diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 79ce0d60a744cde6b7438fb2fd18f49d207df877..bcf1734d506d573d3b989a7418a03d8a5906589e 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -79,7 +79,10 @@
<li><a href="promod3.html">promod3</a></li>
<ul><li><a href="promod3/core/helper.html">promod3.core.helper</a></li>
<li><a href="promod3/core/pm3argparse.html">promod3.core.pm3argparse</a></li>
-<li><a href="promod3/loop/_loop.html">promod3.loop._loop</a></li>
+<li><a href="promod3/loop.html">promod3.loop</a></li>
+<ul><li><a href="promod3/loop/_loop.html">promod3.loop._loop</a></li>
+</ul><li><a href="promod3/pipeline/run_engine.html">promod3.pipeline.run_engine</a></li>
+<li><a href="promod3/rawmodel/_closedels.html">promod3.rawmodel._closedels</a></li>
<li><a href="promod3/rawmodel/_rawmodel.html">promod3.rawmodel._rawmodel</a></li>
<li><a href="promod3/sidechain/_sidechain.html">promod3.sidechain._sidechain</a></li>
<li><a href="promod3/sidechain/reconstruct_sidechains.html">promod3.sidechain.reconstruct_sidechains</a></li>
diff --git a/doc/html/_modules/promod3/loop.html b/doc/html/_modules/promod3/loop.html
new file mode 100644
index 0000000000000000000000000000000000000000..5408f9511ea523824804d5a023089aa04462bfcb
--- /dev/null
+++ b/doc/html/_modules/promod3/loop.html
@@ -0,0 +1,117 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>promod3.loop — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+
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+ var DOCUMENTATION_OPTIONS = {
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+
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+
+ </head>
+ <body role="document">
+ <div class="related" role="navigation" aria-label="related navigation">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../../genindex.html" title="General Index"
+ accesskey="I">index</a></li>
+ <li class="right" >
+ <a href="../../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="nav-item nav-item-0"><a href="../../index.html">ProMod3 0 documentation</a> »</li>
+ <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> »</li>
+ <li class="nav-item nav-item-2"><a href="../promod3.html" accesskey="U">promod3</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <h1>Source code for promod3.loop</h1><div class="highlight"><pre>
+<span class="sd">'''__init__.py of the loop module</span>
+<span class="sd">'''</span>
+<span class="kn">from</span> <span class="nn">_loop</span> <span class="kn">import</span> <span class="o">*</span>
+
+<span class="c"># not the best style, but as long as we only have a single function in</span>
+<span class="c"># __init__.py lets ignore this flaw... if there are more general functions</span>
+<span class="c"># coming up, start sth like a 'base.py' and import here properly</span>
+<div class="viewcode-block" id="SetupBackboneScorer"><a class="viewcode-back" href="../../loop/backbone_loop_score.html#promod3.loop.SetupBackboneScorer">[docs]</a><span class="k">def</span> <span class="nf">SetupBackboneScorer</span><span class="p">(</span><span class="n">raw_model</span><span class="p">):</span>
+ <span class="sd">'''Get a scorer for medling with backbones.</span>
+
+<span class="sd"> This one is already tailored towards a certain modelling job.</span>
+
+<span class="sd"> :param raw_model: The raw model this scorer should be dedicated to.</span>
+<span class="sd"> :type raw_model: :class:`~promod3.rawmodel.RawModelingResult`</span>
+
+<span class="sd"> :return: A scorer instance.</span>
+<span class="sd"> :rtype: :class:`~promod3.loop.BackboneLoopScorer`</span>
+<span class="sd"> '''</span>
+ <span class="n">scorer</span> <span class="o">=</span> <span class="n">LoadBackboneLoopScorer</span><span class="p">()</span>
+ <span class="n">seqres</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">raw_model</span><span class="o">.</span><span class="n">seqres</span><span class="p">:</span>
+ <span class="n">seqres</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">GetString</span><span class="p">())</span>
+ <span class="n">scorer</span><span class="o">.</span><span class="n">Initialize</span><span class="p">(</span><span class="n">seqres</span><span class="p">)</span>
+ <span class="n">scorer</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">raw_model</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">scorer</span></div>
+</pre></div>
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
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+ Enter search terms or a module, class or function name.
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+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
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+</html>
\ No newline at end of file
diff --git a/doc/html/_modules/promod3/pipeline/run_engine.html b/doc/html/_modules/promod3/pipeline/run_engine.html
new file mode 100644
index 0000000000000000000000000000000000000000..81612ee7c6681b98cc46ade5bad36a97508adb45
--- /dev/null
+++ b/doc/html/_modules/promod3/pipeline/run_engine.html
@@ -0,0 +1,149 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>promod3.pipeline.run_engine — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../../',
+ VERSION: '0',
+ COLLAPSE_INDEX: false,
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+ <script type="text/javascript" src="../../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../../_static/doctools.js"></script>
+ <link rel="top" title="ProMod3 0 documentation" href="../../../index.html" />
+ <link rel="up" title="promod3" href="../../promod3.html" />
+
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+
+ </head>
+ <body role="document">
+ <div class="related" role="navigation" aria-label="related navigation">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../../../genindex.html" title="General Index"
+ accesskey="I">index</a></li>
+ <li class="right" >
+ <a href="../../../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="nav-item nav-item-0"><a href="../../../index.html">ProMod3 0 documentation</a> »</li>
+ <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
+ <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <h1>Source code for promod3.pipeline.run_engine</h1><div class="highlight"><pre>
+<span class="sd">'''Everything sticked together to build models using ProMod3</span>
+<span class="sd">'''</span>
+
+<span class="kn">import</span> <span class="nn">ost</span>
+
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+
+<div class="viewcode-block" id="BuildFromRawModel"><a class="viewcode-back" href="../../../pipeline/run_engine.html#promod3.pipeline.run_engine.BuildFromRawModel">[docs]</a><span class="k">def</span> <span class="nf">BuildFromRawModel</span><span class="p">(</span><span class="n">raw_model</span><span class="p">,</span> <span class="n">structure_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">fragment_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
+ <span class="n">torsion_sampler</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+ <span class="sd">'''Build a model starting with a</span>
+<span class="sd"> :class:`RawModel <promod3.rawmodel.RawModelingResult>`.</span>
+
+<span class="sd"> :param raw_model: The prepared template coordinates loaded with the input</span>
+<span class="sd"> alignment.</span>
+<span class="sd"> :type raw_model: :class:`~promod3.rawmodel.RawModelingResult`</span>
+
+<span class="sd"> :param structure_db: The structural database. Loads the default one shipped</span>
+<span class="sd"> with |project| if omitted.</span>
+<span class="sd"> :type structure_db: :class:`~promod3.loop.StructureDB`</span>
+
+<span class="sd"> :param fragment_db: A fragment database coupled to the *structure_db*.</span>
+<span class="sd"> Loads the default one shipped with |project| if omitted.</span>
+<span class="sd"> :type fragment_db: :class:`~promod3.loop.FragDB`</span>
+
+<span class="sd"> :param torsion_sampler: A sampler for torsion angles. Loads the default one</span>
+<span class="sd"> shipped with |project| if omitted.</span>
+<span class="sd"> :type torsion_sampler: :class:`~promod3.loop.TorsionSampler`</span>
+
+<span class="sd"> EXAMPLE: obtain raw model, build model</span>
+
+<span class="sd"> :return: Delivers the model as an |ost_s| entity.</span>
+<span class="sd"> :rtype: :class:`Entity <ost.mol.EntityHandle>`</span>
+<span class="sd"> '''</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Starting modelling based on a raw model"</span><span class="p">)</span>
+
+ <span class="c"># a bit of setup</span>
+ <span class="k">if</span> <span class="n">structure_db</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">fragment_db</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="n">fragment_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">torsion_sampler</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
+
+ <span class="n">scorer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">SetupBackboneScorer</span><span class="p">(</span><span class="n">raw_model</span><span class="p">)</span>
+
+ <span class="c"># step 1: close small deletions in the raw model</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Trying to close small deletions."</span><span class="p">)</span>
+ <span class="n">raw_model</span><span class="o">.</span><span class="n">CloseSmallDeletions</span><span class="p">(</span><span class="n">scorer</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">raw_model</span><span class="o">.</span><span class="n">model</span>
+</div>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'BuildProMod3Model'</span><span class="p">)</span>
+
+<span class="c"># LocalWords: BuildProMod ProMod sticked ost promod BuildFromRawModel param</span>
+<span class="c"># LocalWords: RawModel rtype bool LoadStructureDB LogVerbose LoadFragDB</span>
+<span class="c"># LocalWords: LoadTorsionSamplerCoil SetupBackboneScorer</span>
+<span class="c"># LocalWords: CloseSmallDeletions</span>
+</pre></div>
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../../../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ <p class="searchtip" style="font-size: 90%">
+ Enter search terms or a module, class or function name.
+ </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2015, Bienchen.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/_modules/promod3/rawmodel/_closedels.html b/doc/html/_modules/promod3/rawmodel/_closedels.html
new file mode 100644
index 0000000000000000000000000000000000000000..a0a0b425bf023496ca053b7a1ebf6fabe444fa83
--- /dev/null
+++ b/doc/html/_modules/promod3/rawmodel/_closedels.html
@@ -0,0 +1,250 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>promod3.rawmodel._closedels — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../../',
+ VERSION: '0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../../_static/doctools.js"></script>
+ <link rel="top" title="ProMod3 0 documentation" href="../../../index.html" />
+ <link rel="up" title="promod3" href="../../promod3.html" />
+
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+
+ </head>
+ <body role="document">
+ <div class="related" role="navigation" aria-label="related navigation">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../../../genindex.html" title="General Index"
+ accesskey="I">index</a></li>
+ <li class="right" >
+ <a href="../../../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="nav-item nav-item-0"><a href="../../../index.html">ProMod3 0 documentation</a> »</li>
+ <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
+ <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <h1>Source code for promod3.rawmodel._closedels</h1><div class="highlight"><pre>
+<span class="sd">'''Single function to be 'injected' into the RawModellingResult class in the</span>
+<span class="sd">__init__.py file.</span>
+<span class="sd">'''</span>
+
+<span class="kn">import</span> <span class="nn">ost</span>
+<span class="c">#pylint: disable=no-name-in-module</span>
+<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">_rawmodel</span> <span class="k">as</span> <span class="n">rawmodel</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+
+<span class="k">def</span> <span class="nf">_CloseSmallDeletions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span> <span class="n">extension_steps</span><span class="o">=</span><span class="mi">9</span><span class="p">,</span> <span class="n">clash_thresh</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
+ <span class="n">e_thresh</span><span class="o">=</span><span class="mi">200</span><span class="p">):</span>
+ <span class="sd">'''Close small deletions by relaxing neighbouring residues.</span>
+
+<span class="sd"> Small deletions in the template from the target-template alignment have a</span>
+<span class="sd"> good chance to be bridged just by relaxing neighbours around a tiny gap.</span>
+<span class="sd"> Before diving into the more demanding tasks in modeling, those may be closed</span>
+<span class="sd"> already in the raw-model. After closure some checks are done to see if the</span>
+<span class="sd"> solution is stereochemically sensible.</span>
+
+<span class="sd"> Closed gaps are removed from :attr:`self.gaps`.</span>
+
+<span class="sd"> .. testcode:: closesmalldel</span>
+<span class="sd"> :hide:</span>
+
+<span class="sd"> from promod3 import rawmodel</span>
+<span class="sd"> from promod3 import loop</span>
+
+<span class="sd"> tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/gly.pdb')</span>
+<span class="sd"> aln = ost.seq.CreateAlignment(ost.seq.CreateSequence('trg', 'GGG-GGG'),</span>
+<span class="sd"> ost.seq.CreateSequence('tpl', 'GGGAGGG'))</span>
+<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
+<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
+<span class="sd"> assert len(rmodel.gaps) == 1</span>
+<span class="sd"> scorer = loop.SetupBackboneScorer(rmodel)</span>
+<span class="sd"> rmodel.CloseSmallDeletions(scorer)</span>
+<span class="sd"> assert len(rmodel.gaps) == 0</span>
+
+<span class="sd"> .. doctest:: closesmalldel</span>
+
+<span class="sd"> import ost</span>
+<span class="sd"> from promod3 import rawmodel</span>
+<span class="sd"> from promod3 import loop</span>
+
+<span class="sd"> tpl = ost.io.LoadPDB('gly.pdb')</span>
+<span class="sd"> aln = ost.io.LoadAlignment('seq.fasta')</span>
+<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
+<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
+<span class="sd"> scorer = loop.SetupBackboneScorer(rmodel)</span>
+<span class="sd"> rmodel.CloseSmallDeletions(scorer)</span>
+
+<span class="sd"> :param scorer: A scorer dedicated to this raw model.</span>
+<span class="sd"> :type scorer: :class:`~promod3.loop.BackboneLoopScorer`</span>
+
+<span class="sd"> :param extension_steps: Iterations allowed for gap extension. This does not</span>
+<span class="sd"> directly mean 'extended size of gap' but no. of</span>
+<span class="sd"> attempts to extend. Extension works like trying to</span>
+<span class="sd"> increase left, then right, then try more on the</span>
+<span class="sd"> left side again...</span>
+<span class="sd"> :type extension_steps: :class:`int`</span>
+
+<span class="sd"> :param clash_thresh: Threshold for the clash score, acceptance means being</span>
+<span class="sd"> lower than this.</span>
+<span class="sd"> :type clash_thresh: :class:`float`</span>
+
+<span class="sd"> :param e_thresh: Potential energy should be lower than this.</span>
+<span class="sd"> :type e_thresh: :class:`float`</span>
+
+<span class="sd"> :return: If gaps are deleted, the scorer needs to be updated and is</span>
+<span class="sd"> returned.</span>
+<span class="sd"> :rtype: :class:`~promod3.loop.BackboneLoopScorer`</span>
+<span class="sd"> '''</span>
+ <span class="n">current_gap_index</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="c"># iterating self.gaps. The number of gaps may change during the process,</span>
+ <span class="c"># hence we run by 'while', breaking out once we've seen all gaps. If a gap</span>
+ <span class="c"># gets closed, it is deleted from self.gaps, otherwise, current_gap_index</span>
+ <span class="c"># as a counter is increased.</span>
+ <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
+ <span class="c"># check if all gaps were visited</span>
+ <span class="k">if</span> <span class="n">current_gap_index</span> <span class="o">>=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">):</span>
+ <span class="k">break</span>
+
+ <span class="c"># in the end this determines if a gap was closed or not</span>
+ <span class="n">success</span> <span class="o">=</span> <span class="bp">False</span>
+
+ <span class="c"># A deletion is a gap of size 0 in the template, this means that to</span>
+ <span class="c"># transform the template sequence into the target sequence, aa's vanish,</span>
+ <span class="c"># so the target sequence has gap caracters, the template not.</span>
+ <span class="c"># If we are not looking at a deletion, do nothing.</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">]</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c"># work on a copy of the gap, if not closed in the end, no harm done</span>
+ <span class="n">current_gap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+ <span class="n">current_chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
+ <span class="n">current_chain_index</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
+
+ <span class="c"># Try to close gap by relaxation: by checking how far we may extend</span>
+ <span class="c"># the gap, we get the backbone to be stretched. If no more extension</span>
+ <span class="c"># is possible, break out. On first successful relaxation for an</span>
+ <span class="c"># extension, we successfully stop.</span>
+ <span class="n">extender</span> <span class="o">=</span> <span class="n">rawmodel</span><span class="o">.</span><span class="n">GapExtender</span><span class="p">(</span><span class="n">current_gap</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">extension_steps</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">extender</span><span class="o">.</span><span class="n">Extend</span><span class="p">():</span>
+ <span class="k">break</span>
+ <span class="c"># gather residues for backbone relaxation, check that we get a</span>
+ <span class="c"># bunch of actual residues, otherwise jump to next extension</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+ <span class="n">current_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
+ <span class="n">after_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
+ <span class="n">found_residues</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">current_resnum</span> <span class="o">></span> <span class="n">after_resnum</span><span class="p">:</span>
+ <span class="k">break</span>
+ <span class="n">res</span> <span class="o">=</span> <span class="n">current_chain</span><span class="o">.</span><span class="n">FindResidue</span><span class="p">(</span><span class="n">current_resnum</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">res</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
+ <span class="n">found_residues</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">break</span>
+ <span class="n">res_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</span><span class="p">)</span>
+ <span class="n">current_resnum</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">found_residues</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="c"># backbone relaxation, for now we allow 300 steps or stop at</span>
+ <span class="c"># max. force of 0.1</span>
+ <span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">current_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">res_list</span><span class="p">)</span>
+ <span class="n">bb_relaxer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneRelaxer</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span>
+ <span class="n">potential_e</span> <span class="o">=</span> <span class="n">bb_relaxer</span><span class="o">.</span><span class="n">Run</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="mi">300</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
+ <span class="c"># check for clashes</span>
+ <span class="n">score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">CalculateClashScore</span><span class="p">(</span>\
+ <span class="n">bb_list</span><span class="p">,</span>
+ <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="n">current_chain_index</span><span class="p">)</span>
+ <span class="c"># if there is no clash and potential energy is low enough we</span>
+ <span class="c"># just solved a gap, delete it and update the scorer for the</span>
+ <span class="c"># changed model</span>
+ <span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">clash_thresh</span> <span class="ow">and</span> \
+ <span class="n">potential_e</span> <span class="o"><</span> <span class="n">e_thresh</span> <span class="ow">and</span> \
+ <span class="n">scorer</span><span class="o">.</span><span class="n">TransOmegaTorsions</span><span class="p">(</span><span class="n">bb_list</span><span class="p">):</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Closed: </span><span class="si">%s</span><span class="s"> by relaxing </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> \
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">],</span> <span class="n">current_gap</span><span class="p">))</span>
+ <span class="n">chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
+ <span class="n">bb_list</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">(),</span>
+ <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">())</span>
+ <span class="n">scorer</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span>\
+ <span class="n">bb_list</span><span class="p">,</span>
+ <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ClearGaps</span><span class="p">(</span><span class="n">current_gap</span><span class="p">)</span>
+ <span class="n">success</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">break</span>
+ <span class="c"># On closed gap, it is removed so the no. of gaps goes down by itself.</span>
+ <span class="c"># In case of no success, counter needs to be increased to jump to the</span>
+ <span class="c"># next gap.</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">success</span><span class="p">:</span>
+ <span class="n">current_gap_index</span> <span class="o">+=</span> <span class="mi">1</span>
+
+ <span class="k">return</span> <span class="n">scorer</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'_CloseSmallDeletions'</span><span class="p">]</span>
+
+<span class="c"># LocalWords: modeling stereochemically param</span>
+</pre></div>
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../../../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ <p class="searchtip" style="font-size: 90%">
+ Enter search terms or a module, class or function name.
+ </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2015, Bienchen.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index 3775b08b1e6b8f1f5ad1d6cd7c72eed54a9ec829..2dfe453889d674c51753096eb21d7aae1757f201 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -1,5 +1,6 @@
Building |project|
================================================================================
+
--------------------------------------------------------------------------------
Dependencies
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index f9cdb6d7d62a2cd76625bc5d8a661341d49c10e3..6d263eb393e230ee26d774f1877834f32c64d6b2 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -391,11 +391,11 @@ a couple of examples around in this repository. Here is the most basic
.. code-block:: cmake
:linenos:
- set(SIDECHAINS_PYMOD
- __init__.py
- )
+ set(SIDECHAINS_PYMOD
+ __init__.py
+ )
- pymod(NAME sidechains PY ${SIDECHAINS_PYMOD})
+ pymod(NAME sidechains PY ${SIDECHAINS_PYMOD})
Source files should be again listed in a dedicated variable. Later, you
probably add some |C++| code and settings diverging from the defaults via the
@@ -408,7 +408,7 @@ top level :file:`CMakeLists.txt`:
.. code-block:: cmake
:linenos:
- :emphasize-lines: 103
+ :emphasize-lines: 104
#-------------------------------------------------------------------------------
# Author: Bienchen
@@ -532,7 +532,7 @@ top level :file:`CMakeLists.txt`:
" Eigen3 : ${EIGEN3_INCLUDE_DIR}\n")
All that needs to be done for |cmake| to recognise your module is adding its
-directory as shown in line 103.
+directory as shown in line 104.
This was the final step to set up the build system. Running |cmake| at this
point would create the build environment in place. But building software in
@@ -604,16 +604,16 @@ carrying a single test case:
.. code-block:: python
:linenos:
- import unittest
- from promod3.sidechains import something
+ import unittest
+ from promod3.sidechains import something
- class SomethingTests(unittest.TestCase):
- def testFileExistsFalse(self):
- self.assertEquals(something.Else(), 1)
+ class SomethingTests(unittest.TestCase):
+ def testFileExistsFalse(self):
+ self.assertEquals(something.Else(), 1)
- if __name__ == "__main__":
- from ost import testutils
- testutils.RunTests()
+ if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
To hook up your tests with ``make codetest`` (and to create a
``test_something.py_run`` target), everything has to be introduced to |cmake|.
diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.txt
index 387c9b0a510c06a37cedacf69b3f4caa319805ec..260a2e5cc2d0150f0dd528f36ed55cbdbe67c2bb 100644
--- a/doc/html/_sources/developers.txt
+++ b/doc/html/_sources/developers.txt
@@ -11,6 +11,7 @@ Contents:
core/setcompoundschemlib
core/index
+ pipeline/index
rawmodel/index
loop/index
sidechain/index
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.txt
index 923b4790649d7071c84a32ca8a4763f5d067753b..136b870131242c5de878a7601b3f7e6a1dd5e43f 100644
--- a/doc/html/_sources/loop/backbone.txt
+++ b/doc/html/_sources/loop/backbone.txt
@@ -4,7 +4,7 @@ Backbone
.. currentmodule:: promod3.loop
-The most simple representation of structural information in PROMOD3 is the
+The most simple representation of structural information in |project| is the
:class:`Backbone`. It provides a way to store the backbone positions of
a residue. For simple structural manipulations they can be gathered to a
:class:`BackboneList` that can be inserted into or converted to a
@@ -44,7 +44,7 @@ a residue. For simple structural manipulations they can be gathered to a
-The basic building blocks
+The Basic Building Blocks
--------------------------------------------------------------------------------
@@ -140,12 +140,15 @@ The basic building blocks
-Editing full stretches of backbone residues
+Editing Full Stretches Of Backbone Residues
--------------------------------------------------------------------------------
.. class:: BackboneList()
- Container for the positions of the backbone atoms (N,CA,CB,C and O) of a segment. This object basically contains a list of :class:`Backbone` and allows setting or modifying the positions of the atoms by setting/changing torsion angles.
+ Container for the positions of the backbone atoms (N,CA,CB,C and O) of a
+ segment. This object basically contains a list of :class:`Backbone` and
+ allows setting or modifying the positions of the atoms by setting/changing
+ torsion angles.
.. method:: BackboneList()
@@ -203,7 +206,9 @@ Editing full stretches of backbone residues
.. method:: InsertInto(chain,n_stem,c_stem [,reset_stem_positions=True])
- Inserts the backbone list into the **chain**. If the residues corresponding to the :class:`BackboneList` are already present in the entity, they will be replaced, otherwise they will be added to the entity.
+ Inserts the backbone list into the **chain**. If the residues corresponding
+ to the :class:`BackboneList` are already present in the entity, they will
+ be replaced, otherwise they will be added to the entity.
:param chain: The chain
:param n_stem: The residue number of the n_stem
diff --git a/doc/html/_sources/loop/backbone_loop_score.txt b/doc/html/_sources/loop/backbone_loop_score.txt
index 61d20f16b4a5af8e84b60a4fd1338a954f33dd39..4681fca82fd1c0cc4f521051017a4c00540c5fa3 100644
--- a/doc/html/_sources/loop/backbone_loop_score.txt
+++ b/doc/html/_sources/loop/backbone_loop_score.txt
@@ -4,7 +4,7 @@ Loop Scoring
.. currentmodule:: promod3.loop
-PROMOD3 provides several terms to assess a loop conformations plausibility.
+|project| provides several terms to assess a loop conformations plausibility.
This is done using the :class:`BackboneLoopScorer`. To be used, the scorer
must be initialized with a seqres. After initialization the structural
environment can be set. This environment defines the particles a certain
@@ -24,6 +24,8 @@ of these potentials have to be set manually.
The BackboneLoopScorer
--------------------------------------------------------------------------------
+.. autofunction:: SetupBackboneScorer
+
.. class:: BackboneLoopScorer
.. method:: Save(filename)
diff --git a/doc/html/_sources/loop/load_loop_objects.txt b/doc/html/_sources/loop/load_loop_objects.txt
index 9cff788d79f8c6449c6b249b31ae2aec56c3bcaf..0a5d8bb7e51f973ca739c3a91f849ee934a79051 100644
--- a/doc/html/_sources/loop/load_loop_objects.txt
+++ b/doc/html/_sources/loop/load_loop_objects.txt
@@ -5,7 +5,7 @@ Load Loop Objects
Several data objects are used throughout the loop module.
-PROMOD3 offers to load precomputed instances for direct usage.
+|project| offers to load precomputed instances for direct usage.
.. method:: LoadTorsionSampler([seed = 0])
@@ -94,7 +94,7 @@ PROMOD3 offers to load precomputed instances for direct usage.
potentials.
:returns: The scorer
- :rtype: :class:`BackboneLoopScore`
+ :rtype: :class:`~promod3.loop.BackboneLoopScorer`
[1] A. D. Solis and S. Rackovsky. Improvement of statistical potentials and
threading score functions using information maximization.
diff --git a/doc/html/_sources/loop/loop_closing.txt b/doc/html/_sources/loop/loop_closing.txt
index 96f09ba05ce14c857d42c16497245fa1e62784c5..00fd52ae8a77085167002797145808817818db68 100644
--- a/doc/html/_sources/loop/loop_closing.txt
+++ b/doc/html/_sources/loop/loop_closing.txt
@@ -6,7 +6,7 @@ Loop Closing
Loops, represented as :class:`BackboneList` objects, often need to undergo
conformational changes to fit into gaps defined by stem residues.
-PROMOD3 implements two algorithms performing this task.
+|project| implements two algorithms performing this task.
There is cyclic coordinate descent (CCD):
Adrian A. Canutescu and Roland L. Dunbrack Jr. "Cyclic coordinate descent: A robotics algorithm for protein loop closure." Protein Sci. 12(5):963–972. (2003)
@@ -23,7 +23,7 @@ also consider the :class:`BackboneRelaxer`.
CCD
--------------------------------------------------------------------------------
-The PROMOD3 implementation of the cyclic coordinate descent first superposes
+The |project| implementation of the cyclic coordinate descent first superposes
the n-stem of the input :class:`BackboneList` with the provided n-stem
positions. In every iteration of the algorithm, one residue of the
:class:`BackboneList` gets randomly selected. If the residue is not the n-stem,
diff --git a/doc/html/_sources/loop/monte_carlo.txt b/doc/html/_sources/loop/monte_carlo.txt
index 3fbcc4070ea6b8fcf4d48ce099686c60b469e5af..fb7973e19b6e68dd74868b86ec235a353d964fb2 100644
--- a/doc/html/_sources/loop/monte_carlo.txt
+++ b/doc/html/_sources/loop/monte_carlo.txt
@@ -3,7 +3,7 @@ Monte Carlo Sampling
.. currentmodule:: promod3.loop
-The monte carlo capabilities of PROMOD3 are mainly targeted at generating de
+The monte carlo capabilities of |project| are mainly targeted at generating de
novo structure candidates for loops or N-/C-Termini. Every iteration of the
sampling process consists basically of four steps.
@@ -15,7 +15,7 @@ sampling process consists basically of four steps.
These steps are performed by sampler, closer, scorer and cooler objects, that
can be arbitrarily combined to generate custom monte carlo sampling pipelines.
This combination either happens manually or by using a convenient function
-provided by PROMOD3.
+provided by |project|.
diff --git a/doc/html/_sources/pipeline/index.txt b/doc/html/_sources/pipeline/index.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74e684f49abdafcef6d23eb96fc8c967101a7f78
--- /dev/null
+++ b/doc/html/_sources/pipeline/index.txt
@@ -0,0 +1,14 @@
+:mod:`~promod3.pipeline` - ProMod3 Modelling Pipeline
+================================================================================
+
+.. module:: promod3.pipeline
+ :synopsis: Everything needed for building actual models.
+
+This module gathers the different aspects of creating coordinates for a
+homology model. The intention is to provide easy access to the modelling engine
+for external applications.
+
+.. toctree::
+ :maxdepth: 2
+
+ run_engine
diff --git a/doc/html/_sources/pipeline/run_engine.txt b/doc/html/_sources/pipeline/run_engine.txt
new file mode 100644
index 0000000000000000000000000000000000000000..753130aa5394271613865df4e5e5daa224caa646
--- /dev/null
+++ b/doc/html/_sources/pipeline/run_engine.txt
@@ -0,0 +1,20 @@
+:mod:`~promod3.pipeline.run_engine` - Build Models From Various Starting Points
+================================================================================
+
+.. currentmodule:: promod3.pipeline.run_engine
+
+Introduction
+--------------------------------------------------------------------------------
+This is a collection of functions to just build models. All steps needed to go from various starting points to a complete model are wrapped in single function calls. That way, if something changes in the default pipeline, e.g. on general improvements, there is no need to change code depending on |project| to adapt.
+
+
+- also convenient for developing new stuff
+- e.g. you want to transform the template coordinates in some way, but then just
+ want to see them in a model, go by BuildFromRawModel
+- or if you have a fancy way of post-processing, sth like a new way of going
+ ligand, build a model easily here, then do whatever you want with the result
+- examples should come with the API
+
+.. autofunction:: BuildFromRawModel
+
+.. LocalWords: currentmodule BuildFromRawModel API autofunction
diff --git a/doc/html/_sources/rawmodel/index.txt b/doc/html/_sources/rawmodel/index.txt
index 0e95c1b6efb9e8857f8c58cac31fcd0c36f057bf..212678315510e6771675cabee9df2062138ac346 100644
--- a/doc/html/_sources/rawmodel/index.txt
+++ b/doc/html/_sources/rawmodel/index.txt
@@ -91,9 +91,12 @@ Raw Coordinate Modeling API
gaps may be the result of insertions/deletions in the alignment or due to
missing or incomplete backbone coordinates in the template structure.
-
:type: :class:`StructuralGapList`
+ .. automethod:: CloseSmallDeletions
.. LocalWords: currentmodule promod aln AttachView BuildRawModel pdb calpha
-.. LocalWords: RawModelingResult StructuralGapList
+.. LocalWords: RawModelingResult StructuralGapList rawmodel Modeling os ost
+.. LocalWords: testcode tempfile io LoadAlignment LoadPDB fh fn doctest API
+.. LocalWords: modeling phosphoserine param exc RuntimeError automethod
+.. LocalWords: CloseSmallDeletions
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 9fe77cccca1e1ff200178a70836dee1ce944d163..2ebb7b5993849c76ca4647ae9f8d2d076e39b82d 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -392,11 +392,11 @@ a couple of examples around in this repository. Here is the most basic
2
3
4
-5</pre></div></td><td class="code"><div class="highlight"><pre> <span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAINS_PYMOD</span>
- <span class="s">__init__.py</span>
- <span class="p">)</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAINS_PYMOD</span>
+<span class="s">__init__.py</span>
+<span class="p">)</span>
- <span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">sidechains</span> <span class="s">PY</span> <span class="o">${</span><span class="nv">SIDECHAINS_PYMOD</span><span class="o">}</span><span class="p">)</span>
+<span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">sidechains</span> <span class="s">PY</span> <span class="o">${</span><span class="nv">SIDECHAINS_PYMOD</span><span class="o">}</span><span class="p">)</span>
</pre></div>
</td></tr></table></div>
<p>Source files should be again listed in a dedicated variable. Later, you
@@ -627,9 +627,9 @@ top level <code class="file docutils literal"><span class="pre">CMakeLists.txt</
<span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
-<span class="hll"><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">rawmodel</span><span class="p">)</span>
-</span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
-<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">loop</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">rawmodel</span><span class="p">)</span>
+<span class="hll"><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
+</span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">loop</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">actions</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">extras</span><span class="p">)</span>
@@ -648,7 +648,7 @@ top level <code class="file docutils literal"><span class="pre">CMakeLists.txt</
</pre></div>
</td></tr></table></div>
<p>All that needs to be done for CMake to recognise your module is adding its
-directory as shown in line 103.</p>
+directory as shown in line 104.</p>
<p>This was the final step to set up the build system. Running CMake at this
point would create the build environment in place. But building software in
your code repository has several drawbacks. First of all, it puts all kind of
@@ -700,16 +700,16 @@ carrying a single test case:</p>
7
8
9
-10</pre></div></td><td class="code"><div class="highlight"><pre> <span class="kn">import</span> <span class="nn">unittest</span>
- <span class="kn">from</span> <span class="nn">promod3.sidechains</span> <span class="kn">import</span> <span class="n">something</span>
+10</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">unittest</span>
+<span class="kn">from</span> <span class="nn">promod3.sidechains</span> <span class="kn">import</span> <span class="n">something</span>
- <span class="k">class</span> <span class="nc">SomethingTests</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
- <span class="k">def</span> <span class="nf">testFileExistsFalse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">assertEquals</span><span class="p">(</span><span class="n">something</span><span class="o">.</span><span class="n">Else</span><span class="p">(),</span> <span class="mi">1</span><span class="p">)</span>
+<span class="k">class</span> <span class="nc">SomethingTests</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
+ <span class="k">def</span> <span class="nf">testFileExistsFalse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">assertEquals</span><span class="p">(</span><span class="n">something</span><span class="o">.</span><span class="n">Else</span><span class="p">(),</span> <span class="mi">1</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span>
- <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
- <span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
+<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span>
+ <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
+ <span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
</pre></div>
</td></tr></table></div>
<p>To hook up your tests with <code class="docutils literal"><span class="pre">make</span> <span class="pre">codetest</span></code> (and to create a
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 083829335c38302c8904d9f200e50285de867f8b..422dd95c123f64a5e89ac34af1ab8984bfc937ee 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -25,7 +25,7 @@
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
- <link rel="next" title="rawmodel - Coordinate Modeling" href="../rawmodel/index.html" />
+ <link rel="next" title="pipeline - ProMod3 Modelling Pipeline" href="../pipeline/index.html" />
<link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
@@ -43,7 +43,7 @@
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="../rawmodel/index.html" title="rawmodel - Coordinate Modeling"
+ <a href="../pipeline/index.html" title="pipeline - ProMod3 Modelling Pipeline"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="pm3argparse.html" title="pm3argparse - Parsing Command Lines"
@@ -231,8 +231,8 @@ script will terminate if a gzip file is found.</li>
<p class="topless"><a href="pm3argparse.html"
title="previous chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></p>
<h4>Next topic</h4>
- <p class="topless"><a href="../rawmodel/index.html"
- title="next chapter"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a></p>
+ <p class="topless"><a href="../pipeline/index.html"
+ title="next chapter"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></p>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
diff --git a/doc/html/developers.html b/doc/html/developers.html
index fda5a23f13e8615656491dede2fe5302ea58a755..7fa8a012229c42873f68649572f07bf5a7a6dda2 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -67,6 +67,10 @@
<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
</ul>
</li>
+<li class="toctree-l1"><a class="reference internal" href="pipeline/index.html"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pipeline/run_engine.html"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="rawmodel/index.html"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
</ul>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index b54cdcf18c51fc58e9702d3ca269019c5d7f174f..240c69668425693c0a517fe6e168aef385186ffe 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -306,6 +306,10 @@
</dt>
+ <dt><a href="pipeline/run_engine.html#promod3.pipeline.run_engine.BuildFromRawModel">BuildFromRawModel() (in module promod3.pipeline.run_engine)</a>
+ </dt>
+
+
<dt><a href="rawmodel/index.html#promod3.rawmodel.BuildRawModel">BuildRawModel() (in module promod3.rawmodel)</a>
</dt>
@@ -411,12 +415,12 @@
<dt><a href="loop/loop_closing.html#promod3.loop.CCD">CCD() (in module promod3.loop)</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[1]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[2]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[3]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[4]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[5]</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/monte_carlo.html#promod3.loop.CCDCloser">CCDCloser (class in promod3.loop)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo.chain_index">chain_index (promod3.loop.FragmentInfo attribute)</a>
</dt>
@@ -456,6 +460,10 @@
</dl></dd>
+ <dt><a href="rawmodel/index.html#promod3.rawmodel.RawModelingResult.CloseSmallDeletions">CloseSmallDeletions() (promod3.rawmodel.RawModelingResult method)</a>
+ </dt>
+
+
<dt><a href="loop/loop_candidate.html#promod3.loop.LoopCandidates.ClusterCandidates">ClusterCandidates() (promod3.loop.LoopCandidates method)</a>
</dt>
@@ -1282,6 +1290,10 @@
</dt>
+ <dt><a href="pipeline/index.html#module-promod3.pipeline">promod3.pipeline (module)</a>
+ </dt>
+
+
<dt><a href="rawmodel/index.html#module-promod3.rawmodel">promod3.rawmodel (module)</a>
</dt>
@@ -1545,6 +1557,10 @@
</dt>
+ <dt><a href="loop/backbone_loop_score.html#promod3.loop.SetupBackboneScorer">SetupBackboneScorer() (in module promod3.loop)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig1">sig1 (promod3.sidechain.RotamerLibEntry attribute)</a>
</dt>
diff --git a/doc/html/index.html b/doc/html/index.html
index 9b487eccbb4524dd5919a8b61cd743b98692eedb..d5591f4553da35bcc5680a7834460a1451fc7df6 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -61,6 +61,7 @@
<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a><ul>
<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="pipeline/index.html"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></li>
<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 8658b4b42582062f7a20250b0f570f308c102eb6..1d95887a4d2db82334c1dccf8f2752a1a7858fd1 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -61,7 +61,7 @@
<div class="section" id="backbone">
<h1>Backbone<a class="headerlink" href="#backbone" title="Permalink to this headline">¶</a></h1>
-<p>The most simple representation of structural information in PROMOD3 is the
+<p>The most simple representation of structural information in ProMod3 is the
<a class="reference internal" href="#promod3.loop.Backbone" title="promod3.loop.Backbone"><code class="xref py py-class docutils literal"><span class="pre">Backbone</span></code></a>. It provides a way to store the backbone positions of
a residue. For simple structural manipulations they can be gathered to a
<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> that can be inserted into or converted to a
@@ -98,7 +98,7 @@ a residue. For simple structural manipulations they can be gathered to a
</pre></div>
</div>
<div class="section" id="the-basic-building-blocks">
-<h2>The basic building blocks<a class="headerlink" href="#the-basic-building-blocks" title="Permalink to this headline">¶</a></h2>
+<h2>The Basic Building Blocks<a class="headerlink" href="#the-basic-building-blocks" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.DihedralPair">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">DihedralPair</code><a class="headerlink" href="#promod3.loop.DihedralPair" title="Permalink to this definition">¶</a></dt>
@@ -260,11 +260,14 @@ a residue. For simple structural manipulations they can be gathered to a
</div>
<div class="section" id="editing-full-stretches-of-backbone-residues">
-<h2>Editing full stretches of backbone residues<a class="headerlink" href="#editing-full-stretches-of-backbone-residues" title="Permalink to this headline">¶</a></h2>
+<h2>Editing Full Stretches Of Backbone Residues<a class="headerlink" href="#editing-full-stretches-of-backbone-residues" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.BackboneList">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">BackboneList</code><a class="headerlink" href="#promod3.loop.BackboneList" title="Permalink to this definition">¶</a></dt>
-<dd><p>Container for the positions of the backbone atoms (N,CA,CB,C and O) of a segment. This object basically contains a list of <a class="reference internal" href="#promod3.loop.Backbone" title="promod3.loop.Backbone"><code class="xref py py-class docutils literal"><span class="pre">Backbone</span></code></a> and allows setting or modifying the positions of the atoms by setting/changing torsion angles.</p>
+<dd><p>Container for the positions of the backbone atoms (N,CA,CB,C and O) of a
+segment. This object basically contains a list of <a class="reference internal" href="#promod3.loop.Backbone" title="promod3.loop.Backbone"><code class="xref py py-class docutils literal"><span class="pre">Backbone</span></code></a> and
+allows setting or modifying the positions of the atoms by setting/changing
+torsion angles.</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>
@@ -367,7 +370,9 @@ providing all necessary positions.</p>
<dl class="method">
<dt id="promod3.loop.BackboneList.InsertInto">
<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>chain</em>, <em>n_stem</em>, <em>c_stem</em><span class="optional">[</span>, <em>reset_stem_positions=True</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.InsertInto" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inserts the backbone list into the <strong>chain</strong>. If the residues corresponding to the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> are already present in the entity, they will be replaced, otherwise they will be added to the entity.</p>
+<dd><p>Inserts the backbone list into the <strong>chain</strong>. If the residues corresponding
+to the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> are already present in the entity, they will
+be replaced, otherwise they will be added to the entity.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -682,8 +687,8 @@ providing all necessary positions.</p>
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Backbone</a><ul>
-<li><a class="reference internal" href="#the-basic-building-blocks">The basic building blocks</a></li>
-<li><a class="reference internal" href="#editing-full-stretches-of-backbone-residues">Editing full stretches of backbone residues</a></li>
+<li><a class="reference internal" href="#the-basic-building-blocks">The Basic Building Blocks</a></li>
+<li><a class="reference internal" href="#editing-full-stretches-of-backbone-residues">Editing Full Stretches Of Backbone Residues</a></li>
</ul>
</li>
</ul>
diff --git a/doc/html/loop/backbone_loop_score.html b/doc/html/loop/backbone_loop_score.html
index 25097d04474229b184459aa89087cb43dea32b80..cd9b56214e274f0e22dd27a07533528ed30400b8 100644
--- a/doc/html/loop/backbone_loop_score.html
+++ b/doc/html/loop/backbone_loop_score.html
@@ -61,7 +61,7 @@
<div class="section" id="loop-scoring">
<h1>Loop Scoring<a class="headerlink" href="#loop-scoring" title="Permalink to this headline">¶</a></h1>
-<p>PROMOD3 provides several terms to assess a loop conformations plausibility.
+<p>ProMod3 provides several terms to assess a loop conformations plausibility.
This is done using the <a class="reference internal" href="#promod3.loop.BackboneLoopScorer" title="promod3.loop.BackboneLoopScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneLoopScorer</span></code></a>. To be used, the scorer
must be initialized with a seqres. After initialization the structural
environment can be set. This environment defines the particles a certain
@@ -73,6 +73,25 @@ When setting up an empty scorer, the parametrization and the score values
of these potentials have to be set manually.</p>
<div class="section" id="the-backboneloopscorer">
<h2>The BackboneLoopScorer<a class="headerlink" href="#the-backboneloopscorer" title="Permalink to this headline">¶</a></h2>
+<dl class="function">
+<dt id="promod3.loop.SetupBackboneScorer">
+<code class="descclassname">promod3.loop.</code><code class="descname">SetupBackboneScorer</code><span class="sig-paren">(</span><em>raw_model</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/loop.html#SetupBackboneScorer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.loop.SetupBackboneScorer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get a scorer for medling with backbones.</p>
+<p>This one is already tailored towards a certain modelling job.</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>raw_model</strong> (<a class="reference internal" href="../rawmodel/index.html#promod3.rawmodel.RawModelingResult" title="promod3.rawmodel.RawModelingResult"><code class="xref py py-class docutils literal"><span class="pre">RawModelingResult</span></code></a>) – The raw model this scorer should be dedicated to.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A scorer instance.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.BackboneLoopScorer" title="promod3.loop.BackboneLoopScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneLoopScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
<dl class="class">
<dt id="promod3.loop.BackboneLoopScorer">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">BackboneLoopScorer</code><a class="headerlink" href="#promod3.loop.BackboneLoopScorer" title="Permalink to this definition">¶</a></dt>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 8c9c026b5aa1b5914ce29f677c5325ea54644315..d9fd10519c577a0a5750b8f8d324eef841ce56be 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -65,8 +65,8 @@
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="backbone.html">Representing Loops</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="backbone.html#the-basic-building-blocks">The basic building blocks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="backbone.html#editing-full-stretches-of-backbone-residues">Editing full stretches of backbone residues</a></li>
+<li class="toctree-l2"><a class="reference internal" href="backbone.html#the-basic-building-blocks">The Basic Building Blocks</a></li>
+<li class="toctree-l2"><a class="reference internal" href="backbone.html#editing-full-stretches-of-backbone-residues">Editing Full Stretches Of Backbone Residues</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="torsion_sampler.html">Have a closer look at backbone dihedral angles</a><ul>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index f4e6d44fda1d6d0297d477362328450df176edb7..ff96687abf44f55831af0063b1627aac1e0a4a36 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -62,7 +62,7 @@
<div class="section" id="load-loop-objects">
<h1>Load Loop Objects<a class="headerlink" href="#load-loop-objects" title="Permalink to this headline">¶</a></h1>
<p>Several data objects are used throughout the loop module.
-PROMOD3 offers to load precomputed instances for direct usage.</p>
+ProMod3 offers to load precomputed instances for direct usage.</p>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSampler">
<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSampler</code><span class="sig-paren">(</span><span class="optional">[</span><em>seed = 0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSampler" title="Permalink to this definition">¶</a></dt>
@@ -194,7 +194,7 @@ potentials.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The scorer</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">BackboneLoopScore</span></code></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="backbone_loop_score.html#promod3.loop.BackboneLoopScorer" title="promod3.loop.BackboneLoopScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneLoopScorer</span></code></a></td>
</tr>
</tbody>
</table>
diff --git a/doc/html/loop/loop_closing.html b/doc/html/loop/loop_closing.html
index 928b1947d59e6dbf8f945ccccfe192ce563556c2..4b8643e7c3908886d6ffbb0e4e59dd533b6dbf90 100644
--- a/doc/html/loop/loop_closing.html
+++ b/doc/html/loop/loop_closing.html
@@ -63,7 +63,7 @@
<h1>Loop Closing<a class="headerlink" href="#loop-closing" title="Permalink to this headline">¶</a></h1>
<p>Loops, represented as <a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> objects, often need to undergo
conformational changes to fit into gaps defined by stem residues.
-PROMOD3 implements two algorithms performing this task.</p>
+ProMod3 implements two algorithms performing this task.</p>
<p>There is cyclic coordinate descent (CCD):
Adrian A. Canutescu and Roland L. Dunbrack Jr. “Cyclic coordinate descent: A robotics algorithm for protein loop closure.” Protein Sci. 12(5):963–972. (2003)</p>
<p>and kinematic closure (KIC):
@@ -72,7 +72,7 @@ Mandell DJ, Coutsias EA and Kortemme T. “Sub-angstrom accuracy in protein
also consider the <a class="reference internal" href="#promod3.loop.BackboneRelaxer" title="promod3.loop.BackboneRelaxer"><code class="xref py py-class docutils literal"><span class="pre">BackboneRelaxer</span></code></a>.</p>
<div class="section" id="ccd">
<h2>CCD<a class="headerlink" href="#ccd" title="Permalink to this headline">¶</a></h2>
-<p>The PROMOD3 implementation of the cyclic coordinate descent first superposes
+<p>The ProMod3 implementation of the cyclic coordinate descent first superposes
the n-stem of the input <a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> with the provided n-stem
positions. In every iteration of the algorithm, one residue of the
<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> gets randomly selected. If the residue is not the n-stem,
diff --git a/doc/html/loop/monte_carlo.html b/doc/html/loop/monte_carlo.html
index 21b47f57392dcc5fc8ec87b86ba6df08200ffd93..1c0f635fda7458071b923ac6a0e6bd422fdb134f 100644
--- a/doc/html/loop/monte_carlo.html
+++ b/doc/html/loop/monte_carlo.html
@@ -61,7 +61,7 @@
<div class="section" id="monte-carlo-sampling">
<h1>Monte Carlo Sampling<a class="headerlink" href="#monte-carlo-sampling" title="Permalink to this headline">¶</a></h1>
-<p>The monte carlo capabilities of PROMOD3 are mainly targeted at generating de
+<p>The monte carlo capabilities of ProMod3 are mainly targeted at generating de
novo structure candidates for loops or N-/C-Termini. Every iteration of the
sampling process consists basically of four steps.</p>
<ul class="simple">
@@ -73,7 +73,7 @@ sampling process consists basically of four steps.</p>
<p>These steps are performed by sampler, closer, scorer and cooler objects, that
can be arbitrarily combined to generate custom monte carlo sampling pipelines.
This combination either happens manually or by using a convenient function
-provided by PROMOD3.</p>
+provided by ProMod3.</p>
<dl class="method">
<dt id="promod3.loop.MonteCarloSampler">
<code class="descclassname">promod3.loop.</code><code class="descname">MonteCarloSampler</code><span class="sig-paren">(</span><em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>steps</em>, <em>bb_list</em>, <em>initialize</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MonteCarloSampler" title="Permalink to this definition">¶</a></dt>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 3bf7f7d91131adee98eb7071b1aecc2f664d8841..c87d249947abf17cd63ea0633a647ae9cefe6436 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/pipeline/index.html b/doc/html/pipeline/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..a534352b622da24ce87d49051ccd947ab4624eb3
--- /dev/null
+++ b/doc/html/pipeline/index.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>pipeline - ProMod3 Modelling Pipeline — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
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+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="top" title="ProMod3 0 documentation" href="../index.html" />
+ <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="next" title="run_engine - Build Models From Various Starting Points" href="run_engine.html" />
+ <link rel="prev" title="helper - Shared Functionality For the Everything" href="../core/helper.html" />
+
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+
+ </head>
+ <body role="document">
+ <div class="related" role="navigation" aria-label="related navigation">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../genindex.html" title="General Index"
+ accesskey="I">index</a></li>
+ <li class="right" >
+ <a href="../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="right" >
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+ accesskey="P">previous</a> |</li>
+ <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="module-promod3.pipeline">
+<span id="pipeline-promod3-modelling-pipeline"></span><h1><a class="reference internal" href="#module-promod3.pipeline" title="promod3.pipeline: Everything needed for building actual models."><code class="xref py py-mod docutils literal"><span class="pre">pipeline</span></code></a> - ProMod3 Modelling Pipeline<a class="headerlink" href="#module-promod3.pipeline" title="Permalink to this headline">¶</a></h1>
+<p>This module gathers the different aspects of creating coordinates for a
+homology model. The intention is to provide easy access to the modelling engine
+for external applications.</p>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="run_engine.html"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="run_engine.html#introduction">Introduction</a></li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="../core/helper.html"
+ title="previous chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="run_engine.html"
+ title="next chapter"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></p>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/pipeline/index.txt"
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+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ <p class="searchtip" style="font-size: 90%">
+ Enter search terms or a module, class or function name.
+ </p>
+</div>
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+
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+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
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+
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+ <a href="../_sources/pipeline/index.txt"
+ rel="nofollow">Page source</a></li>
+ </div>
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\ No newline at end of file
diff --git a/doc/html/pipeline/run_engine.html b/doc/html/pipeline/run_engine.html
new file mode 100644
index 0000000000000000000000000000000000000000..a8e0caa280d199c0db09f1e310faed14708b3b18
--- /dev/null
+++ b/doc/html/pipeline/run_engine.html
@@ -0,0 +1,174 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>run_engine - Build Models From Various Starting Points — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="top" title="ProMod3 0 documentation" href="../index.html" />
+ <link rel="up" title="pipeline - ProMod3 Modelling Pipeline" href="index.html" />
+ <link rel="next" title="rawmodel - Coordinate Modeling" href="../rawmodel/index.html" />
+ <link rel="prev" title="pipeline - ProMod3 Modelling Pipeline" href="index.html" />
+
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+
+ </head>
+ <body role="document">
+ <div class="related" role="navigation" aria-label="related navigation">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../genindex.html" title="General Index"
+ accesskey="I">index</a></li>
+ <li class="right" >
+ <a href="../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="right" >
+ <a href="../rawmodel/index.html" title="rawmodel - Coordinate Modeling"
+ accesskey="N">next</a> |</li>
+ <li class="right" >
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+ accesskey="P">previous</a> |</li>
+ <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
+ <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="run-engine-build-models-from-various-starting-points">
+<h1><code class="xref py py-mod docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points<a class="headerlink" href="#run-engine-build-models-from-various-starting-points" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="introduction">
+<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
+<p>This is a collection of functions to just build models. All steps needed to go from various starting points to a complete model are wrapped in single function calls. That way, if something changes in the default pipeline, e.g. on general improvements, there is no need to change code depending on ProMod3 to adapt.</p>
+<ul class="simple">
+<li>also convenient for developing new stuff</li>
+<li>e.g. you want to transform the template coordinates in some way, but then just
+want to see them in a model, go by BuildFromRawModel</li>
+<li>or if you have a fancy way of post-processing, sth like a new way of going
+ligand, build a model easily here, then do whatever you want with the result</li>
+<li>examples should come with the API</li>
+</ul>
+<dl class="function">
+<dt id="promod3.pipeline.run_engine.BuildFromRawModel">
+<code class="descclassname">promod3.pipeline.run_engine.</code><code class="descname">BuildFromRawModel</code><span class="sig-paren">(</span><em>raw_model</em>, <em>structure_db=None</em>, <em>fragment_db=None</em>, <em>torsion_sampler=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/pipeline/run_engine.html#BuildFromRawModel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.pipeline.run_engine.BuildFromRawModel" title="Permalink to this definition">¶</a></dt>
+<dd><p>Build a model starting with a
+<a class="reference internal" href="../rawmodel/index.html#promod3.rawmodel.RawModelingResult" title="promod3.rawmodel.RawModelingResult"><code class="xref py py-class docutils literal"><span class="pre">RawModel</span></code></a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>raw_model</strong> (<a class="reference internal" href="../rawmodel/index.html#promod3.rawmodel.RawModelingResult" title="promod3.rawmodel.RawModelingResult"><code class="xref py py-class docutils literal"><span class="pre">RawModelingResult</span></code></a>) – The prepared template coordinates loaded with the input
+alignment.</li>
+<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – The structural database. Loads the default one shipped
+with ProMod3 if omitted.</li>
+<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – A fragment database coupled to the <em>structure_db</em>.
+Loads the default one shipped with ProMod3 if omitted.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. Loads the default one
+shipped with ProMod3 if omitted.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>EXAMPLE: obtain raw model, build model</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">Returns:</th><td class="field-body">Delivers the model as 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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+ <h3><a href="../index.html">Table Of Contents</a></h3>
+ <ul>
+<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a><ul>
+<li><a class="reference internal" href="#introduction">Introduction</a></li>
+</ul>
+</li>
+</ul>
+
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="index.html"
+ title="previous chapter"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="../rawmodel/index.html"
+ title="next chapter"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a></p>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/pipeline/run_engine.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
+ </div>
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ <p class="searchtip" style="font-size: 90%">
+ Enter search terms or a module, class or function name.
+ </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2015, Bienchen.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+
+ |
+ <a href="../_sources/pipeline/run_engine.txt"
+ rel="nofollow">Page source</a></li>
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index f3fad5495f79353e7f8fcec9b348330d1b945cea..4b355acda60de50d8a03c1bfce4430e7690fc706 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -84,6 +84,11 @@
<td>
<a href="loop/index.html#module-promod3.loop"><code class="xref">promod3.loop</code></a></td><td>
<em>Loop Modelling</em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="pipeline/index.html#module-promod3.pipeline"><code class="xref">promod3.pipeline</code></a></td><td>
+ <em>Everything needed for building actual models.</em></td></tr>
<tr class="cg-1">
<td></td>
<td>
diff --git a/doc/html/rawmodel/index.html b/doc/html/rawmodel/index.html
index 1f3150676f9749b68076ddb3656241ad886c8903..7cf292f13cd6c31bbecd3ec9974bf7af2066dc4f 100644
--- a/doc/html/rawmodel/index.html
+++ b/doc/html/rawmodel/index.html
@@ -26,7 +26,7 @@
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developes" href="../developers.html" />
<link rel="next" title="loop - Loop Modelling" href="../loop/index.html" />
- <link rel="prev" title="helper - Shared Functionality For the Everything" href="../core/helper.html" />
+ <link rel="prev" title="run_engine - Build Models From Various Starting Points" href="../pipeline/run_engine.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
@@ -46,7 +46,7 @@
<a href="../loop/index.html" title="loop - Loop Modelling"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="../core/helper.html" title="helper - Shared Functionality For the Everything"
+ <a href="../pipeline/run_engine.html" title="run_engine - Build Models From Various Starting Points"
accesskey="P">previous</a> |</li>
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@@ -150,6 +150,56 @@ missing or incomplete backbone coordinates in the template structure.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.rawmodel.RawModelingResult.CloseSmallDeletions">
+<code class="descname">CloseSmallDeletions</code><span class="sig-paren">(</span><em>scorer</em>, <em>extension_steps=9</em>, <em>clash_thresh=1.0</em>, <em>e_thresh=200</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.rawmodel.RawModelingResult.CloseSmallDeletions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Close small deletions by relaxing neighbouring residues.</p>
+<p>Small deletions in the template from the target-template alignment have a
+good chance to be bridged just by relaxing neighbours around a tiny gap.
+Before diving into the more demanding tasks in modeling, those may be closed
+already in the raw-model. After closure some checks are done to see if the
+solution is stereochemically sensible.</p>
+<p>Closed gaps are removed from <code class="xref py py-attr docutils literal"><span class="pre">self.gaps</span></code>.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ost</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">rawmodel</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'gly.pdb'</span><span class="p">)</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s">'seq.fasta'</span><span class="p">)</span>
+<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
+<span class="n">rmodel</span> <span class="o">=</span> <span class="n">rawmodel</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
+<span class="n">scorer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">SetupBackboneScorer</span><span class="p">(</span><span class="n">rmodel</span><span class="p">)</span>
+<span class="n">rmodel</span><span class="o">.</span><span class="n">CloseSmallDeletions</span><span class="p">(</span><span class="n">scorer</span><span class="p">)</span>
+</pre></div>
+</div>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>scorer</strong> (<a class="reference internal" href="../loop/backbone_loop_score.html#promod3.loop.BackboneLoopScorer" title="promod3.loop.BackboneLoopScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneLoopScorer</span></code></a>) – A scorer dedicated to this raw model.</li>
+<li><strong>extension_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Iterations allowed for gap extension. This does not
+directly mean ‘extended size of gap’ but no. of
+attempts to extend. Extension works like trying to
+increase left, then right, then try more on the
+left side again...</li>
+<li><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Threshold for the clash score, acceptance means being
+lower than this.</li>
+<li><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Potential energy should be lower than this.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">If gaps are deleted, the scorer needs to be updated and is
+returned.</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 internal" href="../loop/backbone_loop_score.html#promod3.loop.BackboneLoopScorer" title="promod3.loop.BackboneLoopScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneLoopScorer</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
</div>
@@ -170,8 +220,8 @@ missing or incomplete backbone coordinates in the template structure.</p>
</ul>
<h4>Previous topic</h4>
- <p class="topless"><a href="../core/helper.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></p>
+ <p class="topless"><a href="../pipeline/run_engine.html"
+ title="previous chapter"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="../loop/index.html"
title="next chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a></p>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 83b09be15034d4fbc0bd271c362840cd41cebe04..a324233e403b7da526d396638cd7c3e49d6345f1 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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class=\"docutils literal\"><span class=\"pre\">test_actions.ActionTestCase</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Contributing","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","Documentation For Developes","Welcome To ProMod3’s Documentation!","Backbone","Loop Scoring","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Modelling","Load Loop Objects","Loop Candidates","Loop Closing","Monte Carlo Sampling","Structural Database","Torsion Sampler","<code class=\"docutils literal\"><span class=\"pre\">pipeline</span></code> - ProMod3 Modelling Pipeline","<code class=\"docutils literal\"><span class=\"pre\">run_engine</span></code> - Build Models From Various Starting Points","<code class=\"docutils literal\"><span class=\"pre\">rawmodel</span></code> - Coordinate Modeling","Disulfid Bond Evaluation","Frame","Coming to a solution","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Rotamers","RotamerID","Rotamer Library","Rotamer Settings","Documentation For Users"],titleterms:{"class":19,"function":[3,5,6,24,27],acid:19,action:[0,3,4],actiontestcas:0,amino:19,api:[0,22],argument:7,backbon:[11,16,29],backboneloopscor:12,base:18,basic:11,block:[11,27],bond:23,branch:4,build:[1,11,21,27],can:28,candid:15,carlo:17,catchphras:[],ccd:16,chain:18,chang:2,changelog:2,close:16,closer:17,cmake:[0,1,3,4],come:25,command:7,construct:[24,27],contribut:4,conveni:[24,27],cooler:17,coordin:22,core:6,creat:0,databas:18,defin:[18,19],depend:[1,29],develop:9,directori:4,disulfid:23,document:[3,4,9,10,31],edit:11,entri:29,evalu:23,everyth:5,execut:0,featur:18,file:5,find:18,fragment:18,frame:24,from:21,full:11,geometr:18,get:28,git:4,graph:25,group:27,have:0,helper:5,hook:4,how:[4,28],indic:10,integr:0,interact:25,introduct:[3,5,7,21],iou:[],issu:4,kic:16,librari:29,licens:4,line:7,load:14,loop:[12,13,14,15,16],mainten:3,make:[0,1],messag:5,model:[13,20,21,22,26],modul:[3,4],mont:17,must:0,object:[14,17,24],output:0,own:4,pars:7,parser:7,parti:4,particl:27,pipelin:20,pm3argpars:7,point:21,promod3:[1,3,6,10,20],raw:22,rawmodel:22,relax:16,releas:2,residu:[11,24],rotam:[27,29,30],rotamerid:28,run:[0,1],run_engin:21,sampl:17,sampler:[17,19],score:12,scorer:17,script:0,sequenc:18,set:30,setcompoundschemlib:8,share:[3,5],sidechain:26,smallest:27,solut:25,stage:4,start:[4,21],stretch:11,structur:[4,18],subclass:0,tabl:10,test:[0,3,4,5],test_act:0,third:4,torsion:19,triplet:19,type:29,unit:[0,3,4],user:31,variou:21,welcom:10,write:4,your:4}})
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