""]},"promod3.loop.FragmentInfo":{chain_index:[26,6,1,""],length:[26,6,1,""],offset:[26,6,1,""]},"promod3.loop.MmSystemCreator":{ExtractLoopPositions:[25,4,1,""],GetCpuPlatformSupport:[25,4,1,""],GetDisulfidBridges:[25,4,1,""],GetForcefieldAminoAcids:[25,4,1,""],GetIndexing:[25,4,1,""],GetLoopLengths:[25,4,1,""],GetLoopStartIndices:[25,4,1,""],GetNumLoopResidues:[25,4,1,""],GetNumResidues:[25,4,1,""],GetSimulation:[25,4,1,""],SetCpuPlatformSupport:[25,4,1,""],SetupSystem:[25,4,1,""],UpdatePositions:[25,4,1,""]},"promod3.loop.PsipredPrediction":{Add:[26,4,1,""],Extract:[26,4,1,""],FromHHM:[26,4,1,""],FromHoriz:[26,4,1,""],GetConfidence:[26,4,1,""],GetConfidences:[26,4,1,""],GetPrediction:[26,4,1,""],GetPredictions:[26,4,1,""],PsipredPrediction:[26,4,1,""],__len__:[26,4,1,""]},"promod3.loop.StructureDB":{AddCoordinates:[26,4,1,""],GenerateStructureProfile:[26,4,1,""],GetBackboneList:[26,4,1,""],GetCoordIdx:[26,4,1,""],GetCoordInfo:[26,4,1,""],GetDSSPStates:[26,4,1,""],GetDihedralAngles:[26,4,1,""],GetNumCoords:[26,4,1,""],GetResidueDepths:[26,4,1,""],GetSequence:[26,4,1,""],GetSequenceProfile:[26,4,1,""],GetSolventAccessibilitites:[26,4,1,""],GetStructureProfile:[26,4,1,""],GetSubDB:[26,4,1,""],HasData:[26,4,1,""],Load:[26,5,1,""],LoadPortable:[26,5,1,""],PrintStatistics:[26,4,1,""],RemoveCoordinates:[26,4,1,""],Save:[26,4,1,""],SavePortable:[26,4,1,""],SetStructureProfile:[26,4,1,""]},"promod3.loop.TorsionSampler":{Draw:[27,4,1,""],DrawPhiGivenPsi:[27,4,1,""],DrawPsiGivenPhi:[27,4,1,""],ExtractStatistics:[27,4,1,""],GetBinSize:[27,4,1,""],GetBinsPerDimension:[27,4,1,""],GetHistogramIndex:[27,4,1,""],GetHistogramIndices:[27,4,1,""],GetPhiProbabilityGivenPsi:[27,4,1,""],GetProbability:[27,4,1,""],GetPsiProbabilityGivenPhi:[27,4,1,""],Load:[27,5,1,""],LoadPortable:[27,5,1,""],Save:[27,4,1,""],SavePortable:[27,4,1,""],UpdateDistributions:[27,4,1,""]},"promod3.modelling":{AFDBModel:[28,1,1,""],AFDBTPLSearch:[28,1,1,""],AddModellingIssue:[35,1,1,""],AllAtomRelaxer:[32,3,1,""],BackboneRelaxer:[32,3,1,""],BuildFromRawModel:[35,1,1,""],BuildRawModel:[35,1,1,""],BuildSidechains:[35,1,1,""],CCD:[32,3,1,""],CCDCloser:[34,3,1,""],CTerminalCloser:[34,3,1,""],CheckFinalModel:[35,1,1,""],ClearGaps:[29,1,1,""],CloseGaps:[35,1,1,""],CloseLargeDeletions:[35,1,1,""],CloseSmallDeletions:[35,1,1,""],CloserBase:[34,3,1,""],CoolerBase:[34,3,1,""],CountEnclosedGaps:[29,1,1,""],CountEnclosedInsertions:[29,1,1,""],DeNovoCloser:[34,3,1,""],DeleteGapCols:[35,1,1,""],DirtyCCDCloser:[34,3,1,""],ExponentialCooler:[34,3,1,""],FSStructureServer:[28,3,1,""],FillLoopsByDatabase:[35,1,1,""],FillLoopsByMonteCarlo:[35,1,1,""],FilterCandidates:[33,1,1,""],FilterCandidatesWithSC:[33,1,1,""],FindMotifs:[28,4,1,""],FraggerHandle:[28,3,1,""],FragmentSampler:[34,3,1,""],FullGapExtender:[29,3,1,""],GapExtender:[29,3,1,""],GenerateDeNovoTrajectories:[28,1,1,""],GetNonPlanarRings:[33,1,1,""],GetRingPunches:[33,1,1,""],GetRings:[33,1,1,""],HasNonPlanarRings:[33,1,1,""],HasRingPunches:[33,1,1,""],InsertLoop:[35,1,1,""],InsertLoopClearGaps:[29,1,1,""],IsAllAtomScoringSetUp:[35,1,1,""],IsBackboneScoringSetUp:[35,1,1,""],KIC:[32,3,1,""],KICCloser:[34,3,1,""],LinearScorer:[34,3,1,""],LoopCandidates:[31,3,1,""],MergeGaps:[29,1,1,""],MergeGapsByDistance:[35,1,1,""],MergeMHandle:[35,1,1,""],MinimizeModelEnergy:[35,1,1,""],ModelTermini:[35,1,1,""],ModellingHandle:[35,3,1,""],ModellingIssue:[35,3,1,""],MotifMatch:[28,3,1,""],MotifQuery:[28,3,1,""],NTerminalCloser:[34,3,1,""],PentaMatch:[28,3,1,""],PhiPsiSampler:[34,3,1,""],PullTerminalDeletions:[35,1,1,""],ReconstructSidechains:[36,1,1,""],RemoveTerminalGaps:[35,1,1,""],ReorderGaps:[35,1,1,""],ReportMolProbityScores:[33,1,1,""],RigidBlocks:[28,4,1,""],RunMolProbity:[33,1,1,""],RunMolProbityEntity:[33,1,1,""],SampleMonteCarlo:[34,1,1,""],SamplerBase:[34,3,1,""],ScoreContainer:[31,3,1,""],ScorerBase:[34,3,1,""],ScoringGapExtender:[29,3,1,""],ScoringWeights:[31,3,1,""],SetFraggerHandles:[35,1,1,""],SetPsipredPredictions:[35,1,1,""],SetSequenceProfiles:[35,1,1,""],SetupDefaultAllAtomScoring:[35,1,1,""],SetupDefaultBackboneScoring:[35,1,1,""],ShiftExtension:[29,3,1,""],SidechainReconstructionData:[36,3,1,""],SidechainReconstructor:[36,3,1,""],SoftSampler:[34,3,1,""],StructuralGap:[29,3,1,""],StructuralGapList:[29,3,1,""]},"promod3.modelling.AllAtomRelaxer":{GetSystemCreator:[32,4,1,""],Run:[32,4,1,""],UpdatePositions:[32,4,1,""]},"promod3.modelling.BackboneRelaxer":{AddCARestraint:[32,4,1,""],AddCBRestraint:[32,4,1,""],AddCRestraint:[32,4,1,""],AddNRestraint:[32,4,1,""],AddORestraint:[32,4,1,""],GetNonBondedCutoff:[32,4,1,""],Run:[32,4,1,""],SetNonBondedCutoff:[32,4,1,""]},"promod3.modelling.CCD":{CCD:[32,4,1,""],Close:[32,4,1,""]},"promod3.modelling.CCDCloser":{Close:[34,4,1,""]},"promod3.modelling.CTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.CloserBase":{Close:[34,4,1,""]},"promod3.modelling.CoolerBase":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.DeNovoCloser":{Close:[34,4,1,""]},"promod3.modelling.DirtyCCDCloser":{Close:[34,4,1,""]},"promod3.modelling.ExponentialCooler":{GetTemperature:[34,4,1,""],Reset:[34,4,1,""]},"promod3.modelling.FSStructureServer":{FromDataChunks:[28,5,1,""],GetIdx:[28,4,1,""],GetOMF:[28,4,1,""],GetOMFByIdx:[28,4,1,""],chunk:[28,6,1,""],data:[28,6,1,""],indexer:[28,6,1,""],length:[28,6,1,""],n_entries:[28,6,1,""],pos:[28,6,1,""],search_keys:[28,6,1,""]},"promod3.modelling.FraggerHandle":{Get:[28,4,1,""],GetList:[28,4,1,""],LoadCached:[28,4,1,""],SaveCached:[28,4,1,""]},"promod3.modelling.FragmentSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.FullGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.GapExtender":{Extend:[29,4,1,""]},"promod3.modelling.KIC":{Close:[32,4,1,""],KIC:[32,4,1,""]},"promod3.modelling.KICCloser":{Close:[34,4,1,""]},"promod3.modelling.LinearScorer":{GetScore:[34,4,1,""]},"promod3.modelling.LoopCandidates":{Add:[31,4,1,""],AddFragmentInfo:[31,4,1,""],ApplyCCD:[31,4,1,""],ApplyKIC:[31,4,1,""],CalculateAllAtomScores:[31,4,1,""],CalculateBackboneScores:[31,4,1,""],CalculateSequenceProfileScores:[31,4,1,""],CalculateStemRMSDs:[31,4,1,""],CalculateStructureProfileScores:[31,4,1,""],Extract:[31,4,1,""],FillFromDatabase:[31,5,1,""],FillFromMonteCarloSampler:[31,5,1,""],GetClusteredCandidates:[31,4,1,""],GetClusters:[31,4,1,""],GetFragmentInfo:[31,4,1,""],GetLargestCluster:[31,4,1,""],GetSequence:[31,4,1,""],HasFragmentInfos:[31,4,1,""],Remove:[31,4,1,""]},"promod3.modelling.ModellingHandle":{Copy:[35,4,1,""],all_atom_scorer:[35,6,1,""],all_atom_scorer_env:[35,6,1,""],all_atom_sidechain_env:[35,6,1,""],backbone_scorer:[35,6,1,""],backbone_scorer_env:[35,6,1,""],fragger_handles:[35,6,1,""],gaps:[35,6,1,""],model:[35,6,1,""],modelling_issues:[35,6,1,""],profiles:[35,6,1,""],psipred_predictions:[35,6,1,""],seqres:[35,6,1,""],sidechain_reconstructor:[35,6,1,""]},"promod3.modelling.ModellingIssue":{Severity:[35,3,1,""],is_major:[35,4,1,""],residue_list:[35,6,1,""],severity:[35,6,1,""],text:[35,6,1,""]},"promod3.modelling.ModellingIssue.Severity":{MAJOR:[35,6,1,""],MINOR:[35,6,1,""]},"promod3.modelling.MotifMatch":{alignment:[28,6,1,""],mat:[28,6,1,""],query_idx:[28,6,1,""]},"promod3.modelling.MotifQuery":{GetIdentifiers:[28,4,1,""],GetN:[28,4,1,""],GetPositions:[28,4,1,""],Load:[28,5,1,""],Save:[28,4,1,""]},"promod3.modelling.NTerminalCloser":{Close:[34,4,1,""]},"promod3.modelling.PentaMatch":{FromSeqList:[28,5,1,""],N:[28,6,1,""],TopN:[28,4,1,""],indexer:[28,6,1,""],length:[28,6,1,""],pos:[28,6,1,""]},"promod3.modelling.PhiPsiSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.SamplerBase":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.ScoreContainer":{Contains:[31,4,1,""],Copy:[31,4,1,""],Extend:[31,4,1,""],Extract:[31,4,1,""],Get:[31,4,1,""],GetNumCandidates:[31,4,1,""],IsEmpty:[31,4,1,""],LinearCombine:[31,4,1,""],Set:[31,4,1,""]},"promod3.modelling.ScorerBase":{GetScore:[34,4,1,""]},"promod3.modelling.ScoringGapExtender":{Extend:[29,4,1,""]},"promod3.modelling.ScoringWeights":{GetAllAtomScoringKeys:[31,5,1,""],GetAllAtomWeights:[31,5,1,""],GetBackboneScoringKeys:[31,5,1,""],GetBackboneWeights:[31,5,1,""],GetSequenceProfileScoresKey:[31,5,1,""],GetStemRMSDsKey:[31,5,1,""],GetStructureProfileScoresKey:[31,5,1,""],GetWeights:[31,5,1,""],SetAllAtomScoringKeys:[31,5,1,""],SetBackboneScoringKeys:[31,5,1,""],SetSequenceProfileScoresKey:[31,5,1,""],SetStemRMSDsKey:[31,5,1,""],SetStructureProfileScoresKey:[31,5,1,""],SetWeights:[31,5,1,""]},"promod3.modelling.ShiftExtension":{Extend:[29,4,1,""]},"promod3.modelling.SidechainReconstructionData":{disulfid_bridges:[36,6,1,""],env_pos:[36,6,1,""],is_c_ter:[36,6,1,""],is_n_ter:[36,6,1,""],loop_lengths:[36,6,1,""],loop_start_indices:[36,6,1,""],rotamer_res_indices:[36,6,1,""]},"promod3.modelling.SidechainReconstructor":{AttachEnvironment:[36,4,1,""],Reconstruct:[36,4,1,""]},"promod3.modelling.SoftSampler":{Initialize:[34,4,1,""],ProposeStep:[34,4,1,""]},"promod3.modelling.StructuralGap":{Copy:[29,4,1,""],ExtendAtCTerm:[29,4,1,""],ExtendAtNTerm:[29,4,1,""],GetChain:[29,4,1,""],GetChainIndex:[29,4,1,""],GetChainName:[29,4,1,""],GetLength:[29,4,1,""],IsCTerminal:[29,4,1,""],IsNTerminal:[29,4,1,""],IsTerminal:[29,4,1,""],ShiftCTerminal:[29,4,1,""],after:[29,6,1,""],before:[29,6,1,""],full_seq:[29,6,1,""],length:[29,6,1,""],seq:[29,6,1,""]},"promod3.scoring":{AllAtomClashScorer:[39,3,1,""],AllAtomInteractionScorer:[39,3,1,""],AllAtomOverallScorer:[39,3,1,""],AllAtomPackingScorer:[39,3,1,""],AllAtomScorer:[39,3,1,""],BackboneOverallScorer:[41,3,1,""],BackboneScoreEnv:[40,3,1,""],BackboneScorer:[41,3,1,""],CBPackingScorer:[41,3,1,""],CBetaScorer:[41,3,1,""],ClashScorer:[41,3,1,""],ConstraintFunction:[40,3,1,""],ContactFunction:[40,3,1,""],DiscoContainer:[40,3,1,""],HBondScorer:[41,3,1,""],LoadAllAtomInteractionScorer:[39,1,1,""],LoadAllAtomPackingScorer:[39,1,1,""],LoadCBPackingScorer:[41,1,1,""],LoadCBetaScorer:[41,1,1,""],LoadDefaultAllAtomOverallScorer:[39,1,1,""],LoadDefaultBackboneOverallScorer:[41,1,1,""],LoadHBondScorer:[41,1,1,""],LoadReducedScorer:[41,1,1,""],LoadSSAgreementScorer:[41,1,1,""],LoadTorsionScorer:[41,1,1,""],PairwiseFunction:[40,3,1,""],PairwiseFunctionType:[40,3,1,""],PairwiseScorer:[41,3,1,""],ReducedScorer:[41,3,1,""],SCWRL3DisulfidScore:[43,4,1,""],SCWRL3PairwiseScore:[43,4,1,""],SSAgreementScorer:[41,3,1,""],TorsionScorer:[41,3,1,""]},"promod3.scoring.AllAtomClashScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""]},"promod3.scoring.AllAtomInteractionScorer":{DoExternalScores:[39,4,1,""],DoInternalScores:[39,4,1,""],DoNormalize:[39,4,1,""],Load:[39,5,1,""],LoadPortable:[39,5,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomOverallScorer":{AttachEnvironment:[39,4,1,""],CalculateLinearCombination:[39,4,1,""],Contains:[39,4,1,""],Get:[39,4,1,""],__getitem__:[39,4,1,""],__setitem__:[39,4,1,""]},"promod3.scoring.AllAtomPackingScorer":{DoNormalize:[39,4,1,""],Load:[39,5,1,""],LoadPortable:[39,5,1,""],Save:[39,4,1,""],SavePortable:[39,4,1,""],SetEnergy:[39,4,1,""]},"promod3.scoring.AllAtomScorer":{AttachEnvironment:[39,4,1,""],CalculateScore:[39,4,1,""],CalculateScoreProfile:[39,4,1,""]},"promod3.scoring.BackboneOverallScorer":{AttachEnvironment:[41,4,1,""],Calculate:[41,4,1,""],CalculateLinearCombination:[41,4,1,""],Contains:[41,4,1,""],Get:[41,4,1,""],__getitem__:[41,4,1,""],__setitem__:[41,4,1,""]},"promod3.scoring.BackboneScoreEnv":{AddPairwiseFunction:[40,4,1,""],ApplyPairwiseFunction:[40,4,1,""],ClearEnvironment:[40,4,1,""],Copy:[40,4,1,""],GetSeqres:[40,4,1,""],Pop:[40,4,1,""],SetEnvironment:[40,4,1,""],SetInitialEnvironment:[40,4,1,""],SetPsipredPrediction:[40,4,1,""],Stash:[40,4,1,""]},"promod3.scoring.BackboneScorer":{AttachEnvironment:[41,4,1,""],CalculateScore:[41,4,1,""],CalculateScoreProfile:[41,4,1,""]},"promod3.scoring.CBPackingScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.CBetaScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.ClashScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.DiscoContainer":{AddStructuralInfo:[40,1,1,""],AttachConstraints:[40,1,1,""]},"promod3.scoring.HBondScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.PairwiseFunction":{Score:[40,4,1,""]},"promod3.scoring.PairwiseScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""]},"promod3.scoring.ReducedScorer":{DoExternalScores:[41,4,1,""],DoInternalScores:[41,4,1,""],DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.scoring.SSAgreementScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetScore:[41,4,1,""]},"promod3.scoring.TorsionScorer":{DoNormalize:[41,4,1,""],Load:[41,5,1,""],LoadPortable:[41,5,1,""],Save:[41,4,1,""],SavePortable:[41,4,1,""],SetEnergy:[41,4,1,""]},"promod3.sidechain":{AAToRotID:[49,4,1,""],BBDepRotamerLib:[51,3,1,""],CreateSCWRL3Particle:[49,4,1,""],CreateSCWRL4Particle:[49,4,1,""],CreateVINAParticle:[49,4,1,""],DihedralConfiguration:[51,3,1,""],DisulfidScore:[44,4,1,""],FRMRotamer:[49,3,1,""],FRMRotamerGroup:[49,3,1,""],Frame:[45,3,1,""],FrameResidue:[45,3,1,""],GetDihedralConfiguration:[51,4,1,""],GetRotamericConfiguration:[51,4,1,""],GetVINAWeightGaussian1:[49,4,1,""],GetVINAWeightGaussian2:[49,4,1,""],GetVINAWeightHBond:[49,4,1,""],GetVINAWeightHydrophobic:[49,4,1,""],GetVINAWeightRepulsion:[49,4,1,""],LoadBBDepLib:[48,4,1,""],LoadLib:[48,4,1,""],PScoringFunction:[49,3,1,""],Particle:[49,3,1,""],RRMRotamer:[49,3,1,""],RRMRotamerGroup:[49,3,1,""],ReadDunbrackFile:[48,4,1,""],ResolveCysteins:[44,4,1,""],RotamerConstructor:[50,3,1,""],RotamerGraph:[46,3,1,""],RotamerID:[49,3,1,""],RotamerLib:[51,3,1,""],RotamerLibEntry:[51,3,1,""],SCWRL3RotamerConstructor:[50,3,1,""],SCWRL4ParticleType:[49,3,1,""],SCWRL4RotamerConstructor:[50,3,1,""],SetVINAWeightGaussian1:[49,4,1,""],SetVINAWeightGaussian2:[49,4,1,""],SetVINAWeightHBond:[49,4,1,""],SetVINAWeightHydrophobic:[49,4,1,""],SetVINAWeightRepulsion:[49,4,1,""],SubrotamerOptimizer:[52,4,1,""],TLCToRotID:[49,4,1,""],VINAParticleType:[49,3,1,""],VINARotamerConstructor:[50,3,1,""]},"promod3.sidechain.BBDepRotamerLib":{AddRotamer:[51,4,1,""],Load:[51,5,1,""],LoadPortable:[51,5,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""],SetInterpolate:[51,4,1,""]},"promod3.sidechain.FRMRotamer":{AddFrameEnergy:[49,4,1,""],AddSubrotamerDefinition:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetActiveSubrotamer:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetNumSubrotamers:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],GetSubrotamerDefinition:[49,4,1,""],GetTemperature:[49,4,1,""],SetActiveSubrotamer:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],SetTemperature:[49,4,1,""],ToFrameResidue:[49,4,1,""],ToRRMRotamer:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.FrameResidue":{__getitem__:[45,4,1,""],__len__:[45,4,1,""]},"promod3.sidechain.Particle":{GetCollisionDistance:[49,4,1,""],GetName:[49,4,1,""],GetPos:[49,4,1,""],GetScoringFunction:[49,4,1,""],PairwiseScore:[49,4,1,""]},"promod3.sidechain.RRMRotamer":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],GetFrameEnergy:[49,4,1,""],GetInternalEnergy:[49,4,1,""],GetInternalEnergyPrefactor:[49,4,1,""],GetProbability:[49,4,1,""],GetSelfEnergy:[49,4,1,""],SetFrameEnergy:[49,4,1,""],SetInternalEnergy:[49,4,1,""],SetInternalEnergyPrefactor:[49,4,1,""],SetProbability:[49,4,1,""],ToFrameResidue:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RRMRotamerGroup":{AddFrameEnergy:[49,4,1,""],ApplyOnResidue:[49,4,1,""],ApplySelfEnergyThresh:[49,4,1,""],Merge:[49,4,1,""],SetFrameEnergy:[49,4,1,""],__getitem__:[49,4,1,""],__len__:[49,4,1,""]},"promod3.sidechain.RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructBackboneFrameResidue:[50,4,1,""],ConstructRRMRotamerGroup:[50,4,1,""],ConstructSidechainFrameResidue:[50,4,1,""]},"promod3.sidechain.RotamerGraph":{CreateFromFRMList:[46,5,1,""],CreateFromRRMList:[46,5,1,""]},"promod3.sidechain.RotamerLib":{AddRotamer:[51,4,1,""],Load:[51,5,1,""],LoadPortable:[51,5,1,""],MakeStatic:[51,4,1,""],QueryLib:[51,4,1,""],Save:[51,4,1,""],SavePortable:[51,4,1,""]},"promod3.sidechain.RotamerLibEntry":{FromResidue:[51,5,1,""],IsSimilar:[51,4,1,""],SimilarDihedral:[51,4,1,""],chi1:[51,6,1,""],chi2:[51,6,1,""],chi3:[51,6,1,""],chi4:[51,6,1,""],probability:[51,6,1,""],sig1:[51,6,1,""],sig2:[51,6,1,""],sig3:[51,6,1,""],sig4:[51,6,1,""]},"promod3.sidechain.SCWRL3RotamerConstructor":{AssignInternalEnergies:[50,4,1,""]},"promod3.sidechain.SCWRL4RotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFrameResidue:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""]},"promod3.sidechain.VINARotamerConstructor":{AssignInternalEnergies:[50,4,1,""],ConstructFRMRotamerHeuristic:[50,4,1,""],ConstructFrameResidueHeuristic:[50,4,1,""],ConstructRRMRotamerHeuristic:[50,4,1,""]},"test_actions.ActionTestCase":{RunAction:[1,4,1,""],RunExitStatusTest:[1,4,1,""],pm_action:[1,6,1,""],pm_bin:[1,6,1,""],testPMExists:[1,4,1,""]},promod3:{SetCompoundsChemlib:[15,1,1,""],core:[12,2,0,"-"],loop:[23,2,0,"-"],modelling:[30,2,0,"-"],scoring:[42,2,0,"-"],sidechain:[47,2,0,"-"]},test_actions:{ActionTestCase:[1,3,1,""]}},objnames:{"0":["cmake","command","CMake command"],"1":["py","function","Python function"],"2":["py","module","Python module"],"3":["py","class","Python class"],"4":["py","method","Python method"],"5":["py","staticmethod","Python static method"],"6":["py","attribute","Python attribute"],"7":["std","cmdoption","program option"]},objtypes:{"0":"cmake:command","1":"py:function","2":"py:module","3":"py:class","4":"py:method","5":"py:staticmethod","6":"py:attribute","7":"std:cmdoption"},terms:{"0288eced23a9a541a88005a7ed30b8f019e06226":3,"10a":36,"1ake":28,"1aki":26,"1crn":[21,23,25,26,30,31,32,34,35,36,42,47],"1crn_cut":[30,31,35],"1crna":[26,31],"1e2q":28,"1ey":8,"1eye_rec":8,"1ko5":28,"20a":36,"214e6":3,"2e6":28,"2iyw":28,"2jlp":0,"30a":36,"3x3":9,"4tb":3,"655a":26,"abstract":[34,50],"boolean":[11,13,35],"break":[3,4,8,16],"byte":[10,28,37],"case":[0,1,5,8,13,16,22,26,27,28,29,32,34,35,36,37,41,44,47,49,50,51],"catch":26,"char":[22,37],"class":[0,1,3,5,8,9,10,12,13,14,17,20,23,25,28,30,32,34,35,37,42,45,46,49,50,51],"const":37,"default":[0,1,2,3,4,5,8,10,13,14,15,18,21,22,25,26,27,28,30,31,32,33,34,36,39,41,47,49,50],"enum":[26,49],"export":[8,21],"final":[8,18,26,28,30,31,35,40,42,44,46,47,49],"float":[9,10,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,49,50,51,52],"function":[0,1,3,8,10,13,14,15,16,17,19,21,22,25,26,28,30,31,32,33,34,35,37,38,39,41,42,44,46,47,51,54],"import":[0,1,5,7,8,11,13,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,42,47,49,50],"int":[1,9,10,11,14,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,45,49,50,51,52],"long":35,"new":[1,3,7,8,13,16,17,21,22,25,26,28,29,31,32,34,35,36,37,38,47,49],"null":26,"public":[8,37,49],"return":[1,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,44,45,48,49,50,51],"s\u00f6ding":38,"short":[8,16,35,37],"static":[8,14,21,25,26,27,28,31,36,37,39,41,46,48,51],"super":47,"switch":[8,16,40],"throw":[1,37,47,48],"true":[1,11,13,14,21,22,23,25,26,28,29,31,32,33,34,35,36,37,39,41,44,47,50],"try":[1,8,18,29,35,37,51],"void":37,"while":[1,4,8,14,20,21,25,35,37,49],AND:[20,39,41,50],Added:3,Adding:[3,4],And:26,But:[1,4,8,16,28,35,50],CYS:[25,36,49,51],FOR:20,For:[1,2,5,8,12,13,16,18,20,21,25,26,28,31,34,35,36,37,40,41,44,49,50,51],HIS:[21,25,33,49,51],Has:4,IDs:49,ILE:[27,49],Into:[30,54],Its:[4,16,19],LYS:49,NOT:5,Not:20,One:[16,21,22,26,28,35,40,44,49,52],RMS:33,Res:[21,31,34,35,39,40,41],That:[0,1,4,8,11,13,16,26,28,41],Thats:52,The:[0,2,3,4,8,10,11,13,14,17,18,19,20,23,24,25,28,29,30,32,33,34,37,38,39,40,41,42,43,44,46,47,48,52,54],Then:[4,8,11,35],There:[1,4,5,8,10,13,16,25,26,27,34,39,41,48,49],These:[1,2,4,26,28,29,34,35],USE:20,Use:[0,4,25,26,27,35,39,41,51],Used:[31,35],Useful:[21,25,36],Uses:[31,35],Using:[4,17,25,54],Will:35,With:[8,30,35,51],__doc__:[11,13],__getitem__:[26,39,41,45,49],__init__:[1,8,13,16],__len__:[22,26,45,49],__main__:[1,8],__name__:[1,8],__setitem__:[26,39,41],_data:37,_name:4,_run:[1,4],_xml:4,a3m:[0,13],a3mtoprofil:[0,13],aa1:41,aa2:41,aa_aft:26,aa_befor:26,aa_clash:[35,39],aa_interact:[35,39],aa_pack:[35,39],aa_packing_scor:37,aa_relax_test:32,aa_res_idx:50,aa_scor:37,aa_with_rotam:47,aaa1:39,aaa2:39,aaa:[21,39],aaaaaaaa:22,aaaaggggggggggggggggggggaaaaaa:35,aafrequ:26,aafrequenciesstruct:26,aah:21,aatorotid:49,abcd:35,abcdef:35,abcdefghi:35,abcdefghij:35,abcdefghijklmnopqrstuvwxyz0123456789abcdefghijklmnopqrstuvwxyz:35,abil:16,abl:[2,8,35],abort:[8,10,32,35],about:[1,4,8,10,26,28,35],abov:[0,1,5,8,13,16,20,22,29,31,33,35,37,49,51],absolut:[4,5,34],academ:8,accept:[10,13,20,31,32,34,35,36,37],acceptor:[41,49,50],access:[4,5,8,21,22,26,27,28,31,35,39,40,41,49],accessor:26,accord:[0,5,10,16,21,22,25,26,27,28,29,31,34,35,36,39,44,47,49,50,51],accordingli:[26,40],account:[8,53],accumul:28,accur:28,accuraci:[0,28,35,38],achiev:[10,16],acid:[22,23,24,26,28,32,35,36,41,43,46,47,49,51],acknowledg:8,across:[1,51],act:[20,32],acta:38,action:[3,7,13,16,17,18,19,32,54],action_nam:16,action_unit_test:1,actiontest:1,actiontestcas:8,activ:[13,14,16,35,44,49,52],active_internal_energi:52,actual:[3,8,13,16,22,26,28,34,35,36,40,41,42,50,51],actual_posit:34,actual_step:34,adapt:[3,8,25,26,32,34,35,38],add:[1,2,4,6,8,10,13,18,20,21,26,27,28,31,32,35,36,39,40,41,44,47,49,50,53],add_argu:11,add_custom_target:8,add_doc_depend:4,add_doc_sourc:[4,8],add_flag:28,add_subdirectori:8,addalign:13,addcarestraint:32,addcbrestraint:32,addcoordin:26,addcrestraint:32,added:[0,4,8,10,13,21,22,26,28,29,31,33,35,36,39,40,41,49,50,51],addedg:10,addendum:20,addfrag:[13,26],addfragmentinfo:31,addframeenergi:49,addharmonicangl:25,addharmonicbond:25,addharmonicimprop:25,adding:[0,2,4,8,13,14,16,26,45],addit:[3,4,11,13,14,16,20,22,23,25,26,28,33,35,37],addition:[1,4,16,21,25,26,28],addljpair:25,addmodellingissu:35,addnod:10,addnrestraint:32,addorestraint:32,addpairwisefunct:40,addperiodicdihedr:25,addperiodicimprop:25,addprofil:13,addresidu:28,address:37,addrotam:51,addseqidparamet:26,addseqsimparamet:[23,26],addsequenceprofileparamet:26,addssagreeparamet:26,addstructur:13,addstructuralinfo:40,addstructureprofileparamet:26,addsubrotamerdefinit:49,addtorsionprobabilityparamet:26,addureybradleyangl:25,admir:8,advanc:28,advantag:25,advic:[8,16],advis:20,afdb:[3,30],afdb_frag:28,afdb_model:28,afdb_vers:28,afdbmodel:28,afdbtplsearch:28,afdptplsearch:[],affect:[8,22,35,49,50],after:[1,2,4,5,8,10,13,16,21,22,25,26,27,29,31,32,34,35,37,40,51],after_c_stem:22,afterward:[8,26,35],again:[2,3,8,26,28,50],against:[20,28,39],agg:27,agglom:31,ago:1,agre:20,agreement:[13,20,26,28,41],agress:[2,10],aim:19,ala:[22,27,32,47,49,50,51],ala_cb:21,ala_h1:21,ala_h:21,alanin:[3,49],alg:[23,26,28,35],algorithm:[3,10,19,22,23,26,30,31,32,33,34,35,38,42,43,46,47,49,54],alia:29,align:[0,3,13,18,26,28,30,38,40],alignedcuboid:22,alignmenthandl:[28,35,40],alignmentlist:[0,13,35],all:[0,1,2,3,4,7,8,10,13,14,16,18,19,20,22,23,25,26,27,28,29,30,31,33,34,35,36,37,40,41,42,44,45,47,48,49,50,51,52,54],all_atom:[21,22,25,49],all_atom_env:21,all_atom_po:[21,50],all_atom_scor:35,all_atom_scorer_env:35,all_atom_sidechain_env:35,all_po:[21,25,32],all_scor:31,allatom:[32,35,36],allatomclashscor:[35,42],allatomenv:[23,32,35,36,39],allatomenvposit:[23,36],allatominteractionscor:[35,37,42],allatomoverallscor:[31,35,42],allatompackingscor:[35,37,42],allatomposit:[23,25,49,50],allatomrelax:[25,32],allatomscor:42,alleg:20,alloc:26,allow:[0,2,3,5,8,11,16,22,26,27,28,31,34,35,37,39,41,46,51],allow_multitempl:13,allow_prepro_ci:22,almost:[4,32,35],aln:[0,28,30,31,35,40],aln_preprocess:35,aln_sourc:13,alon:[11,20],along:[1,8,20],alongsid:20,alot:8,alpha:[9,22,41,47],alpha_bin:41,alreadi:[1,4,8,10,16,22,25,26,28,31,35,36,39,40,41,49,50,51,52],also:[1,2,3,4,8,11,16,20,26,27,28,31,32,33,34,35,36,44,45,46,50,51],alter:[31,34],altern:[4,5,8,31,34,35,48,50],alwai:[0,1,8,16,29,34,35,37],amber:[21,35],ambig:51,ambigu:[0,13,51],amino:[22,23,24,26,28,32,35,36,41,43,46,47,49,51],aminoacid:[21,22,25,27,41,49,51],aminoacidatom:[21,39],aminoacidhydrogen:21,aminoacidlookup:[21,25],among:31,amount:[3,18,28,51],analog:28,analysi:[32,33,38],analyt:[31,51],anchor:[9,21,35],ancient:[3,15],angl:[0,9,21,22,23,25,26,31,32,33,34,35,41,47,50,51,54],angle_bin:41,angle_bin_s:26,angle_force_const:25,angle_four:9,angle_on:9,angle_thre:9,angle_two:9,angstrom:[26,32],ani:[0,1,4,5,8,10,13,14,15,18,20,21,22,25,26,27,28,29,31,33,34,35,36,37,39,40,41,45,47,49,50],anneal:[10,31,34],annot:20,announc:[1,8],anoth:[4,14,22,29,32,35,36,44],anymor:[3,10,28,35],anyon:[8,16],anyth:[0,2,5,8,13,14,15,28,31,32,36,39,41],anywai:8,anywher:16,apach:[3,20],apart:[1,31,35,36,39,41],api:[8,17],appear:20,append:[0,13,22,26,27,28,35,47],appendix:20,appli:[3,7,10,11,15,16,20,22,26,28,29,31,32,34,35,36,38,40,44,47,49,51],applic:[1,20,32,50],applyccd:31,applyde:10,applyedgedecomposit:10,applyk:31,applylbfg:35,applyonresidu:[47,49],applypairwisefunct:[40,41],applysd:[25,35],applyselfenergythresh:[47,49],applytransform:[22,28],approach:[0,2,10,26,28,35,37,44,47,50],appropri:[10,20,27,28,35,37,50],approx:35,approxim:25,arbitrari:[3,7,21,26,44],arbitrarili:34,archiv:20,arendal:38,arg:[1,4,13,49],arg_ca:21,arg_hd3:21,arg_sorted_scor:31,arginin:49,argpars:13,argument:[0,1,2,4,11,12,34,40],argumentpars:13,argv:13,aris:20,around:[1,4,8,9,16,22,31,32,35,39,40,41,51],arrai:[0,8,37],arrang:28,artifici:26,ascend:29,ask:8,asn:[49,51],asn_c:21,asn_hb2:21,asp:[21,49,51],asp_ha:21,asp_o:21,asparagin:49,aspart:[49,51],ass:34,assembl:13,assemblepars:13,assert:20,assertequ:8,assess:[39,40],assign:[3,10,22,26,31,34,39,41,50,52],assigninternalenergi:50,assignsecstruct:35,associ:[20,26,29,45],assum:[1,4,5,8,20,25,26,32,35,37,40,41,44,50],assur:44,astar:3,astarsolv:10,atom:[3,8,9,22,23,25,26,28,30,31,33,35,36,40,41,42,44,45,49,50,51,54],atom_idx:[21,25],atom_nam:[21,25],atomhandl:50,atomseq:35,atp:28,atp_at:28,atp_idx:28,atp_list:28,atp_r:28,atp_sel:28,atp_view:28,attach:[0,4,8,13,20,21,25,28,29,31,35,36,39,40,41,42],attach_view:13,attachconstraint:40,attachenviron:[31,32,34,36,39,41,42],attachview:[30,31,35],attent:[1,16],attribut:[8,13,20,26,35,36,51],aug2022:3,author:20,authorship:20,autodock:[38,49],autom:[2,4],automat:[1,8,10,11,14,16,26,30,31,37,50,51],automatis:8,avaibl:50,avail:[1,2,3,5,8,15,16,18,20,25,26,28,31,34,35,40,47,49],availab:20,availabl:8,averag:[31,40,44],avg:26,avg_sampling_per_posit:28,avoid:[0,3,6,11,13,15,26,28,32,34],awai:[16,28,36],awar:[0,3,8,35,50],awesom:[1,8],axi:[9,22],back:[1,16,25,34],backbon:[0,3,7,9,18,21,22,26,27,28,29,30,31,34,35,36,38,42,45,47,48,49,50,54],backbone_scor:35,backbone_scorer_env:35,backbonelist:[7,18,21,23,26,28,29,31,32,34,35,40],backboneoverallscor:[28,31,34,35,42],backbonerelax:[32,35],backbonescor:[8,42],backbonescoreenv:[8,28,31,34,35,41,42],backbonescoreenvlisten:8,background:[2,36],backrub:[22,38],backward:[2,3,37],bad:[25,35],bare:26,base:[0,3,4,5,9,11,13,19,20,22,23,27,28,31,32,34,35,37,38,40,42,47,49,50,51],base_target:4,baseclass:47,basel:[8,53],bashrc:8,basi:[4,8,16,20,28,32,33,34,48],basic:[1,2,8,11,16,27,28,34,35,47,51],bb_dep_lib:37,bb_list:[7,18,21,22,23,26,29,31,32,34,35,40],bb_list_on:28,bb_list_two:28,bb_score:31,bbdeprotamerlib:[35,36,37,48,50,51],bcde:35,becaus:[8,16,21,28,35,40],becom:[10,35,51],been:[2,3,10,16,20,24,26,28,31,32,35,39,41,44,51],befor:[0,1,4,7,8,13,16,22,25,26,27,29,31,32,34,35,36,37,50],begin:[1,8,21,22,28,34,40],behalf:20,behav:[1,51],behaviour:[0,13,39,40,49,50,51],behind:8,being:[3,5,8,10,21,26,28,31,34,35,44,51],believ:53,bell:8,belong:[3,4,16,21,22,26,29,31,34,35,36,39,40,41,45,49,50],belov:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,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],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:[1,3,4,8,11,13,28,35,36,42,46,51],command:[0,1,7,8,11,12,16,18,54],commandlin:13,comment:[16,20],commerci:[8,20],commit:[3,8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib:50,compar:[3,8,22,23,26,31,32,51],comparison:[35,38,51],compat:[2,3,16,25,37],compensatori:22,compil:[1,2,3,4,8,14,16,18,20,37,54],complain:1,complaint:16,complet:[14,16,22,25,32,34,35,36,51],complex:[8,16,36,44,49,52],compli:20,complianc:20,complib_dir_contain:[5,7],complib_dir_localhost:[5,7],compon:[5,7,10,15,26,33,41,50],compound:[3,15,50],compoundlib:[5,50],compress:[3,11,26,28],comput:[3,8,19,20,28,31,33,38,39,41],concaten:21,concept:8,concern:8,condit:[8,20,27],conf:[2,8],confid:[26,41],config:[4,8],config_head:4,configur:[2,3,8,10,16,20,31,47],conflict:16,conform:[26,32,34,38,46,51],connect:[4,5,7,10,16,21,25,26,31],connectivi:5,conop:[5,21,22,25,27,41,49,50],conquer:8,consecut:[26,27,35,41],consequenti:20,conserv:[18,29],consid:[0,4,8,10,13,14,16,21,22,26,27,28,31,32,33,34,35,36,39,40,41,44,47,49,50,51,53],consider_all_nod:10,consider_hydrogen:49,consider_ligand:36,consist:[3,8,20,21,25,28,29,31,32,34,35,36,37,40,44,49,51],conspicu:20,constant:[3,25,32,39,41,52],constitut:20,constraint:[13,26,32,34,40],constraintfunct:40,constru:20,construct:[0,3,9,21,22,26,28,29,33,34,35,37,42,43,45,49,50,51],constructatompo:9,constructbackboneframeresidu:[47,50],constructcbetapo:9,constructcterminaloxygen:9,constructetd:10,constructframeresidu:50,constructframeresidueheurist:50,constructfrmrotamergroup:[47,50],constructfrmrotamerheurist:50,constructor:[21,25,28,29,32,34,37,40,41,47,49,54],constructrrmrotamergroup:50,constructrrmrotamerheurist:50,constructsidechainframeresidu:50,contact:[40,53],contactfunct:40,contain:[0,1,2,3,4,5,7,8,9,11,13,16,18,19,20,21,22,24,25,26,27,28,31,33,34,35,36,39,40,41,42,44,45,47,49,50,51,54],content:[8,12,17,20,23,26,42,47,54],contigu:[25,36,37],continu:[1,21,29,32,47],contract:20,contrast:45,contribut:[4,10,16,17,19,20,54],contributor:20,contributori:20,control:[0,3,8,10,20,31,34,36,40,49,50,51,52],conveni:[1,8,18,28,31,34,35,42,49,50,51],convent:[1,49],converg:[28,31,32,34],convers:[20,37],convert:[4,5,22,25,26,27,35,37,39,41,51,52],convert_module_data:4,convertbasetyp:37,cooler:[3,30,31],coolerbas:34,cooling_factor:[10,34],coord:[26,31],coord_idx:26,coordin:[3,9,26,28,31,32,34,35,38,39,47],coordinfo:26,cope:16,copi:[2,3,4,8,16,18,20,21,22,28,29,31,34,35,40],copyright:20,copyright_cmak:20,core:[0,8,9,10,11,13,14,19,35,37,46,53,54],correct:[5,25,50],correctli:35,correspond:[0,10,16,21,22,25,26,27,28,31,37,49,50,51],corrupt:[21,40],could:[1,4,5,8,13,16,25,26,35],couldn:35,count:[14,28,29,34,35,39,41],countenclosedgap:29,countenclosedinsert:29,counter:[28,34],counterclaim:20,counterpart:[31,41,50],coupl:[1,8,16,35],cours:8,coutsia:38,coutsias2005:[32,38],coval:49,cover:[0,1,8,12,13,14,21,25,28,30,34,35],coverag:[0,3,35],cparticl:49,cpp:4,cpr:[49,51],cpu:[18,25,35],cpu_platform_support:25,crambin:[26,31,34],crash:47,creat:[2,4,5,7,8,9,10,13,16,17,21,22,23,26,27,28,30,34,35,39,41,47,48,49,50,51],createalign:[31,35],createemptyview:28,createentityfromview:[28,36,47],createfromfrmlist:[46,47],createfromrrmlist:46,createfullview:[30,31,35],createscwrl3particl:49,createscwrl4particl:49,createsequ:[26,31,35],createvinaparticl:49,creation:[25,28,32,49],creator:[25,28,32],criteria:36,criterion:[10,34],criterium:31,croak:16,cross:[20,28],crucial:8,crude:[0,35],cryst:38,cterminalclos:34,cumul:50,current:[2,4,5,8,10,14,16,21,22,25,26,31,34,35,37,40,41,42,49,50,52],custom:[8,26,34,35,36,37,48,49],customari:20,cutoff:[24,25,31,32,36,39,41],cycl:29,cyclic:[31,32,38],cyd:[49,51],cyh:[49,51],cys_hb3:21,cys_sg:21,cystein:[25,36,44,47,49],d_bin:41,dai:11,damag:20,dampen:25,danc:38,dare:4,dat:[26,28,37],data1:4,data2:4,data:[0,1,3,4,8,16,17,21,23,24,25,28,29,30,31,32,34,35,36,40,42,47,49,54],data_:37,data_gener:[3,28,37,48],data_to_stor:26,data_typ:26,databas:[0,3,9,23,24,28,31,35],databs:26,datatyp:26,date:[5,7,16,20],davi:38,davis2006:[22,38],db_dir:28,dbg:8,dcmake_install_prefix:2,deactiv:10,dead:[10,38],deal:[35,36],debug:[8,10,21],decent:15,decid:[3,8,32,50],decis:27,declar:[4,8,16],decod:13,decompos:[3,10],decomposit:[10,28,33,46],decreas:[28,34],dedic:[4,8,16],dee:10,deep:[22,35],def:[1,8,21,35],def_angl:21,defend:20,defin:[1,4,8,9,13,14,15,20,21,22,23,24,25,28,29,31,32,33,34,35,36,37,39,40,41,44,49,50,51],definem:8,definit:[8,20,26,27,31,41,49],degre:[22,26,27],deleg:28,delet:[0,2,8,22,35,49],deletegapcol:35,deliber:20,deliv:[1,26,34,35],delta_scor:34,demand:35,demonstr:26,denovoclos:34,densiti:[22,32,38],dep1:4,dep2:4,dep:4,depend:[0,3,4,8,10,13,18,22,25,26,27,28,31,35,36,37,38,39,40,41,47,48,49,54],dependency1:4,dependency2:4,depends_on:4,depth:[26,38],deriv:[1,20,26,28,33,38,43,44],descend:35,descent:[31,32,38],describ:[0,4,7,8,10,11,17,20,21,22,26,28,29,30,32,33,37,39,41,44,47,48,49,50,51,54],descript:[0,5,13,16,20,34,35,51],descriptor:[26,28],descsrib:10,design:[1,3,19,20],desir:[9,18,25,26,31,32,34,35,39,40,41],despit:3,detail:[0,3,9,13,16,20,25,26,27,28,31,33,34,35,39,41,48,49,51],detect:[0,3,11,28,30,38,44],determin:[8,11,20,25,26,31,34,40,41],determinist:28,deuterium:[35,50],develop:[1,3,8,16,19,53],deviat:[22,33,34,51],devot:12,dict:[4,28,31,33,34,39,41],dictionari:[4,5,13,15,33,38],did:[8,26,31,35],didn:[7,28],didnt:5,diff:10,differ:[1,2,4,7,8,10,15,16,20,21,26,28,29,31,35,39,41,47,49,51],differenti:49,dihedr:[7,9,18,22,23,25,26,32,34,35,41,50,51,54],dihedral_angl:22,dihedral_bin:41,dihedral_idx:51,dihedral_pair:27,dihedralconfigur:51,dill:38,dimens:27,dimension:38,dir:[4,8,18],direct:[8,20,22,24,26,33,41,49,50],directli:[8,10,18,26,31,35,36,40,44,49,51,53],directori:[1,2,4,5,7,8,17,26,28,48],dirti:1,dirtyccdclos:34,disabl:[1,16,35],disable_doctest:2,disable_document:2,disable_linkcheck:2,discard:26,disclaim:20,discocontain:40,disconnect:3,discret:[28,39,41],discuss:[20,26],disk:[8,25,28,39,41,51],displai:[7,11,13,14,20],displaystyl:10,dissimilar:28,dist:41,dist_bin:41,dist_bin_s:26,distanc:[7,9,22,26,28,31,33,35,36,39,40,41,43,49],distance_thresh:28,distant:40,distinct:[21,28,36,51],distinguish:[3,23,25,37,39,41,51],distribut:[1,8,20,25,26,27,34,37,39,41,48,51],disulfid:[0,25,32,36,43,47,49,51,54],disulfid_bridg:[25,36],disulfid_score_thresh:36,disulfidscor:[36,44],dive:[16,35],diverg:8,divers:[26,28],divid:28,dng:18,do_it:[39,41],doc:[2,4,8,16,20,28],dock:38,docker:[3,6,7,54],dockerfil:[5,7],docstr:13,doctest:[2,8,16],document:[1,2,7,16,20,26,28,53],doe:[1,3,4,8,9,10,11,13,15,16,20,22,26,30,31,34,35,37,40,48],doesn:[8,16,29,32,34,35,51],doesnt:51,doexternalscor:[39,41],doing:[1,5,16,28],dointernalscor:[39,41],domain:28,domin:10,don:[2,10,20,31,35,50],done:[1,8,11,13,16,23,25,27,28,31,33,34,35,37],donor:[41,49,50],donorm:[39,41],dont:[0,34],dont_write_bytecod:1,dost_root:2,doubl:28,doubt:13,down:[13,22,26,28,34],download:5,dpm3_runtime_profiling_level:14,draw:[22,27,34],drawback:8,drawn:[27,34],drawphigivenpsi:27,drawpsigivenphi:27,drop:[3,8],dssp:[3,26,41],dssp_state:41,dtype:28,due:[0,26,31,32,35,44],dump:[28,51],dunbrack:[3,38,48],duplic:[6,28],dure:[1,3,21,32,35,37,45,51],dynam:51,dynamicspatialorgan:3,e_cut:10,e_thresh:[10,35],e_tresh:10,each:[0,7,8,10,13,14,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,41],earli:3,earlier:2,easi:8,easier:[1,8,20],easili:[4,16,35],echo:8,edg:[10,28],edge_idx:10,editor:1,editori:20,editxc:28,edu:3,educ:8,effect:[4,8,10,25,36,44],effici:[21,28,34,38,42],egg:26,eigen3_include_dir:2,eigen:[2,3],either:[0,7,8,13,16,18,20,21,22,27,29,31,32,34,35,36,37,39,40,41,45,49,51],elabor:[8,20],electron:20,electrostat:[25,32],element:[1,10,21,22,26,28,31,33,37,40,44,50],elimin:[10,38],els:[8,16,36,37],emerg:1,empir:[43,44],emploi:16,empti:[8,11,13,22,26,28,31,35,49],enabl:[1,2,3,11,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,52],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,28,33,35,42,47],entityhandl:[13,21,22,26,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,28,31,32,33,36,41,47,50],entries_from_seqnam:28,entrypoint:5,enumer:[8,10,21,25,26,28,31,35,40,47,49,50,51],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39,41,42,54],epsilon:[10,25,36,52],equal:[28,34,39,41,44,50],equidist:51,equip:5,equival:[28,35,39,41],error:[0,11,13,14,26,28,32,35,37],especi:28,estim:[10,28,33,34,35,38,41,44,49,50,51],etc:[1,3,8,16,22,26,31,40],evalu:[4,8,32,35,39,40,41,46,47,49,51,54],evaluategromacsposrul:9,even:[2,8,10,20,22,25,29,35],event:[20,28],eventu:13,ever:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,51,52],everyth:[1,2,3,7,8,12,13,16,28,32,35,36,37,39,54],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,49],exampl:[0,1,2,3,8,11,13,16,17,18,20,21,23,25,26,27,28,30,32,34,35,36,42,47,48,49],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35],exclud:[8,20,26],exclus:[1,8,20,25],execut:[0,2,3,4,7,8,16,18,20,26,33,35],exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,28,31,32,33,34,35,37,39,40,41,48,49,51],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:[10,34],expect:[1,3,7,21,25,26,33,35,36,40,44,50,52],expens:26,experiment:[33,35],explain:[1,8],explan:8,explicit:2,explicitli:20,explor:[5,38],exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28,30,31,35,41,46],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,28,29,35],extension_penalti:29,extent:26,extern:[3,4,5,8,28,34],external_script:[3,8],extra:[2,3,8,16,22,28,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,49,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:[3,22,28],eye:1,f_i:26,f_idx:40,f_vinaparticl:49,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,35,51],fall:32,fallback:51,fals:[1,8,10,11,13,22,25,26,28,29,31,34,35,36,44,47,49,50],fantast:8,far:[31,35],fast:[0,9,18,19,21,25,26,27,28,37,39,40,41,51],fasta:[0,13,28,30,35],fasta_fil:28,faster:[10,25,26,28,32,33,40],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,filesystem:28,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:[0,3,5,13,20,26,28,48],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],fromdatachunk:28,fromhhm:26,fromhoriz:26,fromresidu:51,fromseqlist:28,front:[1,11,16],fs_data_:28,fs_server:28,fsstructureserv:[3,28],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:[0,3,9,18,24,25,28,30,31,33,35,36,54],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:[3,9,23,28,31,33,38,44],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,getattachedview:28,getaveragescor:31,getbackbonelist:[23,26],getbackbonescoringkei:31,getbackboneweight:31,getbins:27,getbinsperdimens:27,getbound:22,getc:22,getca:22,getcb:22,getchain:29,getchainindex:29,getchainnam:29,getchains:8,getcharg:25,getclust:31,getclusteredcandid:31,getcollisiondist:49,getconfid:26,getcoordidx:26,getcoordinfo:26,getcpuplatformsupport:25,getcreationd:5,getdefault:[25,32,35],getdefaultlib:5,getdihedralangl:26,getdihedralconfigur:51,getdistbins:26,getdisulfidbridg:25,getdisulfidconnect:25,getdsspstat:26,getel:21,getenviron:21,getenvsetdata:8,getepsilon:25,getfirstindex:21,getforcefieldaminoacid:25,getfragmentinfo:[26,31],getframeenergi:49,getfudgelj:25,getfudgeqq:25,geth1index:21,geth2index:21,geth3index:21,getheavyindex:25,gethistogramindex:[22,27],gethistogramindic:27,gethnindex:21,gethydrogenindex:[21,25],getidentifi:28,getidx:28,getindex:[21,25],getinternalconnect:25,getinternalenergi:49,getinternalenergyprefactor:49,getlargestclust:31,getlastindex:21,getlength:29,getlist:28,getlooplength:25,getloopstartindic:25,getmass:25,getmaxnumatom:21,getmaxnumhydrogen:21,getn:[22,28],getnam:[28,47,49],getnonbondedcutoff:32,getnonplanar:33,getnum:31,getnumatom:[21,25],getnumb:31,getnumcandid:31,getnumchain:8,getnumcoord:26,getnumfrag:26,getnumhydrogen:21,getnumloopresidu:25,getnumresidu:[8,21,25],getnumstempair:26,getnumsubrotam:49,geto:22,getolc:[21,22],getomegators:[21,22],getomf:28,getomfbyidx:28,getoxtindex:25,getpeptideboundconnect:25,getphiprobabilitygivenpsi:27,getphitors:[21,22,47],getpo:[21,28,49],getposit:28,getpotentialenergi:25,getpredict:26,getprob:[27,49],getpsiprobabilitygivenphi:27,getpsitors:[21,22,47],getr:33,getresidu:28,getresiduedepth:26,getringpunch:33,getrotamericconfigur:51,getscor:[26,34],getscoringfunct:49,getselfenergi:49,getseqr:[21,40],getsequ:[21,22,26,28,31],getsequenceprofil:26,getsequenceprofilescoreskei:31,getsigma:25,getsimul:25,getsolventaccessibilitit:26,getstemrmsdskei:31,getstructureprofil:26,getstructureprofilescoreskei:31,getsubdb:26,getsubrotamerdefinit:49,getsystemcr:32,gettemperatur:[34,49],gettransform:22,getversionnumb:37,getvinaweightgaussian1:49,getvinaweightgaussian2:49,getvinaweighthbond:49,getvinaweighthydrophob:49,getvinaweightrepuls:49,getweight:[28,31],gggg:35,ggggagggg:35,gggggggggggggggggggg:35,git:[1,4,8,17,18,19,53],git_root:28,gitignor:8,gitlab:[5,53],give:[4,8,16,20,23,28,31,34,35,49],given:[0,1,3,4,8,9,10,11,13,14,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51],glass:38,gln:[49,51],gln_ne2:21,global:[15,26,31,35,37,49],glu:[21,49,51],glu_oe1:21,glutam:49,glutamin:49,gly:[35,36,47,49,50],gly_n:21,glycin:[3,22,26,32,36,49],goal:[1,10,28,30],goe:[2,8,14,16,35,51],going:[8,9],goldfarb:35,goldstein1994:[10,38],goldstein:[10,38],good:[4,8,18,25,26,35],goodwil:20,got:2,govern:20,grain:8,grant:20,graph:[3,12,38,47,54],graph_initial_epsilon:36,graph_intial_epsilon:36,graph_max_complex:36,graphminim:[10,46],greatest:5,grep:2,grid:26,gromac:9,grossli:20,group:[4,14,24,26,27,28,41,44,45,46,47,50,52],group_definit:[27,41],group_idx:41,guarante:[26,28,31,34,36,37],gui:[8,27],guid:32,guidelin:[8,37],gzip:[0,5,11,13,28],haa:38,hand:[0,2,4,13],handl:[3,8,9,13,19,22,28,30,36,40,44,54],handler:28,happen:[1,8,25,28,29,34,35,49],hard:[43,49],hardwar:18,harmless:20,harmon:[25,32],harmonic_angl:25,harmonic_bond:25,harmonic_improp:25,has:[0,1,2,3,4,5,8,10,11,13,16,20,21,22,23,24,25,26,28,29,31,32,34,35,36,39,40,41,44,46,49,50,52],hasattr:35,hasdata:26,hasfraglength:26,hasfragmentinfo:31,hash:[3,26,28],hash_thresh:28,hash_tresh:28,hasnonplanar:33,hasringpunch:33,have:[0,2,3,4,5,7,8,10,13,14,16,18,20,21,22,25,26,28,29,31,33,34,35,36,37,39,40,41,44,46,47,50,51,52],hbond:[28,35,41,49,50],hbond_scor:37,hbondscor:[35,37,42],headach:8,header1:4,header2:4,header3:4,header4:4,header:[0,2,4,16,17],header_output_dir:4,headlin:8,heavi:[21,25,36,39,49,50],heavili:[26,47],helic:[22,24,25,28,35,41],helix:[7,18,22,34,47],hell:28,hello:37,hello_world:8,hellyeah:[7,18],help:[0,1,2,3,4,7,8,13,16,18,25,41],helpactiontest:1,helper:[4,12,16,17,21,25,31,36,37,54],hen:26,henc:[8,14,21,26,37],here:[0,1,2,3,4,8,11,13,14,16,18,19,21,22,25,26,27,28,30,31,32,33,34,35,37,39,41,44,48,51],herebi:20,herein:20,het:35,heurist:[3,28,35,50],heuristicprocessor:21,hg_po:49,hgfhvhefgdntngcmssgphfnpygkehgapvdenrhlg:0,hhblit:[0,13],hhm:[0,13,26,31],hhsearch:26,hide:[8,16],hierarch:[31,40],hierarchi:15,high:[3,8,16,28,30,35],high_resolut:22,higher:[31,40,41],highest:[15,33],highli:[2,8],hint:13,histidin:[25,49],histogram:[27,34],histori:16,hit:[1,10,16,27,28,32],hmm:38,hold:[20,28],home:[4,5],homo:[0,13],homolog:[0,12,18,19,35,38],homologu:26,honor:35,honour:35,hook:[8,17],horiz:26,horribl:50,host:[4,7,8,16],hotfix:16,how:[1,16,17,20,26,31,34,35,38,40,48,54],howev:[5,20,26],hparticl:49,hpp:37,hsd:[49,51],hse:[49,51],html:[2,3,8,16],http:[3,8,18,19,20,53],huge:28,hybrid:51,hydrogen:[3,21,22,25,35,38,41,49,50],hydrophob:49,hyphen:1,i_loop:[25,36],i_vinaparticl:49,id_:37,idea:[1,8,21,23,25,26,35,40,49,52],ideal:[22,32,52],ident:[3,26,27,28,41,51],identif:20,identifi:[0,3,13,14,20,26,28,31,35,36,39,41,49,50,51],ids:47,idx:[10,21,22,25,26,28,32,40,49],idx_ca_res_37:21,idxhandl:8,iff:[26,29,33],ifstream:37,ignor:[0,25,28,32,35],iii:20,illustr:26,imag:7,image_nam:5,imagehandl:22,imagin:8,imaginari:1,img:[7,22],immedi:[1,8,15,16],impact:[0,25,26],implement:[3,16,19,26,28,29,32,34,35,37,43,44,46,47,49,50,53],impli:20,implicit:2,improp:25,improv:[3,20,25,35,38,44],in_dir:4,in_fil:8,in_path:4,in_stream:37,in_stream_:37,inabl:20,inaccur:25,inaccurate_pot_energi:25,inact:52,inactive_internal_energi:52,incident:20,incl:[25,26,35],includ:[2,3,7,8,11,16,18,20,21,25,26,28,29,31,33,35,37,39,41,47],include_atom:28,include_ligand:35,inclus:[20,35],incompat:[31,32],incomplet:[35,48],inconsist:[10,13,21,22,25,26,29,31,32,36,40,49],inconveni:16,incorpor:[3,20],increas:[0,3,10,28,31,32,35,50],increment:28,incur:20,indemn:20,indemnifi:20,independ:[0,3,25,36,48],index:[8,10,21,22,25,26,27,28,29,31,32,33,34,35,39,40,41,45,49,50,51],index_four:25,index_on:25,index_thre:25,index_two:25,indic:[8,10,11,13,20,21,22,25,26,27,28,29,31,32,35,36,40,44,47,49],indirect:20,individu:[7,20,39,41],inf:[10,32,35],infin:32,infinit:32,influenc:[13,28,40,50],info:[26,28,31,35,40],inform:[0,5,7,8,13,16,20,22,23,26,28,29,31,34,35,38,40,41,42,53],infring:20,inherit:[1,39,40,41,46],init:16,init_bb_list:34,init_frag:34,initi:[3,10,21,22,26,28,31,32,34,35,36,39,40,41,46,49,50,51],initial_bb:31,initial_epsilon:[10,52],initialis:1,inlin:37,inner:14,input:[0,1,3,13,16,18,25,26,27,28,32,34,35,36,39,40,41,44,48,52],insert:[21,22,29,31,34,35,52],insertinto:[21,22,31],insertloop:[29,35],insertloopcleargap:[29,31,35],insid:[1,4],insight:16,instal:[8,16,37,54],instanc:[3,8,13,24,25,37,53],instead:[0,1,2,3,4,8,11,26,28,29,31,34,35,50],institut:20,instruct:2,int16:28,int16_t:37,int32:28,int32_t:37,int64:28,int_32_t:37,integ:[8,13,21,28,40],integr:[4,8,38],intend:[1,8,34,49],intent:26,intention:20,interact:[3,8,25,32,39,40,41,43,44,45,49],intercept:[39,41],interest:[1,10,25,26,34,37,49,51],interfac:[0,3,4,8,20,50],intermedi:8,intern:[0,1,3,4,5,8,16,21,24,25,26,27,28,31,32,33,34,35,36,37,38,39,40,41,46,49,50,52],internal_e_prefac:50,internal_e_prefactor:49,internal_energi:49,internet:8,interpl:51,interpol:[40,51],interpret:[8,11],intervent:8,intrins:2,introduc:[1,3,4,8,16,32,35],introduct:[12,17],invalid:[8,21,25,26,28,29,32,35,36,39,40,41,45,49,51],invalid_vinaparticl:49,invok:[2,4,8,15,16],involv:[16,30,44,49],iodin:49,ios:37,iostream:37,ipython:7,irrevoc:20,is_c_ter:[25,36],is_cter:25,is_hbond_acceptor:50,is_hbond_donor:50,is_major:35,is_n_ter:[25,36],is_nter:25,isallatomscoringsetup:[31,35],isallset:21,isanyset:21,isbackbonescoringsetup:35,isctermin:29,isempti:31,isen:14,isntermin:29,isoleucin:49,isset:21,issimilar:51,issourc:37,issu:[3,12,16,17,20,32,35,37],istermin:29,isvalid:47,item:[1,8,16,21,22,25,26,35,40],iter:[10,26,27,28,31,32,34,35,49],its:[0,1,2,4,5,8,11,16,20,25,26,30,31,33,34,35,41,48,49,50,51],itself:[3,4,8,16,26,28,34,36,37,39,41],januari:20,job:[8,26,34,35],johner:38,join:[8,21,23,26,31,32,34,36],jone:[38,49],jones1999:[26,38],journal:38,json:[0,13],jupyt:7,just:[1,2,8,13,15,16,23,25,26,28,29,31,35,50],kabsch1983:[26,38],kabsch:38,keep:[0,1,2,4,5,8,13,16,28,30,35,47],keep_non_converg:31,keep_sidechain:[8,36],kei:[0,13,26,28,31,34,35,39,40,41],kept:[8,16,25,31,32,36,45,49],kernel:[7,38],keyword:27,kic:[30,31,34],kicclos:34,kick:13,kill_electrostat:25,kind:[1,8,20],kinemat:32,kmer:3,kmer_search:3,know:[2,51],knowledg:51,known:[4,11,21,40,50],krivov2009:[10,38,47,49],krivov:38,kwarg:1,l_e:49,lab:48,label:[16,25],lack:35,languag:[4,20],larg:[3,5,27,32,35],larger:[10,14,22,26,28,35,50],largest:[28,31,44],last:[1,2,3,4,21,22,25,29,31,32,34,35,40,41,48],last_psi:22,later:[1,8,10,21,28,47],latest:[2,3,5,8],latter:[0,5,16,28,35],launcher:[4,8],law:20,lawsuit:20,layer:44,layout:[26,28,37],lbfg:35,lbfgs_toler:[],lddt:7,leach1998:[10,38],leach:38,lead:[0,8,9,11,22,25,31,32,36,39,41,48],learn:28,least:[0,2,4,8,10,16,20,22,25,26,35,39,41,44],leav:1,left:[10,11,32],legal:[8,20],lemon:38,len:[22,23,25,26,28,31,35,36,41,47],length:[0,9,10,21,24,25,26,27,28,29,31,32,34,35,36,37,39,40,44],length_dep_weight:35,length_depend:31,lennard:49,less:[0,10,16,22,25,26,27,28,31,35,39,41,50,51],let:[1,8,22,26,28,31,47],letter:[3,5,21,22,26,27,34,49],leu:49,leu_h:21,leucin:49,level:[2,3,8,14,15,16,30,35],lexicograph:35,liabil:20,liabl:20,lib64:8,lib:[5,7,37],libexec:[4,8],libpromod3_nam:4,librari:[0,3,4,8,15,28,33,36,38,47,50,54],library1:4,library2:4,licenc:48,licens:[3,17,19],licensor:20,lies:26,life:16,ligand:[3,35,36,49,50],like:[0,1,4,8,16,35,37,48],limit:[0,3,20,26,28,32,35],line:[0,1,7,8,9,12,16,27,41,54],linear:[26,28,31,34,39,40,41],linear_weight:[31,34,39,41],linearcombin:31,linearli:[28,49],linearscor:34,link:[0,2,4,8,16,20,21,25,26,28,34,36,39,40,41,42],link_cmd:4,linkcheck:[2,8,16],linker:[4,35],linker_length:35,list:[0,1,2,3,4,7,8,9,10,11,13,20,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,45,46,47,49,50,51,52],listen:8,literalinclud:8,litig:20,littl:[4,8,16,37],live:[4,8],lj_pair:25,load:[1,8,13,15,21,23,25,26,27,28,31,32,35,36,37,39,41,42,47,51,54],loadalign:[30,35],loadallatominteractionscor:39,loadallatompackingscor:39,loadamberforcefield:35,loadbb:26,loadbbdeplib:[0,36,47,48],loadcach:28,loadcbetascor:[31,34,41,42],loadcbpackingscor:41,loadcharmm:25,loadcharmmforcefield:35,loaddefaultallatomoverallscor:39,loaddefaultbackboneoverallscor:41,loadent:[0,13],loadfragdb:[23,24,31,35],loadhbondscor:41,loadlib:[0,36,48],loadpdb:[8,21,23,25,26,28,30,31,32,34,35,36,42,47],loadport:[25,26,27,37,39,41,51],loadreducedscor:41,loadsequenceprofil:[13,26,31],loadssagreementscor:41,loadstructuredb:[23,24,26,31,35],loadtorsionsampl:[22,24,27,34],loadtorsionsamplercoil:[24,31,35],loadtorsionsamplerextend:24,loadtorsionsamplerhel:24,loadtorsionscor:41,local:[2,5,7,25,26,27,39,41,51],localalign:28,localhost:7,locat:[2,3,4,5,10,22,24,26,28,29,37,39,41,49],log:[11,16,33,35,49,50],logic:0,loginfo:33,lone:49,lone_pair:49,longest:26,look:[5,8,11,16,22,26,36,40,50],lookup:[9,21,23,28,42],looooooong:10,loop:[0,3,7,8,13,18,19,21,24,26,27,28,29,30,33,35,36,37,38,39,40,41,50,54],loop_candid:31,loop_length:[25,26,31,36],loop_main:8,loop_po:25,loop_seq:31,loop_start_indic:[25,36],loopcandid:[28,30,33],loss:[16,20],lossi:26,lost:[1,16],lot:[1,8,13,16],low:[1,3,8,10,28,50],lower:[31,34,35,39,41],lowest:[31,33,34,49],lowest_energy_conform:34,lying:40,lysin:49,m_idx:28,m_vinaparticl:[49,50],mac:3,machin:[25,26,27,37,39,41,51],macro:[4,8],macromolecul:38,made:[4,5,20,51],magic:[8,37],mai:[0,1,2,4,8,11,13,16,20,21,25,29,32,35],mail:20,main:[8,35,37,51],mainli:[21,34,49],maintain:[8,16],mainten:17,maintin:34,major:[16,35],make:[3,4,7,8,11,13,16,18,20,21,22,26,37,40,48,54],makefil:[2,8],makestat:51,malfunct:20,malici:16,man:[2,8],manag:[4,8,20,42],mani:[11,13,26,28,32,33,35,50],manipul:22,manner:[8,10,34],manual:[1,2,5,8,9,16,26,31,34,35,37,49],map:[0,13,21,22,26,28,33,36],mariani:38,mark:[4,20,50],mass:25,massiv:28,master:[8,16],mat3:9,mat4:[9,22,28,35],mat:28,match:[0,4,13,22,25,26,27,28,31,32,34,35,40,41],materi:[1,8],math:33,mathemat:[31,32],matplotlib:27,matric:38,matrix:[9,26,28],matter:[4,7,28,53],max:[9,10,21,29,33,35,36,41,51,52],max_alpha:41,max_beta:41,max_complex:[10,52],max_count:[39,41],max_d:41,max_dev:34,max_dist:[31,40],max_dist_thresh:33,max_extens:35,max_gamma:41,max_iter:[28,31,35],max_iter_lbfg:35,max_iter_sd:35,max_length:29,max_loops_to_search:35,max_n:10,max_num_all_atom:35,max_p:50,max_prob:49,max_res_extens:35,max_step:32,max_to_show:14,max_triangle_edge_length:28,max_visited_nod:10,maxfraglength:26,maxim:[10,26,28,31,32,34,35,38,40,41],maximum:[10,26,31,32,33,34,49,50],mc_closer:34,mc_cooler:34,mc_num_loop:35,mc_sampler:34,mc_scorer:34,mc_step:[10,35],mcsolv:10,mean:[4,8,13,16,20,21,25,28,32,35,36],meaning:[26,31],meant:[18,21,26,33,35,50],measur:28,mechan:[18,20,28,31,32,34,35,40],meddl:[7,35],media:20,medium:20,meet:20,member:[8,13,31,35],memori:[10,26,28,35,37],mention:[1,2],mer:3,merchant:20,mere:20,merg:[16,25,28,29,31,35,36,40,49],merge_dist:35,mergegap:29,mergegapsbydist:35,mergemhandl:35,mess:[8,16,40],messag:[12,13,37],messi:16,met:49,meta:28,metal:49,methionin:[35,49],method:[0,1,10,13,21,25,26,27,28,32,35,36,37,50],metric:40,metropoli:[10,31,34],mhandl:[29,30,31,35],middl:16,might:[3,10,25,26,28,31,32,34,40,50,52],min:[28,31,41],min_alpha:41,min_beta:41,min_candid:31,min_d:41,min_dist:40,min_gamma:41,min_loops_requir:35,min_scor:31,min_terminal_anchor_s:35,min_triangle_edge_length:28,mincadist:22,mind:[1,8],minim:[3,12,18,22,25,26,31,32,35,39,40,41,46,47,54],minimizemodelenergi:35,minimum:[22,26,28,44],minor:[3,25,35],mirror:37,miser:14,mismatch:[21,35,40],miss:[0,11,13,25,28,35],mix:[0,4],mkdir:[2,8],mm_sy:[25,32],mm_sys_output:25,mm_system_cr:32,mmap:28,mmcif:[5,11],mmsystemcr:[25,32],mod:8,mode:[1,51],model:[1,3,7,8,12,13,14,19,21,25,26,29,32,34,36,40,41,42,45,46,49,50,52,53,54],model_termini:35,modelling_issu:35,modellinghandl:[3,29,31,35],modellingissu:35,modeltermini:35,modif:[20,35],modifi:[8,16,20,22,31,35],modified_crambin:31,modul:[1,3,11,12,15,16,17,18,23,24,28,30,37,44,47,49],modular:19,module_data:4,mol:[8,9,18,21,22,23,26,27,28,29,31,32,34,35,36,38,40,47,49,50,51,54],molck:7,molecular:[7,18,32,35],molprob:30,molprobity_bin:33,molprobity_execut:33,moment:8,monitor:1,monolith:8,mont:[0,3,10,28,31,34,35,46],montecarlo:3,mood:8,more:[1,2,4,7,8,10,13,14,16,20,28,35,44,49,53],most:[0,3,4,5,8,22,25,26,27,28,31,32,35,39,41,48,50],mostli:[4,16],motif:[3,30,38],motiffind:28,motifmatch:28,motifqueri:28,motion:[22,38],mount:[5,7],movabl:25,move:[2,3,8,16,25,31,32,34,35,37],movement:28,mpscore:33,msg:11,msgerrorandexit:11,msm:3,msse4:2,much:[10,26,28,35],multi:18,multipl:[0,2,3,4,8,13,14,18,25,28,31,35,36,39,41],multipli:[10,34],multitempl:13,multithread:38,must:[0,2,4,8,10,13,14,16,20,22,25,26,28,29,31,32,33,34,35,36,37,39,40,41,44,51],mutlipl:13,my_db_on:26,my_db_two:26,my_script:7,myclass:37,myclassptr:37,mytrg:0,n_a_vinaparticl:49,n_ad_vinaparticl:49,n_coord:9,n_d_vinaparticl:49,n_entri:28,n_i:10,n_j:10,n_num:29,n_po:[9,22,41],n_stem:[9,23,26,29,31,32,34],n_stem_phi:34,n_stem_plddt:28,n_ter:[32,50],n_vinaparticl:49,naivesolv:10,name:[0,1,3,4,5,7,8,11,13,14,20,21,25,26,27,28,29,31,33,35,44,48,49,51],name_pymod:4,namespac:[13,37],nan:[32,35,51],nativ:37,ndarrai:28,necessari:[8,22,34,40],necessarili:[20,52],need:[1,2,3,4,5,8,11,13,15,16,22,25,26,27,28,31,32,35,36,37,39,40,41,47,50],need_config_head:4,neg:[1,10,25,32,40],negelect:[0,35],neglect:[28,32,45,49,50],neglect_size_on:31,neglig:20,neighbor:[8,21,35],neighbour:[28,35,51],network:[22,44],never:[13,16,26,31,35,36,37,39,41],nevertheless:8,new_default:25,new_env_po:21,new_po:21,new_res_nam:49,new_siz:22,newli:[5,21,34],next:[1,8,16,22,27,28,29,37],next_aa:34,nglview:7,nice:8,nitrogen:[9,22,32,43,49,50],nobodi:1,node:10,node_idx:10,node_idx_on:10,node_idx_two:10,non:[0,3,4,10,13,16,20,24,25,27,28,29,30,31,32,35,37,47,48,50],non_rotamer:51,nonbonded_cutoff:[25,32],none:[13,26,28,33,34,35,36,49],nonredund:26,nonzero:51,norm:[28,41],normal:[20,33,39,41],normalis:40,notabl:26,note:[0,2,8,13,14,21,22,25,26,28,31,32,34,35,36,37,39,40,41,47,49,50],notebook:7,noth:[0,4,8,13,14,20,28,34,49],notic:[1,4,16,20],notwithstand:20,novel:[19,38],novo:[3,30,54],now:[3,8,14,16,18,22,26],nparticl:49,nterminalclos:34,null_model:31,num:[23,28,31,32,36],num_frag:[26,35],num_gap_extens:29,num_loop:31,num_residu:[21,25,34,36,39,40,41],num_residues_list:36,num_trajectori:28,number:[0,1,3,8,9,10,13,14,18,21,22,24,25,26,27,28,29,31,32,34,35,36,37,39,40,41,42,44,45,49,51],numer:35,numpi:[27,34],nussinov1991:[28,38],nussinov:[28,38],o_a_vinaparticl:[49,50],o_ad_vinaparticl:49,o_d_vinaparticl:49,o_po:22,o_vinaparticl:49,object:[0,3,8,13,14,20,21,22,23,25,26,27,28,30,31,32,35,36,37,39,41,44,46,47,49,50,54],oblig:20,observ:[10,26,28,32,50,52],obtain:[10,18,20,23,28,35],obviou:16,occupi:[45,50],occur:[21,28,35,40,41],ocparticl:49,odd:26,off:[1,8,14,35],offend:33,offer:[6,20,24,30,49,51],offset:[0,3,13,26,31,35],ofstream:37,often:[8,11,13,32],og_po:49,olc:22,old:[33,35],oligom:[0,13,30],oligomer:3,olson:38,omega:[21,22],omf:[3,28],omit:35,onc:[1,3,8,16,25,28,31,32,34,46,51,52],one:[0,1,2,4,5,6,8,9,10,13,14,15,16,20,21,22,25,26,28,29,31,32,34,35,36,39,40,41,44,49,50,51,52],one_letter_cod:[21,23,26,31,32,33,34,36],ones:[22,28,31,34,50,51],onli:[0,1,2,3,4,8,10,11,13,14,15,16,20,21,22,25,26,28,29,31,33,34,35,36,37,39,41,44,47,48,49,50],only_longest_stretch:26,onto:[1,22,26,28],oparticl:49,open:[13,25,26,27,37,39,41,51,53],openmm:[2,18,25,32],openstructur:[2,3,5,7,19,38],oper:[3,10,16,18,21,26,28,40],opt:[11,13,16],optim:[0,2,3,10,13,25,26,27,31,33,35,38,39,41,44,47,48,51,54],optimis:8,optimize_subrotam:[36,44],option:[0,2,3,5,7,13,26,31,32,35,51],order:[0,5,13,21,25,26,29,31,35,37,40],org:[3,20],organ:[8,26,51],orient:[9,32,41],orig_indic:[31,33],origin:[5,7,9,13,16,20,22,26,31,34,35,40,52],orthogon:[28,33],ost:[0,1,2,3,4,5,7,8,9,11,13,15,18,21,22,23,26,27,28,29,30,31,32,33,34,35,36,37,40,41,42,43,44,47,49,50,51,54],ost_double_precis:2,ost_ent:33,ost_librari:4,ost_root:[2,8],other:[0,1,2,3,4,8,10,14,16,20,21,22,31,32,35,36,39,41,42,49,50,51,52,53,54],other_index:22,other_particl:49,other_res_index:21,otherwis:[1,4,8,10,14,16,20,21,22,25,26,28,29,31,32,34,35,39,40,41,49,51],our:[3,4,5,8,16,26,28,31],out:[0,1,2,4,8,14,16,20,21,25,26,27,28,29,31,34,47,51],out_path:4,out_po:25,out_stream:37,out_stream_:37,outdat:[3,5,7],outer:[14,26],outlier:33,output:[0,5,8,11,13,25,27,28,32],output_dir:4,outsid:[8,40],outstand:20,over:[2,4,13,16,26,28,32,34,35,49],overal:[10,34,40,46],overhead:25,overlap:[25,34,35,36],overli:16,overload:37,overrid:[2,5,25,35,50],overridden:4,overriden:5,overview:[8,16],overwrit:[31,49],overwritten:25,own:[1,3,4,16,17,20,25,26,35,48,49,50],owner:20,ownership:20,oxt:[9,21,25],oxygen:[22,35,43,49,50],p_vinaparticl:49,pack:21,packag:[4,8,16],pad:[22,37],page:[2,8,20],pai:1,pair:[9,10,25,26,27,28,32,34,36,37,39,40,41,44,49,51],pairwis:[3,8,10,22,28,31,35,39,41,42,43,44,46,47,49,50,52],pairwise_energi:10,pairwisefunct:[40,41],pairwisefunctiontyp:40,pairwisescor:[8,35,42,49],paper:[43,44,47,49],paragraph:[1,8],parallel:26,paramet:[1,4,8,9,10,11,13,14,15,21,22,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,43,44,45,46,48,49,50,51,52],parameter_index:26,parametr:[3,32,35,36,49,50],parent:35,pars:[0,11,12,25,26,27,28,39,41,51,54],parser:12,part:[0,1,8,16,18,20,21,26,34,35,40,44,46,47,49,54],parti:[16,17,20],partial:29,particip:[36,44],particl:[3,25,26,32,41,43,44,45,47,50],particle_typ:49,particular:[8,10,20,26,31,32,34,49,51],partner:[39,40,41],pass:[13,16,21,25,26,28,29,32,34,35,44,45,49,50],past:[8,16,22,29],patent:20,path:[1,2,4,5,7,8,11,16,18,25,26,27,28,33,39,41,51],path_to_chemlib:15,path_to_dockerfile_dir:5,path_to_promod3_checkout:6,pattern:[28,38],paus:14,pdb:[0,5,7,8,11,13,18,21,22,23,24,25,26,28,30,31,32,33,34,35,36,42,47],penal:[29,35],penalti:[29,35],pentam:28,pentamatch:[3,28],pentamatch_n:28,pentamermatch:[],penultim:3,peopl:16,pep:[1,16],peptid:[3,21,23,25,26,28,35,36,47],peptide_sel:28,per:[4,8,10,12,16,21,27,31,34,35,39,40,41,44],percent:20,percentag:33,perfect:8,perfectli:8,perform:[0,10,16,18,19,20,25,28,31,32,33,34,35,37,40,44],period:25,periodic_dihedr:25,periodic_improp:25,permiss:[8,20],permut:10,perpetu:20,perspect:33,pertain:20,phase:25,phe:[33,49,51],phenix:33,phenylalanin:49,phi:[21,22,26,27,32,34,41,47,50,51],phi_bin:[41,51],phi_handl:47,philippsen:38,phipsisampl:34,phosphoru:49,phosphoserin:35,phrase:8,pick:[31,34],pickl:28,pictur:8,piec:[8,28],pipelin:[0,3,14,19,26,28,29,30,33,34,47,53,54],pivot:[31,32,34],pivot_on:[31,32],pivot_thre:[31,32],pivot_two:[31,32],place:[1,2,4,8,11,13,16,20,26],plain:[0,13],plan:16,planar:[3,30,35],plane:33,platform:[18,25],playground:7,plddt:28,pleas:[2,8,16,28,31,32,35,53],plot:27,plt:27,plu:[8,13,15,26,44,49],pluribu:28,pm3_csc:16,pm3_openmm_cpu_thread:[18,25,35],pm3_runtime_profiling_level:14,pm3argpars:[0,11,12,54],pm3argumentpars:[0,11,13],pm_action:[1,4,8],pm_action_init:8,pm_bin:1,pna:38,png:27,pocket:28,pocket_view:28,point:[2,8,13,15,21,26,28,33,34,35,40,49,51],pointer:[2,8,37],polar:[49,50],polar_direct:49,polici:8,pop:[16,31,34,40],popul:[2,16],port_str_db:26,portabl:[4,17,25,26,27,39,41,51],portable_binary_seri:37,portable_fil:4,portablebinarydatasink:37,portablebinarydatasourc:37,pos:[21,22,26,28,32,49],pos_end:28,pos_on:28,pos_start:28,pos_two:28,posit:[3,8,9,22,23,25,26,27,28,29,31,32,34,35,36,38,39,40,41,43,44,45,46,49,50,54],possibl:[0,3,8,10,13,16,20,22,25,26,27,28,29,31,32,34,35,36,37,39,40,41,44,46,49,51],post:13,postprocess:36,pot:25,pot_:32,potenti:[3,10,23,25,26,28,31,32,35,36,37,38,41,49],power:[7,20],pqhpg:0,practic:[4,8,25,26],pre:[8,16,35],pre_commit:[8,16],preceed:36,precis:[2,31,35],precomput:[23,54],pred:40,predefin:[4,18,25,35,39,41],predict:[13,26,28,35,38,40,41],prefactor:49,prefer:[2,4,20,26,51,52],prefilt:35,prefix:[1,4,8,11],prepar:[8,20,35],preprocess:28,present:[3,22,28,32,36,49,50,51],prev_aa:34,prevent:[1,8],previous:[25,26,31,36,40],primary_rot_angl:22,principl:[3,34,40],print:[1,2,5,20,22,23,25,26,31,32,33,35,42],printstatist:26,printsummari:14,prior:35,privat:[1,37],pro:[21,27,49,51],probabilist:[26,50],probability_cutoff:50,probabl:[4,8,10,13,16,26,27,28,31,32,34,49,50,51],problem:[3,7,10,13,16,26,28,31,32,34,35,40,42,44,46,48,52],problemat:[3,5,28],proce:42,procedur:[10,28,34,36,50],process:[1,3,13,16,21,25,28,32,34,35,37,40,45,49,51],processor:5,produc:[0,1,2,4,8,10,26,29,33,35],product:[1,3,16,20],prof:[0,26,31],prof_dir:26,prof_path:26,profil:[0,3,12,13,26,28,31,35,38,54],profiledb:26,profilehandl:[13,26,28,31,35],prog:13,program:[4,5,8,12],project:[3,4,5,8,16],prolin:[22,33,49],promin:[0,20],promod3:[1,3,7,9,10,11,13,14,15,17,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54],promod3_checkout:7,promod3_mod:4,promod3_nam:4,promod3_name_head:4,promod3_path:8,promod3_root:8,promod3_shared_data_path:[8,37],promod3_unittest:[1,4,8],promod:[5,7],promot:8,propag:[8,22],proper:[16,26,50],properli:[1,35,39,41,50],properti:[21,22,35,50,51],propos:[29,31,32,34,44],proposed_posit:34,proposestep:34,prot:[8,23,26,28,32,34,36,47],prot_rec:8,protein:[0,18,19,24,25,28,33,34,35,36,38,45,47,49,54],proteinogen:26,proton:[21,25,49,51],prototyp:19,provid:[0,1,2,3,4,5,7,8,13,16,20,21,22,23,25,26,28,29,31,32,33,34,35,36,37,40,48,49,50,51],prune:[10,52],pscoringfunct:49,pseudo:[34,35,39,41],psi:[21,22,26,27,32,34,41,47,50,51],psi_bin:[41,51],psi_handl:47,psipr:[13,26,28,40,41],psipred_confid:41,psipred_pr:28,psipred_predict:[26,28,35],psipred_st:41,psipredpredict:[23,28,35,40],pssm:[0,13],publicli:20,pull:[5,8,16,18],pullterminaldelet:35,punch:[1,3,30,35],pure:0,purpos:[8,10,20,35,51],push:16,pushverbositylevel:13,put:[1,4,8,11,13,33,35],pwd:5,py_run:[1,4,8],pyc:1,pylint:16,pylintrc:16,pymod:[4,8,16],pyplot:27,pytest:8,python3:8,python:[1,2,3,4,5,7,8,11,14,15,16,18,21,22,25,28,32,37,49,50],python_root_dir:2,pythonpath:8,qmeandisco:40,qualiti:35,quantum:38,queri:[26,28,51],query_idx:28,query_list:28,querylib:51,question:[3,27],quick:17,quickli:[5,8,32],quit:[8,13],rackovski:38,radian:[9,22,25,27],radii:[33,43],radiu:[8,33,39,41,49],raihvhqfgdlsqgcestgphynplavph:0,rais:[0,9,10,13,21,22,25,26,27,28,29,31,32,33,34,35,36,39,40,41,44,45,49,50,51],rama_iffi:33,ramachandran:33,random:[10,22,24,27,31,32,34],random_se:31,randomized_frag:22,randomli:[27,34],rang:[8,9,21,22,23,25,26,27,28,29,32,34,35,39,40,41,51],rank:31,rapid:38,rare:8,rather:[5,7,8,11,16,34,51],raw:[7,18,25,26,27,28,30,31,37,39,41,44,51],rawmodel:[3,8],rbvi:3,reach:[0,28,29,32],read:[0,8,11,13,16,25,26,27,28,29,36,37,39,41,48,51],readabl:[0,8,13,20,51],readdunbrackfil:48,reader:[16,18],readi:[2,5,51],readm:[2,8,48],real:[8,13,37],realli:[1,2,8,11,16],reappear:16,reason:[8,16,20,32,34,52],rebas:16,rebuild:[2,8],recalcul:27,receiv:20,recent:[3,16],recip:[3,6],recipi:20,recoginz:49,recogn:[0,13],recognis:[1,8,16],recognit:38,recommend:[2,5,8,20,25,35],reconstruct:[0,3,8,18,21,22,25,30,32,35,44,47,49,52,54],reconstructcbetaposit:22,reconstructcstemoxygen:22,reconstructor:[32,35,36],reconstructoxygenposit:22,reconstructsidechain:[0,3,8,35,36],reconstructtest:8,record:[1,35],recreat:16,redistribut:20,redo:28,reduc:[3,25,28,35,41],reduced_scor:37,reducedscor:[35,37,42],redund:[24,31,33],ref_backbon:[23,26],ref_fil:8,refactor:3,refer:[1,4,8,18,19,21,22,23,25,26,28,34],referenc:8,refin:28,refine_thresh:28,refresh:31,regard:[20,32,44],region:[0,25,28,29,32,34,35,45,50],regist:[4,8],regress:38,regularli:5,reinterpret_cast:37,reintroduc:3,reject:[31,32,34],rel:[4,5,9,10,26,28,32,41],relat:[4,8,13,26,28,37,38,49],relax:[30,35],releas:[2,5,8,16],relev:[2,3,4,7,25,28,36,49],reli:5,remain:[20,30,34,35],rememb:[1,8,34],remodel:[28,31,36],remodel_cutoff:36,remov:[2,3,10,22,25,26,29,31,33,35,36,40,47,49],removecoordin:26,removeterminalgap:35,renumb:[26,35],reorder:35,reordergap:35,repeat:28,replac:[3,20,21,22,34,35],replacefrag:22,report:[1,3,8,35],reportmolprobityscor:33,repositori:[1,4,8,16,53],repres:[10,20,21,23,26,27,28,29,40,41,44,45,46,47,50,52,54],represent:[22,23,25,26,27,37,39,41,49,51],reproduc:[3,20,35],reproduct:20,repuls:49,request:[26,28,48,51],requir:[0,2,3,5,8,13,16,19,20,21,22,26,27,28,31,32,35,36,37,42,49,50,51],reread:26,res:[9,21,22,25,28,31,32,33,36,40,49,50,51],res_depth:26,res_idx:[49,50],res_index:21,res_indic:[21,25,36],res_list:[21,25,32,36],res_num:21,resembl:[16,28],reserv:11,reset:[10,21,25,32,34,40,49],resid:5,residu:[0,3,8,9,21,22,23,24,25,26,27,28,29,31,32,33,34,35,36,38,39,40,41,42,44,45,47,49,50,51],residue_depth:26,residue_index:[45,49,50],residue_list:35,residuedepth:26,residuehandl:[9,21,22,26,29,31,32,33,34,35,49,50,51],residuehandlelist:21,residueview:[33,35],resiz:[22,37],resnum:[21,22,29,31,35,36,40],resnum_on:40,resnum_rang:35,resnum_two:40,resolut:[22,32],resolv:[16,21,32,35],resolvecystein:44,resort:35,respect:[9,25,28,35],respons:[8,16,20],rest:[1,8,16,36],restor:[22,31,34,40],restraint:[26,32],restrict:[8,16,29],restructuredtext:[4,8],result:[0,2,3,8,10,20,25,27,28,31,32,33,34,35,36,38,44,51],resum:14,retain:[20,28,35],retriev:28,return_count:28,reus:[35,36],review:[16,53],revis:20,reviv:16,rewrit:1,richardson:38,ridig:36,right:[1,2,8,10,13,20],rigid:[0,3,30,32,34,36,46,47,49,51,52,54],rigid_frame_cutoff:36,rigidblock:28,rij:43,ring:[3,30,35],ring_punch_detect:35,risk:20,rmsd:[22,23,26,28,31,32],rmsd_cutoff:[26,31,32],rmsd_thresh:[26,28],rname:28,rnum:40,robot:38,role:13,root:[2,4,8,16],rosetta:41,rot:36,rot_constructor:47,rot_group:[47,50],rot_lib:50,rot_lib_entri:50,rota_out:33,rotam:[0,3,33,36,38,44,45,47,52,54],rotamer:[48,51],rotamer_group:[44,46,47],rotamer_id:47,rotamer_librari:[3,35,36,48],rotamer_model:36,rotamer_on:44,rotamer_res_indic:36,rotamer_two:44,rotamerconstructor:[3,47,49],rotamergraph:[36,46,47,52],rotamergroup:49,rotamerid:[47,50,51],rotamerlib:[35,36,37,48,50,51],rotamerlibentri:[50,51],rotat:[9,22],rotatearoundomegators:22,rotatearoundphipsitors:22,rotatearoundphitors:22,rotatearoundpsitors:22,rotationaroundlin:9,roughli:24,round:51,routin:[1,18,31],royalti:20,rrm:36,rrmrotam:[44,49,50],rrmrotamergroup:[44,46,49,50],rst1:4,rst2:4,rst:[4,8,16],rsync:8,rule:[5,8,9,16],run:[0,4,7,8,10,13,14,15,16,25,26,31,32,33,35,54],runact:1,runexitstatustest:1,runmolprob:33,runmolprobityent:33,runnabl:8,runner:1,runtest:[1,8],runtim:[0,3,10,12,35,50,54],runtimeerror:[9,10,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,44,45,48,49,50,51],runtimeexcept:27,s_id:26,s_vinaparticl:49,safe:[2,8],said:4,same:[0,1,2,4,7,8,10,13,14,20,21,25,26,28,31,32,33,34,35,36,37,39,40,41,42,45,48,49,50,51],samiti:35,sampl:[0,3,8,22,23,28,31,34,35,54],sampled_frag:34,samplemontecarlo:[3,34],sampler:[3,23,24,26,28,30,31,32,35],samplerbas:34,sampling_start_index:34,sander:38,saniti:2,sanity_check:2,satisfi:49,save:[16,22,25,26,27,28,31,34,37,39,40,41,51],savebb:26,savecach:28,savefig:27,savepdb:[7,18,21,22,25,26,28,30,31,32,34,35,36,47],saveport:[25,26,27,37,39,41,51],sc_data:32,sc_rec:[32,36],sc_rec_test:36,sc_result:32,scale:22,scatter:27,scheme:[1,8,13,21,26,29,34],schenk:38,schmidt:38,schwede:[5,8,18,19,38,53],sci:38,scicor:[5,8,18,19,53],scondari:35,scope:14,score:[0,3,8,13,19,23,26,28,29,30,33,34,35,36,37,38,39,41,44,47,54],score_contain:31,score_env:[31,34,42],score_threshold:44,score_vari:35,scorecontain:31,scorer:[3,17,28,30,31,35,40,42,54],scorer_env:[28,31,34],scorerbas:34,scoring_weight:28,scoringgapextend:[29,35],scoringweight:[28,31,35],scratch:[26,34],script:[2,3,4,7,11,13,16,17,18,26,28,37,48,54],scriptnam:11,scriptpath:8,scwrl3:[36,42,50],scwrl3disulfidscor:[43,44],scwrl3pairwisescor:43,scwrl3rotamerconstructor:50,scwrl4:[0,36,38,44,47,50],scwrl4particletyp:49,scwrl4rotamerconstructor:[3,47,50],scwrlrotamerconstructor:3,seamlessli:16,search:[0,2,3,8,21,26,28,31,33,35,36,41,44,49,50],search_kei:28,searchdb:[23,26],second:[8,10,22,25,26,28,31,32,35,39,40,41,43,44],secondari:[3,13,26,28,38,41],secondli:8,section:[1,4,7,17,20,53,54],see:[0,1,3,7,8,9,10,11,13,16,18,20,21,25,26,27,28,29,31,33,34,35,37,39,40,41,51],seed:[10,24,27,31,32,34],seem:16,segment:22,select:[3,10,26,28,34,35,36,47],selenium:35,self:[1,8,10,44,47,49],self_energi:[10,49],sell:20,send:11,sensibl:35,sensit:[3,28],sent:20,seok:38,separ:[1,3,8,10,20,25,27,35,39,41,44],seq:[13,21,23,26,28,29,31,35,40,42],seq_idx_on:28,seq_idx_two:28,seq_one_idx:28,seq_sep:[39,41],seq_tpl:[31,35],seq_trg:[31,35],seq_two_idx:28,seqid:[24,26,28],seqid_thresh:28,seqprof:13,seqr:[0,21,23,26,28,29,31,34,35,36,39,40,41],seqres_str:[21,32,36],seqsim:26,sequenc:[0,3,7,8,13,18,21,22,23,27,28,29,30,31,32,34,35,38,39,40,41],sequencefromchain:42,sequencehandl:[21,26,28,29,35,40],sequencelist:[21,35,40],sequenceprofil:26,sequenti:[22,35],ser:49,serial:[26,37],serializ:37,serin:49,serv:[1,13,26,28,31,34],server:28,servic:[16,20],set:[1,2,4,8,10,11,13,15,16,18,21,22,25,26,28,31,32,33,34,35,36,37,39,40,41,44,47,49,50,51,52],setaa:22,setactivesubrotam:49,setallatomscoringkei:31,setaroundomegators:22,setaroundphipsitors:22,setaroundphitors:22,setaroundpsitors:22,setbackbonescoringkei:31,setbackrub:22,setboolprop:50,setc:22,setca:22,setcb:22,setcharg:25,setcompoundschemlib:[19,54],setcpuplatformsupport:25,setdefault:25,setdisulfidconnect:25,setenergi:[39,41],setenviron:[21,32,36,40],setepsilon:25,setfraggerhandl:35,setframeenergi:[47,49],setfudgelj:25,setfudgeqq:25,setinitialenviron:[21,31,32,34,36,40,42],setinternalconnect:25,setinternalenergi:49,setinternalenergyprefactor:49,setinterpol:51,setmass:25,setn:22,setnonbondedcutoff:32,seto:22,setolc:22,setpeptideboundconnect:25,setphitors:22,setpo:21,setprob:49,setpsipredpredict:[35,40,41],setpsitors:22,setresidu:21,setscor:41,setsequ:22,setsequenceoffset:35,setsequenceprofil:35,setsequenceprofilescoreskei:31,setsigma:25,setstemrmsdskei:31,setstructureprofil:26,setstructureprofilescoreskei:31,settemperatur:49,setup:[0,2,5,8,13,17,25,28,31,32,34,35,37,39,40,41,42],setupdefaultallatomscor:[31,35],setupdefaultbackbonescor:[31,35],setupsystem:25,setvinaweightgaussian1:49,setvinaweightgaussian2:49,setvinaweighthbond:49,setvinaweighthydrophob:49,setvinaweightrepuls:49,setweight:31,sever:[0,2,3,5,8,10,13,24,26,27,28,31,32,35,36,40,41,42,44,48,49,51,52],sg_pos_on:43,sg_pos_two:43,shake:34,shall:20,shanno:35,shapovalov2011:[38,48],shapovalov:38,share:[5,7,12,17,20,25,37,53,54],shared_ptr:37,shebang:8,sheet:35,shelenkov:38,shell:[1,2,7,8,11],shift:[22,26,29,35],shiftctermin:29,shiftextens:29,ship:[5,48],shorten:35,shorter:[28,35],shortest:31,shortli:8,should:[1,2,4,5,7,8,10,11,13,16,18,20,22,23,26,27,28,31,32,34,35,36,37,40,45,47,49],show:[1,8,13,14,31,34,47,50],show_fil:7,showcas:[1,21,25,27],shown:[8,14,35],shrink:22,shrug:38,side:[8,35,38],sidechain:[3,8,18,19,25,30,32,33,35,37,38,43,44,45,46,48,50,51,52,54],sidechain_pymod:8,sidechain_reconstructor:35,sidechain_rst:8,sidechain_test_data:8,sidechain_test_orig:36,sidechain_test_rec:36,sidechain_unit_test:8,sidechainparticl:50,sidechainreconstructiondata:[30,32],sidechainreconstructor:[25,30,32,35],sidenot:[26,36],sig1:51,sig2:51,sig3:51,sig4:51,sigma:25,silent:1,sim:25,similar:[1,2,3,13,16,23,26,28,40,41,51],similardihedr:51,similarli:[2,25,35],simpl:[0,9,22,26,28,34,35,39,40,41,49,51],simpler:[25,35],simplest:[5,8,30],simpli:[5,21,22,28,31,32,34,35,49,50,51],simplic:[23,26],simplif:13,simplifi:[3,22,25,26],simul:[10,25,31,32,34,35],sinc:[1,2,4,8,10,11,16,18,22,25,26,27,28,49],singl:[2,4,8,10,21,22,25,26,28,31,32,34,35,36,40,41,45,48,49,50,52],singleton:25,singular:[3,6,28,33,54],sink:37,sit:8,site:[3,5,8,28],size:[8,21,22,26,27,28,32,34,35,37,39,40,41],sizeof:37,skip:[0,1,8,16,26,28,35,50],slide:28,slight:35,slightli:35,slope:28,slow:37,slower:[18,25,26,27,35,39,41,51],small:[8,26,32,35,36],smaller:[22,26,28,32,35,41],smallest:47,smallish:[2,8],smart:16,smng:3,smooth:38,smtl:35,snippet:7,soding2005:[26,38],softsampl:34,softwar:[8,20,38,49],sol:47,sole:[1,16,20,28],soli:38,solis2006:[24,38],solut:[8,10,28,31,32,34,35,36,46,47],solv:[10,16,47,52],solvent:26,solventaccess:26,solver:3,some:[1,2,4,5,6,7,8,13,16,21,23,26,30,33,34,35,36,37,40,42,47,50,51],somedata:37,someth:[1,8,11,16,26],sometim:16,somewher:4,soon:[10,32,41,47,51],sort:[1,4,10,14,31,34,51],sound:[16,50],sourc:[1,2,4,8,13,16,18,19,20,26,28,31,32,33,35,37,51],source1:[4,16],source2:[4,16],source3:4,source4:4,source_chain_idx:35,source_mhandl:35,sp3:51,space:[3,10,28,34,38],span:35,sparticl:49,spatial:[8,28,42],spawn:[1,8],spdbv:35,spdbv_style:35,special:[1,2,4,8,20,25,34,49,50,51],specif:[1,3,8,20,25,26,27,28,31,34,38,40,47,48,49,51],specifi:[0,2,3,4,5,9,10,22,26,27,28,31,32,35,36,40,49,51],specimen:11,speed:[3,25,35,38],spent:[14,18],sphere:[43,49],sphinx:[2,8],spin:38,spit:[29,34],split:[28,42],sport:8,squar:26,src:[8,16],ss_agreement:41,ss_agreement_scor:37,ssagre:26,ssagreementscor:[37,42],sse:2,sstream:37,stabil:38,stabl:[5,16],stack:16,stage:[1,2,4,8,17,18,28,37,40,51],stai:[1,8,10,16,34],standalon:7,standard:[2,8,12,13,16,21,27,37,41,51],start:[0,1,2,4,7,10,14,16,17,19,21,22,25,26,28,29,31,32,34,35,36,40,41,42,54],start_idx:31,start_resnum:[21,22,26,31,34,35,36,39,40,41],start_resnum_list:36,start_rnum:40,start_temperatur:[10,34],starter:1,startscop:14,stash:[16,31,34,40],state:[1,2,8,20,21,26,31,34,40,41,44,49,51],statement:20,staticruntimeprofil:14,statist:[14,26,38],statu:[1,8],std:37,stderr:1,stdout:1,steadili:[10,34],steepest:[32,35],stem:[9,22,25,26,28,29,31,32,34,35,36],stemcoord:9,stempairorient:9,step:[3,8,10,14,16,18,19,28,29,30,31,32,34,40,44],stereo:35,stereo_chemical_problem_backbon:35,stereochem:[3,35],steric:51,still:[8,14,25,26,35,37],stop:[1,8,14,28,29,32],stop_criterion:32,stoppag:20,storabl:26,storag:[3,8,21,25,28,39,41],store:[0,1,3,7,8,9,16,18,21,22,25,26,27,28,29,31,32,34,35,36,37,47],stori:8,str:[1,11,13,14,15,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,51],str_len:37,straight:16,strategi:51,stream:37,stretch:[21,26,28,31,34,35,40,41],strict:16,strictli:3,string:[0,3,11,13,26,27,29,37],stringstream:37,strip:[0,35],struc:5,struct:[5,26,37],struct_db:23,structral:[21,40],structur:[0,3,8,13,17,18,19,21,22,23,24,25,27,28,29,30,31,33,34,35,36,37,38,40,41,42,47,49,50,52,54],structural_db:31,structuralgap:[29,33],structuralgaplist:[29,35],structure_db:[26,28,31,35,37],structure_db_on:26,structure_db_two:26,structure_dir:26,structure_id:26,structure_path:26,structure_sourc:13,structuredb:[3,13,24,26,28,31,35,37],structuredbdatatyp:26,structureprofil:26,studer:38,stuff:[26,39],style:[35,40,41,49],sub:[8,26],sub_frag:22,sub_res_list:26,subclass:[8,13],subdir:8,subfold:8,subject:[8,20],sublicens:20,submiss:20,submit:20,submodul:8,submodule1:16,subpart:28,subrotam:[0,3,44,47,49,50,54],subrotameroptim:[36,52],subsequ:[10,20,22,35,49],subset:[0,13,25,26,28,31,32,35,36],subst:26,subst_matrix:26,substitut:26,substweightmatrix:26,subtre:[4,8],succeed:29,success:[10,11,34],successfulli:5,sudo:7,suffici:26,suffix:11,sugar:6,suggest:[5,8,43],suit:[1,8,26],sulfur:[43,44,49,50],sum:[14,28,29,35,36,43,44,49],sum_:10,sum_i:10,sum_ie_:10,summari:[14,26],superpos:[22,26,28,31,32,34],superpose_stem:22,superposed_rmsd:[22,31],superposeonto:22,superposit:[3,28,31,34],superpost:28,supersed:20,supervis:1,support:[0,1,2,3,8,11,13,18,20,25,32,35],suppos:[16,34],sure:[2,7,8,13,16,26],surfac:26,surotam:49,surprisingli:50,surround:[25,26,32,36,39,41],swap_thresh:28,symmetr:[26,40,51],symmetri:[39,41],sync:8,syntax:20,sys:[1,13,32],system:[1,2,4,8,16,20,23,26,32,42,54],t_sampler:27,tabl:26,tag:5,tail:22,tailor:[21,35],take:[8,10,21,26,27,28,31,32,34,35,37,41,44,50,52],taken:[0,21,25,32,34,50],talk:1,target:[0,1,2,4,8,13,18,26,28,30,31,32,34,35,40,49],target_chain_idx:35,target_mhandl:35,target_pdb:33,target_posit:28,target_sequ:26,task:[8,16,32,35,37,40],techniqu:[10,38],tell:[1,8,11,13,16,26],temperatur:[10,31,34,49],templat:[0,1,3,13,18,28,30,35,37,40],temporari:[26,35],temporarili:16,term:[8,20,26,49,51,52],termin:[0,1,9,11,18,20,21,22,25,29,31,32,34,35,36,50],terminal_len:34,terminal_seqr:34,termini:[0,3,29,34,35],terminu:[26,34,35],test:[2,7,12,16,17,18,25,26,33,37],test_:8,test_act:[8,17],test_action_:1,test_action_do_awesom:1,test_action_help:1,test_awesome_featur:8,test_check_io:37,test_cod:8,test_doctest:8,test_foo:4,test_portable_binari:37,test_reconstruct_sidechain:8,test_sidechain_reconstruct:8,test_submodule1:16,test_suite_:4,test_suite_your_module_run:8,test_your_modul:16,testcas:[1,8],testcasenam:8,testexit0:1,testpmexist:1,testreconstruct:8,testutil:[1,8],text:[1,13,20,35],than:[4,8,13,14,16,21,22,26,28,31,32,33,35,36,41,44,50],thats:[26,41],thei:[2,5,8,16,21,22,25,26,27,28,31,32,33,34,35,44,49,50,51,53],them:[4,8,16,22,25,26,27,28,29,31,35,36,40,45],themselv:25,theoret:34,theori:[20,38],therefor:[5,8,22,24,26,28,32,34,35,51],thereof:[20,25],thi:[0,1,2,3,4,5,7,8,10,11,12,13,14,15,16,17,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,42,44,47,49,50,51,52,54],thing:[1,2,8,16,26,28,35,51],think:10,third:[16,17,20,31,32],thoroughli:16,those:[0,1,2,4,8,10,13,16,20,25,28,31,35,36,37,39,41,47,50,51],though:[25,35,37],thr:49,thread:[18,25,35,38],three:[1,4,16,21,22,27,28,31,33,34,38,41,49,51],threonin:49,thresh:[22,49,51],threshold:[10,26,28,32,33,35,36,40,51],through:[1,8,9,20,22,26,29,35,39,41],throughout:[13,16,24,25],thrown:26,thu:[5,11,33,49],tidi:16,tightli:16,time:[1,5,8,13,14,16,18,28,35],timer:14,tini:[16,35],titl:[20,27],tlc:[21,49],tlc_an:21,tlctorotid:[47,49],tmp_buf:37,todens:22,toentiti:[7,18,21,22,25,26,32,34,36],toframeresidu:49,togeth:[8,16,26,44],toler:35,tolerance_lbfg:35,tolerance_sd:35,too:[13,16,31,32,35,37],tool:[3,4,23,35,37,42,47],toolbox:16,top:[2,6,8,14,15,16,28,32,35],topic:[1,8,16],topn:28,topolog:[25,32],torrmrotam:49,torsion:[0,13,21,22,23,24,26,28,31,32,34,35,41,47],torsion_angl:47,torsion_bin:41,torsion_plot:27,torsion_sampl:[22,26,31,32,34,35,37],torsion_sampler_coil:[28,37],torsion_sampler_extend:[28,37],torsion_sampler_hel:37,torsion_sampler_helix:28,torsion_sampler_list:26,torsion_scor:37,torsionprob:26,torsionsampl:[22,24,26,27,28,31,32,34,35,37,41],torsionscor:[35,37,42],tort:20,total:[10,14,26,28],touch:[1,8,25,32],toward:[0,3,8,13,26,28,29,32,35,39,41,47,49,50,52],tpl:[0,28,30,31,35],tpl_n:28,tpr:[49,51],trace:35,track:[3,11,20,30,35,47],trade:20,trademark:20,tradition:11,trail:0,train:[24,31,35],trajectori:[28,34],tran:[22,49,51],transfer:[20,28],transfer_bfactor:28,transform:[9,20,22,28,34,35,51],translat:[4,8,20,26,49,51],transomegators:22,treat:[3,8,25,28,35,36,37,51],treatment:50,tree:[1,4,8,10,16,46,47],treepack:3,treesolv:[10,36,47],trg:[0,13,31,35],trg_seq:28,tri:[10,28,29,35,44,51],triangl:28,trick:[1,7,16],trigger:[1,4,8,48],tripeptid:27,tripl:11,triplet:[23,28,34,41],trott2010:[38,49],trott:38,trp:[33,49,51],trustworthi:16,tryptophan:49,ttccpsivarsnfnvcrlpgtpea:[31,35],ttccpsivarsnfnvcrlpgtpeaicatgytciiipgatcpgdyan:35,ttccpsivarsnfnvcrlpgtpeaicatytgciiipgatcpgdyan:[31,35],tupl:[9,10,11,22,25,26,28,29,33,35,36,44],turn:[0,1,11,14,16,35],tutori:8,tweak:35,twice:[14,40],two:[1,7,8,10,16,21,22,25,26,28,29,31,32,35,36,37,39,40,41,43,44,47,49,51],txt:[1,2,4,8,16,20],type:[0,1,8,9,10,11,13,14,20,21,22,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,43,47,48,49,50,52],typedef:37,typenam:37,typic:[22,28,34,35,47,51],tyr:[33,49,51],tyrosin:49,ucsf:3,uint32_t:37,uint:37,ultra:26,uncertain:8,uncharg:50,unclos:35,undefin:25,under:[4,8,20],undergo:[28,32,34,36],underli:[28,29,31,49],underscor:1,understand:16,understood:0,undo:10,unexpect:2,unfavor:[22,32],unfavour:[32,34,44],unfortun:16,unhandl:[0,13],uniba:[5,8,18,19,53],uniform:32,union:20,uniprot:28,uniprot_ac:28,uniprotac:28,uniqu:[0,13,28,31,34,51],unique_pentam:28,unit:[2,16,17,37],unittest:[1,8,16],univers:[8,53],unix:16,unknown:25,unless:[13,20,21,22,25,31,39,41],unlik:47,unrecognis:11,unset:[21,25,36],unsupport:[13,37],until:[8,10,28,32,35,40,50],untouch:22,untrack:1,unum:28,unus:16,upat:5,updat:[3,5,7,8,16,21,25,28,29,31,32,35,36,40,42],updatedistribut:27,updateposit:[25,32],upon:[26,32,34],upper:28,ups:3,urei:25,urey_bradley_angl:25,usabl:16,usag:[0,3,10,13,24,26,31,32,36],use:[0,2,3,4,5,8,10,13,16,18,20,21,22,23,25,26,27,28,30,31,32,34,35,36,37,47,48,49,50],use_amber_ff:35,use_bbdep_lib:36,use_frm:36,use_full_extend:35,use_scoring_extend:35,used:[0,2,3,4,8,9,10,11,13,14,15,16,18,21,24,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,42,45,47,48,49,50],useful:[1,3,8,10,11,22,26,28,30,31,32,35,50],user:[1,5,8,19,28,53],userlevel:1,uses:[5,8,10,22,25,27,28],using:[1,2,3,4,7,8,10,18,20,21,22,25,26,28,31,33,34,35,37,38,39,41,44,45,46,47,49,50,51,54],usr:[2,5,7,8],usual:[1,2,4,8,13,14,16,22,31,35,39],util:18,utilis:[8,16],v_size:37,val:[27,49],valid:[0,10,16,22,26,29,34,35,36,48,51],valin:49,valu:[2,10,11,13,21,22,25,26,28,31,33,34,35,37,39,40,41,44,47,49,50,51,52],valueerror:[28,35],vanish:40,varadarajan:38,vari:[4,37],variabl:[1,2,3,8,14,18,25,33,35,37,49],varianc:33,variant:[25,31],variou:[1,2,4,16,30],vec3:[9,21,22,26,32,33,43,44,49],vec3list:[28,49],vector:[25,27,28,31,37,49],verbal:20,verbos:1,veri:[1,8,11,16,25,28,35,37],verif:13,verifi:[1,11,16],version:[2,3,5,8,16,20,26,28,35,37,48,49],vertic:28,via:[1,5,8,13,15,25],view:[7,13,16,27,35,40],vina:[3,36,38,50],vinaparticletyp:[49,50],vinarotamerconstructor:50,virtual:8,visibl:36,vision:38,visual:18,volum:5,wai:[1,2,4,5,8,16,22,23,25,28,31,41,47,49],wait:8,walk:[1,8],want:[1,2,3,8,15,16,22,26,28,31,32,35,40,49,50,51,52,53],warn:[3,8,16,35],warranti:20,watch:8,web:[2,8],weight:[3,26,28,31,34,35,39,41,49],weird:[28,32,47],well:[0,4,16,21,27,28,29,31,35,37,41,47,50,51],went:[0,8],were:[16,26,31,35],wester:38,wether:10,what:[1,8,11,13,16,23,26,36,40],when:[1,3,4,5,8,10,13,14,21,22,25,26,27,28,29,31,34,35,36,37,38,40,41,44,47,48,49,50,51],whenev:[8,21,31,40],where:[0,1,3,4,5,8,10,11,13,14,16,20,21,22,25,26,27,28,31,35,37,39,40,41,48,49,50,51],wherea:26,wherev:20,whether:[3,5,8,10,11,13,20,22,25,26,31,32,34,35,36,39,40,41,49,50,51],which:[0,1,2,4,8,9,11,12,13,16,18,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,40,41,49,50,51],whistl:8,whitespac:0,who:[10,47],whole:[1,2,8,16,20,22,26,28,35,49],whom:20,why:[1,16],width:[10,37,47],wild:4,window:28,window_length:28,wise:4,wish:[2,17,27,35],with_aa:31,with_db:31,within:[2,3,4,8,14,16,20,21,25,28,29,33,35,36,39,41,51],without:[0,1,3,4,8,11,13,20,25,29,32,35,40,51],wolfson:[28,38],won:[0,35,36,50],word:4,work:[1,2,4,5,7,8,14,16,18,20,25,29,35,37,50],worldwid:20,worst:16,worth:53,would:[1,2,8,11,22,26,27,35,44,49],wrap:26,wrapper:[1,4,8,15,35],write:[0,17,20,26,27,32,37,39,41,51],writebasetyp:37,writemagicnumb:37,writetypes:37,writeversionnumb:37,written:[8,20,28,37],wrong:[2,13],wwpdb:5,www:[3,20],x_1:10,x_2:10,x_i:10,x_j:10,x_n:10,xlabel:27,xlim:27,xml:8,xxx:[22,49],xxx_num_atom:21,xxx_num_hydrogen:21,year:1,yet:[26,31,35],ylabel:27,ylim:27,you:[0,1,2,3,4,5,7,8,10,11,13,14,15,16,18,20,21,22,23,25,26,27,28,30,31,32,33,34,35,36,37,39,40,41,47,48,49,50,51,52,53],your:[1,2,4,5,13,14,16,17,18,20,22,26,28,35,37,48],your_modul:[8,16],yourself:[2,8,10,16,35,50],yyyi:20,zero:[0,26,28,35,51],zhou2005:[26,38],zhou:38,zip:[26,47]},titles:["ProMod3 Actions","<code class=\"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 Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal notranslate\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal notranslate\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"docutils literal notranslate\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],For:[4,11,17,54],Into:32,The:[1,5,7,16,21,22,26,27,31,35,36,45,49,50,51],Using:[2,37],With:33,acid:[21,25,27],action:[0,1,4,5,8],actiontestcas:1,afdb:28,algorithm:28,align:35,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,app:7,argument:13,atom:[21,32,39],avail:7,backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:[1,5],exisit:37,extend:29,featur:[8,26],fiddl:35,file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:5,instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:[33,51],novo:[28,34],object:[24,34,45],optim:52,ost:25,other:43,output:1,own:[5,8],pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],planar:33,pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,5,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,registri:5,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}}) \ No newline at end of file diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html index 0ab78f1095cb968d4b9a1304c5051b111f246d80..0b1d32367613367ccd9963f462f0294ab46c8387 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 3.3.0 documentation</title> + <title>Disulfid Bond Evaluation — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -66,10 +67,10 @@ 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/2.3.1/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> +<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li> </ul> </td> </tr> @@ -102,8 +103,8 @@ 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/2.3.1/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>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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li> <li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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 diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html index 0c4e69f76d9f06ced8b62d5b0b2c9c280f2a3f94..edea19a3247e3b722dcf1ad18c359b6b407ff0f3 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 3.3.0 documentation</title> + <title>Frame - The Rigid Part — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html index cc59c634e77b3fa91f1f7a6d51c173b2fde12acf..e2d8d5341bb8a2674ea6aa3c4c0193f1c9209f50 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 3.3.0 documentation</title> + <title>Rotamer Graph — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html index 855b5a7cd5b033add84bdc7877e501e409fa439b..95b85c1a42d228363605f6ca5fadcc02e63e3df0 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 3.3.0 documentation</title> + <title>sidechain - Sidechain Modelling — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html index a0efe0432eda3eaad35edccfd91602a29bdd5a63..331b5e35c793d00857c02ca38c91cbe82aa43753 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 3.3.0 documentation</title> + <title>Loading Rotamer Libraries — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html index 3ae62751fe7a39fba0b3534fddd0e8f218f99341..4f5f95470c67447688426c01f224c85ac5785104 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 3.3.0 documentation</title> + <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -89,7 +90,7 @@ 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/2.3.1/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 +functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a> enum or from amino acid three letter codes.</p> <dl class="method"> <dt id="promod3.sidechain.TLCToRotID"> @@ -114,12 +115,12 @@ 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/2.3.1/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> +defined in <a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><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/2.3.1/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 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/2.4/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td> </tr> <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td> </tr> @@ -217,7 +218,7 @@ 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/2.3.1/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 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/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td> </tr> </tbody> </table> @@ -275,7 +276,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li> <li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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, @@ -284,7 +285,7 @@ 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/2.3.1/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, +<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle, relevant for the hydrogen bond term. If set, the particle is a potential hydrogen bond donor. An example would be the Serine HG hydrogen. The @@ -316,7 +317,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li> </ul> </td> </tr> @@ -428,7 +429,7 @@ 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/2.3.1/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>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li> </ul> </td> </tr> @@ -506,7 +507,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li> <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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 @@ -782,7 +783,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li> <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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 @@ -1182,7 +1183,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li> <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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 @@ -1316,7 +1317,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li> <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/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 diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html index fc7229f75dd6e2860034418835fc85037e9fc22b..fe7e92accec4a51a4fb9bc4cfccfdb913df87a62 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 3.3.0 documentation</title> + <title>Rotamer Constructor — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -68,7 +69,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li> <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li> <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -123,7 +124,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li> <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li> <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -166,7 +167,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li> <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li> <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -254,7 +255,7 @@ 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/2.3.1/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>. +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>. This can be useful to mark a region occupied by a ligand. Note, that there won’t be any parametrization of hbonds in this function. All heavy atoms of the residue will be represented as carbons and hydrogens are @@ -264,7 +265,7 @@ 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/2.3.1/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 +<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li> <li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -280,7 +281,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using a heuristic treatment of the atoms based on the passed compounds library. This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ConstructFrameResidue()</span></code></a>, which will be called by this function if the residue is not known by the given @@ -298,10 +299,10 @@ 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/2.3.1/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 +<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li> <li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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/2.3.1/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> +<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li> </ul> </td> </tr> @@ -461,7 +462,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using a heuristic treatment of the atoms. It is important that the residue has proper bonds assigned, as they influence the atom typing procedure. Furthermore, you need hydrogens to automatically estimate the correct @@ -479,7 +480,7 @@ 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/2.3.1/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 +properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling at.SetBoolProp(“is_hbond_donor”, False) and at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</li> @@ -503,7 +504,7 @@ 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/2.3.1/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 +<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></li> <li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/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> @@ -525,7 +526,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td> </tr> <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td> @@ -545,7 +546,7 @@ 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/2.3.1/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 +<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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td> </tr> <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td> diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html index b2f7c4e36626f8ea03dbea899ead36b5eda4d1d4..b80adf5fcd6fc600a1a69f50ef35dca9e5b91c9c 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 3.3.0 documentation</title> + <title>Rotamer Library — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> @@ -433,7 +434,7 @@ 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/2.3.1/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 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/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td> </tr> <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> @@ -457,7 +458,7 @@ 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/2.3.1/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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.4/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li> <li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></li> </ul> </td> diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html index c1ae5456ea803a5af66a4d12bbfd122efe321a03..949fd907f452a5907e0f0998185ae9d8e5996a1a 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 3.3.0 documentation</title> + <title>Subrotamer Optimization — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html index 109d865d4bafda395c30bb65af8b2f9c7a6bf7d5..49966f020f6e8e44efb4b2b91ada8de7565b709a 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 3.3.0 documentation</title> + <title>Contributing — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/html/users.html b/doc/html/users.html index 82c3ffa195f703025db6ebc0aa823dcc98d19534..bdc7e621c50e2c92c330c6c9c07997bc491343cb 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 3.3.0 documentation</title> + <title>Documentation For Users — ProMod3 3.3.1 documentation</title> <link rel="stylesheet" href="_static/alabaster.css" type="text/css" /> <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script> @@ -14,6 +14,7 @@ <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" /> diff --git a/doc/tests/scripts/model.pdb b/doc/tests/scripts/model.pdb new file mode 100644 index 0000000000000000000000000000000000000000..b5ea368f1b2291f9882223d144bb28d67622e9a8 --- /dev/null +++ b/doc/tests/scripts/model.pdb @@ -0,0 +1,329 @@ +ATOM 1 N THR A 1 17.058 14.169 3.566 1.00 13.79 N +ATOM 2 CA THR A 1 16.973 12.869 4.357 1.00 10.80 C +ATOM 3 C THR A 1 15.717 12.792 5.167 1.00 9.19 C +ATOM 4 O THR A 1 15.267 13.818 5.673 1.00 9.85 O +ATOM 5 CB THR A 1 18.173 12.733 5.294 1.00 13.02 C +ATOM 6 OG1 THR A 1 19.350 12.622 4.511 1.00 15.06 O +ATOM 7 CG2 THR A 1 18.155 11.517 6.244 1.00 14.23 C +ATOM 8 N THR A 2 15.107 11.597 5.303 1.00 7.81 N +ATOM 9 CA THR A 2 13.850 11.417 6.016 1.00 8.31 C +ATOM 10 C THR A 2 14.082 10.710 7.328 1.00 5.80 C +ATOM 11 O THR A 2 14.790 9.711 7.408 1.00 6.94 O +ATOM 12 CB THR A 2 12.773 10.665 5.243 1.00 10.32 C +ATOM 13 OG1 THR A 2 13.155 9.360 4.828 1.00 12.81 O +ATOM 14 CG2 THR A 2 12.512 11.409 3.939 1.00 11.90 C +ATOM 15 N CYS A 3 13.486 11.239 8.408 1.00 5.24 N +ATOM 16 CA CYS A 3 13.663 10.729 9.754 1.00 5.39 C +ATOM 17 C CYS A 3 12.279 10.484 10.319 1.00 4.45 C +ATOM 18 O CYS A 3 11.411 11.343 10.183 1.00 6.54 O +ATOM 19 CB CYS A 3 14.383 11.769 10.648 1.00 5.99 C +ATOM 20 SG CYS A 3 15.922 12.435 9.949 1.00 0.00 S +ATOM 21 N CYS A 4 11.999 9.322 10.938 1.00 3.90 N +ATOM 22 CA CYS A 4 10.657 8.992 11.396 1.00 4.24 C +ATOM 23 C CYS A 4 10.614 8.772 12.908 1.00 3.72 C +ATOM 24 O CYS A 4 11.593 8.320 13.497 1.00 5.30 O +ATOM 25 CB CYS A 4 10.102 7.733 10.692 1.00 4.41 C +ATOM 26 SG CYS A 4 9.789 7.997 8.918 1.00 0.00 S +ATOM 27 N PRO A 5 9.505 9.080 13.592 1.00 3.96 N +ATOM 28 CA PRO A 5 9.448 9.070 15.054 1.00 4.25 C +ATOM 29 C PRO A 5 9.251 7.675 15.608 1.00 4.96 C +ATOM 30 O PRO A 5 9.386 7.479 16.814 1.00 7.44 O +ATOM 31 CB PRO A 5 8.230 9.953 15.377 1.00 5.11 C +ATOM 32 CG PRO A 5 7.326 9.804 14.155 1.00 5.24 C +ATOM 33 CD PRO A 5 8.341 9.760 13.022 1.00 5.20 C +ATOM 34 N SER A 6 8.879 6.698 14.769 1.00 4.83 N +ATOM 35 CA SER A 6 8.653 5.339 15.213 1.00 4.45 C +ATOM 36 C SER A 6 8.769 4.410 14.030 1.00 4.99 C +ATOM 37 O SER A 6 8.733 4.831 12.877 1.00 4.61 O +ATOM 38 CB SER A 6 7.283 5.108 15.930 1.00 5.05 C +ATOM 39 OG SER A 6 6.146 5.113 15.053 1.00 6.39 O +ATOM 40 N ILE A 7 8.892 3.091 14.300 1.00 4.94 N +ATOM 41 CA ILE A 7 8.902 2.051 13.277 1.00 6.33 C +ATOM 42 C ILE A 7 7.613 2.022 12.458 1.00 5.32 C +ATOM 43 O ILE A 7 7.644 1.935 11.236 1.00 6.85 O +ATOM 44 CB ILE A 7 9.210 0.696 13.915 1.00 8.43 C +ATOM 45 CG1 ILE A 7 10.706 0.687 14.311 1.00 9.78 C +ATOM 46 CG2 ILE A 7 8.869 -0.480 12.968 1.00 11.70 C +ATOM 47 CD1 ILE A 7 11.139 -0.531 15.134 1.00 9.92 C +ATOM 48 N VAL A 8 6.437 2.160 13.117 1.00 5.02 N +ATOM 49 CA VAL A 8 5.133 2.251 12.460 1.00 6.93 C +ATOM 50 C VAL A 8 5.066 3.419 11.487 1.00 5.39 C +ATOM 51 O VAL A 8 4.619 3.284 10.349 1.00 6.30 O +ATOM 52 CB VAL A 8 4.013 2.392 13.499 1.00 9.64 C +ATOM 53 CG1 VAL A 8 2.674 2.856 12.881 1.00 13.85 C +ATOM 54 CG2 VAL A 8 3.807 1.039 14.203 1.00 11.97 C +ATOM 55 N ALA A 9 5.561 4.603 11.904 1.00 3.73 N +ATOM 56 CA ALA A 9 5.593 5.781 11.066 1.00 3.56 C +ATOM 57 C ALA A 9 6.462 5.613 9.825 1.00 4.13 C +ATOM 58 O ALA A 9 6.064 5.996 8.723 1.00 4.36 O +ATOM 59 CB ALA A 9 6.048 6.985 11.906 1.00 4.80 C +ATOM 60 N ARG A 10 7.647 4.976 9.963 1.00 3.73 N +ATOM 61 CA ARG A 10 8.499 4.612 8.843 1.00 3.38 C +ATOM 62 C ARG A 10 7.854 3.632 7.870 1.00 3.47 C +ATOM 63 O ARG A 10 7.907 3.808 6.658 1.00 4.67 O +ATOM 64 CB ARG A 10 9.841 4.010 9.325 1.00 3.95 C +ATOM 65 CG ARG A 10 10.806 3.565 8.198 1.00 4.55 C +ATOM 66 CD ARG A 10 11.252 4.676 7.243 1.00 5.89 C +ATOM 67 NE ARG A 10 12.159 5.572 8.019 1.00 6.20 N +ATOM 68 CZ ARG A 10 12.820 6.616 7.512 1.00 7.52 C +ATOM 69 NH1 ARG A 10 12.666 6.960 6.233 1.00 10.68 N +ATOM 70 NH2 ARG A 10 13.624 7.329 8.286 1.00 9.48 N +ATOM 71 N SER A 11 7.196 2.575 8.390 1.00 5.19 N +ATOM 72 CA SER A 11 6.481 1.606 7.566 1.00 4.60 C +ATOM 73 C SER A 11 5.350 2.226 6.765 1.00 4.84 C +ATOM 74 O SER A 11 5.209 1.984 5.568 1.00 5.84 O +ATOM 75 CB SER A 11 5.907 0.439 8.404 1.00 5.91 C +ATOM 76 OG SER A 11 6.971 -0.314 8.986 1.00 8.38 O +ATOM 77 N ASN A 12 4.555 3.111 7.401 1.00 3.54 N +ATOM 78 CA ASN A 12 3.526 3.896 6.735 1.00 4.57 C +ATOM 79 C ASN A 12 4.089 4.861 5.690 1.00 4.14 C +ATOM 80 O ASN A 12 3.526 5.027 4.612 1.00 5.52 O +ATOM 81 CB ASN A 12 2.682 4.695 7.759 1.00 6.42 C +ATOM 82 CG ASN A 12 1.855 3.749 8.622 1.00 8.25 C +ATOM 83 OD1 ASN A 12 1.587 2.604 8.263 1.00 12.72 O +ATOM 84 ND2 ASN A 12 1.391 4.246 9.794 1.00 9.92 N +ATOM 85 N PHE A 13 5.243 5.511 5.979 1.00 3.43 N +ATOM 86 CA PHE A 13 5.953 6.388 5.058 1.00 3.49 C +ATOM 87 C PHE A 13 6.374 5.670 3.781 1.00 3.40 C +ATOM 88 O PHE A 13 6.177 6.176 2.680 1.00 4.07 O +ATOM 89 CB PHE A 13 7.201 6.982 5.781 1.00 5.48 C +ATOM 90 CG PHE A 13 7.975 7.989 4.964 1.00 5.57 C +ATOM 91 CD1 PHE A 13 8.957 7.576 4.042 1.00 6.99 C +ATOM 92 CD2 PHE A 13 7.727 9.360 5.111 1.00 6.52 C +ATOM 93 CE1 PHE A 13 9.600 8.508 3.218 1.00 8.20 C +ATOM 94 CE2 PHE A 13 8.396 10.297 4.314 1.00 6.34 C +ATOM 95 CZ PHE A 13 9.292 9.866 3.335 1.00 6.84 C +ATOM 96 N ASN A 14 6.934 4.451 3.911 1.00 3.64 N +ATOM 97 CA ASN A 14 7.340 3.628 2.785 1.00 4.31 C +ATOM 98 C ASN A 14 6.170 3.203 1.900 1.00 3.98 C +ATOM 99 O ASN A 14 6.267 3.250 0.681 1.00 6.22 O +ATOM 100 CB ASN A 14 8.141 2.389 3.256 1.00 5.81 C +ATOM 101 CG ASN A 14 9.498 2.826 3.806 1.00 6.82 C +ATOM 102 OD1 ASN A 14 10.007 3.912 3.542 1.00 9.43 O +ATOM 103 ND2 ASN A 14 10.145 1.922 4.585 1.00 8.21 N +ATOM 104 N VAL A 15 5.013 2.824 2.494 1.00 3.76 N +ATOM 105 CA VAL A 15 3.788 2.560 1.737 1.00 3.98 C +ATOM 106 C VAL A 15 3.265 3.803 1.032 1.00 3.80 C +ATOM 107 O VAL A 15 2.896 3.764 -0.139 1.00 4.85 O +ATOM 108 CB VAL A 15 2.693 1.938 2.599 1.00 4.71 C +ATOM 109 CG1 VAL A 15 1.361 1.800 1.825 1.00 6.67 C +ATOM 110 CG2 VAL A 15 3.177 0.544 3.039 1.00 6.26 C +ATOM 111 N CYS A 16 3.274 4.969 1.712 1.00 3.79 N +ATOM 112 CA CYS A 16 2.864 6.239 1.129 1.00 3.54 C +ATOM 113 C CYS A 16 3.718 6.650 -0.072 1.00 3.48 C +ATOM 114 O CYS A 16 3.231 7.265 -1.010 1.00 4.63 O +ATOM 115 CB CYS A 16 2.855 7.367 2.202 1.00 4.58 C +ATOM 116 SG CYS A 16 1.908 8.867 1.760 1.00 0.00 S +ATOM 117 N ARG A 17 5.022 6.292 -0.076 1.00 3.99 N +ATOM 118 CA ARG A 17 5.930 6.534 -1.184 1.00 3.83 C +ATOM 119 C ARG A 17 5.812 5.585 -2.365 1.00 3.79 C +ATOM 120 O ARG A 17 6.301 5.914 -3.443 1.00 5.39 O +ATOM 121 CB ARG A 17 7.400 6.484 -0.701 1.00 4.11 C +ATOM 122 CG ARG A 17 7.776 7.683 0.187 1.00 4.69 C +ATOM 123 CD ARG A 17 7.944 8.995 -0.584 1.00 5.10 C +ATOM 124 NE ARG A 17 9.234 8.890 -1.326 1.00 4.71 N +ATOM 125 CZ ARG A 17 9.543 9.583 -2.428 1.00 5.28 C +ATOM 126 NH1 ARG A 17 8.671 10.381 -3.038 1.00 6.67 N +ATOM 127 NH2 ARG A 17 10.776 9.474 -2.924 1.00 6.41 N +ATOM 128 N LEU A 18 5.148 4.416 -2.231 1.00 4.70 N +ATOM 129 CA LEU A 18 4.996 3.463 -3.327 1.00 5.46 C +ATOM 130 C LEU A 18 4.342 3.996 -4.610 1.00 5.13 C +ATOM 131 O LEU A 18 4.869 3.695 -5.680 1.00 5.55 O +ATOM 132 CB LEU A 18 4.208 2.196 -2.900 1.00 6.47 C +ATOM 133 CG LEU A 18 4.950 1.171 -2.026 1.00 7.43 C +ATOM 134 CD1 LEU A 18 3.955 0.076 -1.601 1.00 8.70 C +ATOM 135 CD2 LEU A 18 6.147 0.549 -2.760 1.00 9.39 C +ATOM 136 N PRO A 19 3.254 4.780 -4.621 1.00 4.28 N +ATOM 137 CA PRO A 19 2.734 5.368 -5.849 1.00 5.38 C +ATOM 138 C PRO A 19 3.551 6.545 -6.354 1.00 6.30 C +ATOM 139 O PRO A 19 3.236 7.055 -7.422 1.00 9.62 O +ATOM 140 CB PRO A 19 1.282 5.773 -5.523 1.00 5.87 C +ATOM 141 CG PRO A 19 1.141 5.751 -3.996 1.00 6.47 C +ATOM 142 CD PRO A 19 2.336 4.948 -3.491 1.00 6.45 C +ATOM 143 N GLY A 20 4.580 7.018 -5.617 1.00 4.94 N +ATOM 144 CA GLY A 20 5.391 8.149 -6.052 1.00 5.39 C +ATOM 145 C GLY A 20 5.046 9.438 -5.377 1.00 5.03 C +ATOM 146 O GLY A 20 5.551 10.488 -5.751 1.00 7.34 O +ATOM 147 N THR A 21 4.191 9.388 -4.333 1.00 4.10 N +ATOM 148 CA THR A 21 3.790 10.539 -3.524 1.00 3.94 C +ATOM 149 C THR A 21 4.994 11.363 -3.054 1.00 3.96 C +ATOM 150 O THR A 21 5.943 10.768 -2.527 1.00 5.82 O +ATOM 151 CB THR A 21 2.992 10.121 -2.295 1.00 4.13 C +ATOM 152 OG1 THR A 21 1.942 9.232 -2.646 1.00 5.45 O +ATOM 153 CG2 THR A 21 2.311 11.309 -1.618 1.00 5.41 C +ATOM 154 N PRO A 22 5.091 12.685 -3.239 1.00 5.04 N +ATOM 155 CA PRO A 22 6.160 13.520 -2.704 1.00 4.69 C +ATOM 156 C PRO A 22 6.462 13.281 -1.237 1.00 4.19 C +ATOM 157 O PRO A 22 5.532 13.092 -0.455 1.00 4.47 O +ATOM 158 CB PRO A 22 5.692 14.964 -2.949 1.00 7.12 C +ATOM 159 CG PRO A 22 4.707 14.888 -4.116 1.00 7.03 C +ATOM 160 CD PRO A 22 4.163 13.460 -4.064 1.00 4.90 C +ATOM 161 N GLU A 23 7.740 13.333 -0.819 1.00 5.16 N +ATOM 162 CA GLU A 23 8.148 13.128 0.559 1.00 5.31 C +ATOM 163 C GLU A 23 7.491 14.077 1.558 1.00 4.11 C +ATOM 164 O GLU A 23 7.185 13.710 2.684 1.00 5.11 O +ATOM 165 CB GLU A 23 9.680 13.256 0.670 1.00 6.16 C +ATOM 166 CG GLU A 23 10.443 12.079 0.026 1.00 7.48 C +ATOM 167 CD GLU A 23 11.929 12.078 0.378 1.00 9.40 C +ATOM 168 OE1 GLU A 23 12.463 13.127 0.815 1.00 10.40 O +ATOM 169 OE2 GLU A 23 12.523 10.979 0.229 1.00 13.32 O +ATOM 170 N ALA A 24 7.250 15.342 1.137 1.00 4.56 N +ATOM 171 CA ALA A 24 6.603 16.363 1.942 1.00 4.49 C +ATOM 172 C ALA A 24 5.181 15.997 2.372 1.00 4.10 C +ATOM 173 O ALA A 24 4.780 16.226 3.504 1.00 5.64 O +ATOM 174 CB ALA A 24 6.614 17.716 1.196 1.00 5.80 C +ATOM 175 N ILE A 25 4.393 15.365 1.471 1.00 0.00 N +ATOM 176 CA ILE A 25 3.059 14.858 1.782 1.00 0.00 C +ATOM 177 C ILE A 25 3.119 13.764 2.814 1.00 0.00 C +ATOM 178 O ILE A 25 2.340 13.713 3.763 1.00 0.00 O +ATOM 179 CB ILE A 25 2.395 14.297 0.537 1.00 0.00 C +ATOM 180 CG1 ILE A 25 2.067 15.452 -0.425 1.00 0.00 C +ATOM 181 CG2 ILE A 25 1.147 13.432 0.873 1.00 0.00 C +ATOM 182 CD1 ILE A 25 1.425 14.937 -1.710 1.00 0.00 C +ATOM 183 N CYS A 26 4.092 12.856 2.643 1.00 0.00 N +ATOM 184 CA CYS A 26 4.311 11.762 3.553 1.00 0.00 C +ATOM 185 C CYS A 26 4.647 12.226 4.966 1.00 0.00 C +ATOM 186 O CYS A 26 4.108 11.689 5.919 1.00 0.00 O +ATOM 187 CB CYS A 26 5.440 10.845 3.055 1.00 0.00 C +ATOM 188 SG CYS A 26 5.263 10.218 1.382 1.00 0.00 S +ATOM 189 N ALA A 27 5.487 13.282 5.125 1.00 0.00 N +ATOM 190 CA ALA A 27 5.803 13.900 6.406 1.00 0.00 C +ATOM 191 C ALA A 27 4.561 14.357 7.177 1.00 0.00 C +ATOM 192 O ALA A 27 4.384 14.077 8.358 1.00 0.00 O +ATOM 193 CB ALA A 27 6.730 15.122 6.168 1.00 0.00 C +ATOM 194 N THR A 28 3.634 15.017 6.455 1.00 0.00 N +ATOM 195 CA THR A 28 2.321 15.445 6.937 1.00 0.00 C +ATOM 196 C THR A 28 1.408 14.292 7.325 1.00 0.00 C +ATOM 197 O THR A 28 0.716 14.344 8.336 1.00 0.00 O +ATOM 198 CB THR A 28 1.627 16.339 5.912 1.00 0.00 C +ATOM 199 OG1 THR A 28 2.410 17.506 5.704 1.00 0.00 O +ATOM 200 CG2 THR A 28 0.253 16.829 6.388 1.00 0.00 C +ATOM 201 N TYR A 29 1.380 13.210 6.520 1.00 0.00 N +ATOM 202 CA TYR A 29 0.556 12.034 6.755 1.00 0.00 C +ATOM 203 C TYR A 29 1.029 11.150 7.922 1.00 0.00 C +ATOM 204 O TYR A 29 0.220 10.589 8.656 1.00 0.00 O +ATOM 205 CB TYR A 29 0.432 11.213 5.436 1.00 0.00 C +ATOM 206 CG TYR A 29 -0.619 10.131 5.521 1.00 0.00 C +ATOM 207 CD1 TYR A 29 -0.249 8.777 5.596 1.00 0.00 C +ATOM 208 CD2 TYR A 29 -1.986 10.458 5.550 1.00 0.00 C +ATOM 209 CE1 TYR A 29 -1.222 7.776 5.727 1.00 0.00 C +ATOM 210 CE2 TYR A 29 -2.961 9.454 5.658 1.00 0.00 C +ATOM 211 CZ TYR A 29 -2.576 8.113 5.749 1.00 0.00 C +ATOM 212 OH TYR A 29 -3.541 7.091 5.857 1.00 0.00 O +ATOM 213 N THR A 30 2.361 10.976 8.099 1.00 0.00 N +ATOM 214 CA THR A 30 2.919 9.964 9.002 1.00 0.00 C +ATOM 215 C THR A 30 3.692 10.502 10.184 1.00 0.00 C +ATOM 216 O THR A 30 4.081 9.745 11.071 1.00 0.00 O +ATOM 217 CB THR A 30 3.865 8.993 8.298 1.00 0.00 C +ATOM 218 OG1 THR A 30 4.991 9.632 7.711 1.00 0.00 O +ATOM 219 CG2 THR A 30 3.100 8.329 7.156 1.00 0.00 C +ATOM 220 N GLY A 31 3.953 11.821 10.249 1.00 4.99 N +ATOM 221 CA GLY A 31 4.745 12.407 11.324 1.00 5.50 C +ATOM 222 C GLY A 31 6.234 12.247 11.157 1.00 4.19 C +ATOM 223 O GLY A 31 7.005 12.647 12.019 1.00 6.12 O +ATOM 224 N CYS A 32 6.696 11.661 10.031 1.00 4.30 N +ATOM 225 CA CYS A 32 8.098 11.698 9.639 1.00 4.89 C +ATOM 226 C CYS A 32 8.497 13.099 9.220 1.00 5.50 C +ATOM 227 O CYS A 32 7.656 13.930 8.904 1.00 5.82 O +ATOM 228 CB CYS A 32 8.466 10.716 8.500 1.00 4.66 C +ATOM 229 SG CYS A 32 8.024 8.992 8.876 1.00 0.00 S +ATOM 230 N ILE A 33 9.798 13.416 9.221 1.00 6.02 N +ATOM 231 CA ILE A 33 10.261 14.745 8.877 1.00 5.24 C +ATOM 232 C ILE A 33 11.307 14.643 7.792 1.00 5.16 C +ATOM 233 O ILE A 33 11.935 13.604 7.599 1.00 7.19 O +ATOM 234 CB ILE A 33 10.816 15.514 10.075 1.00 5.49 C +ATOM 235 CG1 ILE A 33 12.052 14.827 10.704 1.00 6.85 C +ATOM 236 CG2 ILE A 33 9.672 15.686 11.098 1.00 6.45 C +ATOM 237 CD1 ILE A 33 12.736 15.667 11.788 1.00 8.94 C +ATOM 238 N ILE A 34 11.516 15.749 7.050 1.00 5.52 N +ATOM 239 CA ILE A 34 12.542 15.857 6.033 1.00 6.82 C +ATOM 240 C ILE A 34 13.537 16.862 6.551 1.00 6.92 C +ATOM 241 O ILE A 34 13.163 17.970 6.943 1.00 9.22 O +ATOM 242 CB ILE A 34 12.013 16.367 4.696 1.00 8.11 C +ATOM 243 CG1 ILE A 34 10.931 15.424 4.143 1.00 9.59 C +ATOM 244 CG2 ILE A 34 13.166 16.514 3.671 1.00 9.73 C +ATOM 245 CD1 ILE A 34 10.163 16.046 2.978 1.00 13.41 C +ATOM 246 N ILE A 35 14.832 16.507 6.576 1.00 7.06 N +ATOM 247 CA ILE A 35 15.900 17.397 6.990 1.00 7.52 C +ATOM 248 C ILE A 35 16.895 17.555 5.839 1.00 6.63 C +ATOM 249 O ILE A 35 17.010 16.646 5.004 1.00 7.90 O +ATOM 250 CB ILE A 35 16.627 16.933 8.255 1.00 8.07 C +ATOM 251 CG1 ILE A 35 17.345 15.572 8.080 1.00 9.41 C +ATOM 252 CG2 ILE A 35 15.604 16.934 9.413 1.00 9.46 C +ATOM 253 CD1 ILE A 35 18.269 15.211 9.249 1.00 9.85 C +ATOM 254 N PRO A 36 17.632 18.673 5.737 1.00 8.07 N +ATOM 255 CA PRO A 36 18.637 18.871 4.698 1.00 8.78 C +ATOM 256 C PRO A 36 19.884 18.038 4.926 1.00 8.31 C +ATOM 257 O PRO A 36 20.550 17.686 3.959 1.00 9.09 O +ATOM 258 CB PRO A 36 18.968 20.380 4.711 1.00 9.67 C +ATOM 259 CG PRO A 36 18.247 20.998 5.919 1.00 10.15 C +ATOM 260 CD PRO A 36 17.388 19.886 6.520 1.00 9.53 C +ATOM 261 N GLY A 37 20.245 17.766 6.197 1.00 8.48 N +ATOM 262 CA GLY A 37 21.414 16.968 6.556 1.00 9.20 C +ATOM 263 C GLY A 37 21.179 15.482 6.482 1.00 10.41 C +ATOM 264 O GLY A 37 20.178 15.006 5.955 1.00 12.06 O +ATOM 265 N ALA A 38 22.111 14.681 7.026 1.00 9.24 N +ATOM 266 CA ALA A 38 22.015 13.238 6.986 1.00 9.24 C +ATOM 267 C ALA A 38 21.913 12.606 8.360 1.00 9.60 C +ATOM 268 O ALA A 38 21.810 11.395 8.492 1.00 13.65 O +ATOM 269 CB ALA A 38 23.257 12.706 6.258 1.00 10.43 C +ATOM 270 N THR A 39 21.883 13.426 9.424 1.00 8.70 N +ATOM 271 CA THR A 39 21.990 12.912 10.778 1.00 9.46 C +ATOM 272 C THR A 39 20.683 13.187 11.461 1.00 8.32 C +ATOM 273 O THR A 39 20.381 14.325 11.828 1.00 9.89 O +ATOM 274 CB THR A 39 23.118 13.577 11.552 1.00 10.72 C +ATOM 275 OG1 THR A 39 24.344 13.437 10.849 1.00 11.66 O +ATOM 276 CG2 THR A 39 23.326 12.909 12.915 1.00 11.81 C +ATOM 277 N CYS A 40 19.839 12.153 11.616 1.00 7.64 N +ATOM 278 CA CYS A 40 18.549 12.273 12.271 1.00 8.05 C +ATOM 279 C CYS A 40 18.683 12.470 13.782 1.00 7.63 C +ATOM 280 O CYS A 40 19.553 11.848 14.390 1.00 9.64 O +ATOM 281 CB CYS A 40 17.636 11.060 11.978 1.00 7.80 C +ATOM 282 SG CYS A 40 17.219 10.907 10.214 1.00 0.00 S +ATOM 283 N PRO A 41 17.894 13.320 14.440 1.00 8.00 N +ATOM 284 CA PRO A 41 17.922 13.457 15.891 1.00 8.96 C +ATOM 285 C PRO A 41 17.385 12.227 16.604 1.00 9.06 C +ATOM 286 O PRO A 41 16.722 11.388 16.007 1.00 8.82 O +ATOM 287 CB PRO A 41 17.063 14.703 16.156 1.00 10.39 C +ATOM 288 CG PRO A 41 16.065 14.729 14.998 1.00 10.99 C +ATOM 289 CD PRO A 41 16.862 14.158 13.828 1.00 10.49 C +ATOM 290 N GLY A 42 17.676 12.109 17.918 1.00 7.55 N +ATOM 291 CA GLY A 42 17.326 10.939 18.720 1.00 8.00 C +ATOM 292 C GLY A 42 15.854 10.667 18.936 1.00 7.22 C +ATOM 293 O GLY A 42 15.487 9.550 19.270 1.00 8.41 O +ATOM 294 N ASP A 43 14.968 11.663 18.745 1.00 5.54 N +ATOM 295 CA ASP A 43 13.534 11.508 18.861 1.00 5.85 C +ATOM 296 C ASP A 43 12.885 11.230 17.500 1.00 5.87 C +ATOM 297 O ASP A 43 11.689 10.973 17.400 1.00 7.29 O +ATOM 298 CB ASP A 43 12.926 12.754 19.574 1.00 6.72 C +ATOM 299 CG ASP A 43 13.238 14.092 18.910 1.00 8.59 C +ATOM 300 OD1 ASP A 43 14.277 14.195 18.201 1.00 9.59 O +ATOM 301 OD2 ASP A 43 12.454 15.039 19.151 1.00 11.45 O +ATOM 302 N TYR A 44 13.695 11.172 16.422 1.00 5.22 N +ATOM 303 CA TYR A 44 13.256 10.771 15.100 1.00 5.56 C +ATOM 304 C TYR A 44 14.244 9.740 14.605 1.00 4.61 C +ATOM 305 O TYR A 44 14.900 9.896 13.577 1.00 6.04 O +ATOM 306 CB TYR A 44 13.176 11.942 14.089 1.00 5.41 C +ATOM 307 CG TYR A 44 12.025 12.846 14.397 1.00 5.34 C +ATOM 308 CD1 TYR A 44 12.132 13.887 15.332 1.00 6.59 C +ATOM 309 CD2 TYR A 44 10.800 12.641 13.747 1.00 5.94 C +ATOM 310 CE1 TYR A 44 11.027 14.699 15.622 1.00 5.97 C +ATOM 311 CE2 TYR A 44 9.696 13.450 14.036 1.00 5.17 C +ATOM 312 CZ TYR A 44 9.812 14.487 14.966 1.00 5.96 C +ATOM 313 OH TYR A 44 8.695 15.301 15.229 1.00 8.60 O +ATOM 314 N ALA A 45 14.374 8.640 15.366 1.00 4.76 N +ATOM 315 CA ALA A 45 15.454 7.695 15.240 1.00 5.89 C +ATOM 316 C ALA A 45 15.168 6.534 14.284 1.00 6.67 C +ATOM 317 O ALA A 45 15.991 5.643 14.126 1.00 7.56 O +ATOM 318 CB ALA A 45 15.705 7.115 16.649 1.00 6.82 C +ATOM 319 N ASN A 46 13.980 6.516 13.642 1.00 5.80 N +ATOM 320 CA ASN A 46 13.548 5.423 12.792 1.00 6.15 C +ATOM 321 C ASN A 46 13.271 5.858 11.325 1.00 6.61 C +ATOM 322 O ASN A 46 13.555 7.019 10.928 1.00 7.18 O +ATOM 323 CB ASN A 46 12.273 4.785 13.398 1.00 7.27 C +ATOM 324 CG ASN A 46 12.512 4.269 14.812 1.00 7.98 C +ATOM 325 OD1 ASN A 46 11.887 4.710 15.772 1.00 11.00 O +ATOM 326 ND2 ASN A 46 13.406 3.262 14.967 1.00 10.32 N +ATOM 327 OXT ASN A 46 12.762 5.007 10.548 1.00 0.00 O +TER 328 ASN A 46 +END