diff --git a/doc/html/.buildinfo b/doc/html/.buildinfo
deleted file mode 100644
index 1b7d1a29551920e9c183442a4d3f965d2e8654a3..0000000000000000000000000000000000000000
--- a/doc/html/.buildinfo
+++ /dev/null
@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 433d99f3c433e3d2ae1ca349a4cb112f
-tags: a205e9ed8462ae86fdd2f73488852ba9
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 8dfb68e7be98f936de1bca25d2812928ebacc4db..bcf62c854ffde1dfabd9ce9bdf829159facfee19 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -87,7 +87,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
new file mode 100644
index 0000000000000000000000000000000000000000..c5edb195b821a7aed0921cc6395b646e16b6fd3d
--- /dev/null
+++ b/doc/html/_modules/promod3.html
@@ -0,0 +1,131 @@
+<!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 — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/default.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="Module code" href="index.html" />
+ </head>
+ <body>
+ <div class="related">
+ <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><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li><a href="index.html" accesskey="U">Module code</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+ <h1>Source code for promod3</h1><div class="highlight"><pre>
+<span class="c"># load compounds library</span>
+<span class="c"># That way we do not need to call our scripts with the OST starter and are more</span>
+<span class="c"># flexible.</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">ost</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+
+<div class="viewcode-block" id="SetCompoundsChemlib"><a class="viewcode-back" href="../core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">[docs]</a><span class="k">def</span> <span class="nf">SetCompoundsChemlib</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="o">=</span><span class="s">"/import/bc2/apps/OpenStructure/1.4.0-goolf-1.4.10_20150123/share/openstructure/compounds.chemlib"</span><span class="p">):</span>
+ <span class="sd">"""SetCompoundsChemlib(path_to_chemlib)</span>
+<span class="sd"> Load a compounds library. Does not return anything, the library is just</span>
+<span class="sd"> enabled globally.</span>
+
+<span class="sd"> :param path_to_chemlib: Points to the file to be loaded.</span>
+<span class="sd"> :type path_to_chemlib: :class:`str`</span>
+<span class="sd"> """</span>
+ <span class="n">compound_lib_path</span> <span class="o">=</span> <span class="n">path_to_chemlib</span>
+ <span class="n">compound_lib</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">CompoundLib</span><span class="o">.</span><span class="n">Load</span><span class="p">(</span><span class="n">compound_lib_path</span><span class="p">)</span>
+ <span class="n">conop</span><span class="o">.</span><span class="n">SetDefaultLib</span><span class="p">(</span><span class="n">compound_lib</span><span class="p">)</span>
+ <span class="n">io</span><span class="o">.</span><span class="n">profiles</span><span class="p">[</span><span class="s">'DEFAULT'</span><span class="p">]</span><span class="o">.</span><span class="n">processor</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">RuleBasedProcessor</span><span class="p">(</span><span class="n">compound_lib</span><span class="p">)</span>
+
+<span class="c"># check if we already have an OST PrefixPath</span></div>
+<span class="k">try</span><span class="p">:</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">GetSharedDataPath</span><span class="p">()</span>
+<span class="k">except</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">rt_err</span><span class="p">:</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">SetPrefixPath</span><span class="p">(</span><span class="s">"/import/bc2/apps/OpenStructure/1.4.0-goolf-1.4.10_20150123"</span><span class="p">)</span>
+<span class="k">except</span><span class="p">:</span>
+ <span class="k">raise</span>
+
+<span class="c"># check if we do have a compounds library</span>
+<span class="k">if</span> <span class="ow">not</span> <span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">():</span>
+ <span class="n">SetCompoundsChemlib</span><span class="p">()</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'SetCompoundsChemlib'</span><span class="p">,)</span>
+
+<span class="c"># LocalWords: OST os ost conop io SetCompoundsChemlib CHEMLIB param chemlib</span>
+<span class="c"># LocalWords: str SetDefaultLib RuleBasedProcessor PrefixPath RuntimeError</span>
+<span class="c"># LocalWords: GetSharedDataPath SetPrefixPath GetDefaultLib</span>
+</pre></div>
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar">
+ <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none">
+ <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="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../genindex.html" title="General Index"
+ >index</a></li>
+ <li class="right" >
+ <a href="../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li><a href="index.html" >Module code</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2014, Bienchen.
+ Last updated on Feb 12 07:23, 2015.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
+ </div>
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index b7a4d0195e35158835e46d3383ba8e96dc4bfd91..0b82516305c9af8803e377d720aafaf56614e42d 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -195,7 +195,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 8ad36d49473b677873dcfc567bda0ab39c1e5e1f..82f521cd6700a8e3817b3d1ad4d265e0238b6244 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -115,7 +115,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3/rawmodel.html b/doc/html/_modules/promod3/rawmodel.html
deleted file mode 100644
index c6e7453f42428ddabe038387b5255f28ac2ef5c8..0000000000000000000000000000000000000000
--- a/doc/html/_modules/promod3/rawmodel.html
+++ /dev/null
@@ -1,97 +0,0 @@
-<!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 — ProMod3 0 documentation</title>
-
- <link rel="stylesheet" href="../../_static/default.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="Module code" href="../index.html" />
- </head>
- <body>
- <div class="related">
- <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><a href="../../index.html">ProMod3 0 documentation</a> »</li>
- <li><a href="../index.html" accesskey="U">Module code</a> »</li>
- </ul>
- </div>
-
- <div class="document">
- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body">
-
- <h1>Source code for promod3.rawmodel</h1><div class="highlight"><pre>
-<span class="sd">"""</span>
-<span class="sd">Initialise the rawmodel module.</span>
-<span class="sd">"""</span>
-<span class="kn">from</span> <span class="nn">_rawmodel</span> <span class="kn">import</span> <span class="n">BuildRawModel</span><span class="p">,</span> <span class="n">StructuralGap</span><span class="p">,</span> <span class="n">GapExtender</span>
-</pre></div>
-
- </div>
- </div>
- </div>
- <div class="sphinxsidebar">
- <div class="sphinxsidebarwrapper">
-<div id="searchbox" style="display: none">
- <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="related">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../genindex.html" title="General Index"
- >index</a></li>
- <li class="right" >
- <a href="../../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li><a href="../../index.html">ProMod3 0 documentation</a> »</li>
- <li><a href="../index.html" >Module code</a> »</li>
- </ul>
- </div>
- <div class="footer">
- © Copyright 2014, Bienchen.
- Last updated on Jan 05 15:48, 2015.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
- </div>
- </body>
-</html>
\ No newline at end of file
diff --git a/doc/html/_sources/core/setcompoundschemlib.txt b/doc/html/_sources/core/setcompoundschemlib.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb0223432967ffc2ed53d542191c52fce4fb770b
--- /dev/null
+++ b/doc/html/_sources/core/setcompoundschemlib.txt
@@ -0,0 +1,17 @@
+:func:`~promod3.SetCompoundsChemlib`
+================================================================================
+
+.. currentmodule:: promod3
+
+This is the one function defined on the highest level of |project|'s module
+hierarchy. It is used to load an |ost_s| compound library to avoid running
+|python| code via the ancient |ost_s| wrapper. Applying this function at
+top-level, we can set a decent default by |cmake| plus the library is
+immediately available just by invoking **any** |project| module. You do not
+need to call this function, only if you want to load a different chemical
+components dictionary.
+
+.. autofunction:: SetCompoundsChemlib
+
+.. LocalWords: func promod SetCompoundsChemlib currentmodule ost cmake
+.. LocalWords: autofunction
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 32595928ad033b9c5826d3d490f1bb7d8ecee6ff..b0ea9d2319ab18fb2f1fc06a28ff917f9c9e3baf 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -212,7 +212,7 @@ builder</li>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index e9ce4ea18ea42181520364e2d7fc7f71b6a49215..7ea457af20b5d85a4d1919370aceb81699029543 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -128,7 +128,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 7fe296a93b06ea23f2c39af1d350b558b9c44fe2..90aef323916916b00fd8bb51dddc0f8daee25e2b 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -194,7 +194,7 @@ build directory.</dd>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 5289e1d205e8e3a1408b448fa8ee24b9534194c6..574a105d7bcdebe27ccc050e872a7aa09f102872 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -836,7 +836,7 @@ contributions to web pages using ProMod3.</p>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index d7268659294297e18375b230aa1fcff5bcc2944f..016616adcc6329ed2ac42437c85fb51c17cdebf3 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -24,9 +24,9 @@
<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="SetCompoundsChemlib()" href="index.html" />
+ <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
- <link rel="prev" title="SetCompoundsChemlib()" href="index.html" />
+ <link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
</head>
<body>
<div class="related">
@@ -42,11 +42,11 @@
<a href="helper.html" title="helper - Shared Functionality For the Everything"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="index.html" title="SetCompoundsChemlib()"
+ <a href="index.html" title="core - ProMod3 Core Functionality"
accesskey="P">previous</a> |</li>
<li><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a> »</li>
+ <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
@@ -169,7 +169,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
<h4>Previous topic</h4>
<p class="topless"><a href="index.html"
- title="previous chapter"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a></p>
+ title="previous chapter"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="helper.html"
title="next chapter"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared Functionality For the Everything</a></p>
@@ -208,16 +208,16 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
<a href="helper.html" title="helper - Shared Functionality For the Everything"
>next</a> |</li>
<li class="right" >
- <a href="index.html" title="SetCompoundsChemlib()"
+ <a href="index.html" title="core - ProMod3 Core Functionality"
>previous</a> |</li>
<li><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li><a href="index.html" ><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a> »</li>
+ <li><a href="index.html" ><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index dc5266d5e9b2c5fcad857a89c3eef541d43e1144..d7bb686a586a0072489d353aabeb38c54e924a11 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -24,7 +24,7 @@
<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="SetCompoundsChemlib()" 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="prev" title="argcheck - Standard Tests For Command Line Arguments" href="argcheck.html" />
</head>
@@ -46,7 +46,7 @@
accesskey="P">previous</a> |</li>
<li><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a> »</li>
+ <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
@@ -155,12 +155,12 @@ traditionally reserved to successful commands.</li>
>previous</a> |</li>
<li><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li><a href="index.html" ><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a> »</li>
+ <li><a href="index.html" ><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 40b88c32dd75733e544b4fd770a083d7c5f835db..1b548a138c86a01af530d53c929411a7a8eb6066 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -129,7 +129,7 @@ modeling per se but cover standard programming issues.</p>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
new file mode 100644
index 0000000000000000000000000000000000000000..54d249a93da4cf1b76ed098daf510f053b01a5d7
--- /dev/null
+++ b/doc/html/core/setcompoundschemlib.html
@@ -0,0 +1,142 @@
+<!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>SetCompoundsChemlib() — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/default.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="Documentation For Developes" href="../developers.html" />
+ <link rel="next" title="core - ProMod3 Core Functionality" href="index.html" />
+ <link rel="prev" title="Documentation For Developes" href="../developers.html" />
+ </head>
+ <body>
+ <div class="related">
+ <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="index.html" title="core - ProMod3 Core Functionality"
+ accesskey="N">next</a> |</li>
+ <li class="right" >
+ <a href="../developers.html" title="Documentation For Developes"
+ accesskey="P">previous</a> |</li>
+ <li><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li><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">
+
+ <div class="section" id="setcompoundschemlib">
+<h1><a class="reference internal" href="#promod3.SetCompoundsChemlib" title="promod3.SetCompoundsChemlib"><tt class="xref py py-func docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a><a class="headerlink" href="#setcompoundschemlib" title="Permalink to this headline">¶</a></h1>
+<p>This is the one function defined on the highest level of ProMod3‘s module
+hierarchy. It is used to load an OST compound library to avoid running
+Python code via the ancient OST wrapper. Applying this function at
+top-level, we can set a decent default by CMake plus the library is
+immediately available just by invoking <strong>any</strong> ProMod3 module. You do not
+need to call this function, only if you want to load a different chemical
+components dictionary.</p>
+<dl class="function">
+<dt id="promod3.SetCompoundsChemlib">
+<tt class="descclassname">promod3.</tt><tt class="descname">SetCompoundsChemlib</tt><big>(</big><em>path_to_chemlib</em><big>)</big><a class="reference internal" href="../_modules/promod3.html#SetCompoundsChemlib"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.SetCompoundsChemlib" title="Permalink to this definition">¶</a></dt>
+<dd><p>Load a compounds library. Does not return anything, the library is just
+enabled globally.</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>path_to_chemlib</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">str</span></tt></a>) – Points to the file to be loaded.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar">
+ <div class="sphinxsidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="../developers.html"
+ title="previous chapter">Documentation For Developes</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="index.html"
+ title="next chapter"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/core/setcompoundschemlib.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
+<div id="searchbox" style="display: none">
+ <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="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../genindex.html" title="General Index"
+ >index</a></li>
+ <li class="right" >
+ <a href="../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="right" >
+ <a href="index.html" title="core - ProMod3 Core Functionality"
+ >next</a> |</li>
+ <li class="right" >
+ <a href="../developers.html" title="Documentation For Developes"
+ >previous</a> |</li>
+ <li><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li><a href="../developers.html" >Documentation For Developes</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2014, Bienchen.
+ Last updated on Feb 12 07:23, 2015.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
+ </div>
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/developers.html b/doc/html/developers.html
index f914a2b2c9fc49013ecb5576a3676798f988ba57..f9ecd800ee803ae598f6038412125bef5c04e402 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -147,7 +147,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index a72eb0ba1f4d1d535efa8d78495747760877fb85..9faafa6d22ca06da3e8d86966c57f71d322e6837 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -240,7 +240,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/index.html b/doc/html/index.html
index fbdc0ab77fe1867779641dc3b5d7dbbf34c43a64..007d58aafa3e0386ace29c9a3c946e4602ff2734 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -134,7 +134,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index fe4469c49e84c9852fce6fab728fd0e642844b7d..3d505f9996a71594ea4f5083cbeda252730edfe1 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/rawmodel/index.html b/doc/html/rawmodel/index.html
index fc694673a0ee181591c6c39d8b919d9263d2fde8..e9ca776e624078f6b385db29ec7b5d316f7332a0 100644
--- a/doc/html/rawmodel/index.html
+++ b/doc/html/rawmodel/index.html
@@ -214,7 +214,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/search.html b/doc/html/search.html
index acfa2b584c4bcdd97b0663d881ad5447fc073610..0379abc37a0b3592f10f19e15550e4dd4c9563ab 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 15:52, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 283e672aa38ffa742a9e3df7742686c82c8834c2..81950fe4e9e0dfcd321686125dc4b288bc63c80a 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:42,terms:{aln:9,all:[8,0,4,11,9],code:[0,4,1,10,8,11],forget:[8,4],chain:[8,9],messi:8,skip:8,forbidden:8,particular:8,ost:[0,1,2,3,4,5,6,7,8,9,10,11],disable_document:[8,4],prefix:[8,0],concept:8,subclass:8,abil:8,follow:[8,9],content:[8,3,6],middl:8,test_foo:11,readabl:8,send:1,init:8,program:[11,7],under:8,introduc:8,emploi:8,sourc:[0,4,1,10,8,11],everi:[8,9],string:0,fals:[8,0,9],internet:8,worst:8,failur:[8,0],veri:[8,0],rawmodel:[8,5],relev:[4,11],tri:9,magic:8,solver:8,did:8,list:[8,0,4,9],assertequ:8,item:[8,9],fileextens:0,align:9,dir:8,pleas:8,malici:8,promod_gcc_45:8,your_modul:8,direct:8,past:8,second:9,pm3_csc:8,design:0,pass:8,download:4,acid:9,even:[8,4],index:[8,3],what:[8,0,4],hide:8,sub:8,resembl:8,section:11,invok:[8,4,10],anywai:8,current:8,delet:9,version:[8,4],"new":[8,9],boost:[0,1,2,3,4,5,6,7,8,9,10,11],meld:5,subtre:[8,11],submodule1:8,honour:9,gener:8,never:8,here:[0,4,1,9,8,11],lib_stage_path:8,let:8,set_directory_properti:8,path:[8,0,4,11],along:8,modifi:[8,9,5],implicit:4,valu:[4,0,1],wait:8,test_someth:8,search:[8,3,4],find_packag:8,executable_output_path:8,setup_boost:8,step:8,promod3_version_minor:8,gly:9,doctest:[8,4],action:8,implement:8,chanc:8,methionin:9,via:[8,10],extra:8,appli:[8,10],modul:5,submodul:8,ask:8,unix:8,api:8,instal:[8,4],smallish:[8,4],unit:4,highli:4,fed:[8,11],from:[0,5,4,1,9,8,11],describ:[0,11],would:[8,4,1],etc:8,regist:[8,11],two:8,next:8,everybodi:8,few:[8,4,9],live:8,call:[8,4,11,10],recommend:4,msg:1,loadalign:9,checkout:8,tell:[8,0],tightli:8,more:[8,4,11,9],sort:11,trustworthi:8,wrapper:10,mol:8,peopl:8,relat:8,pylint:8,notic:[8,11],warn:8,flag:[8,0,11],include_directori:8,sidechains_unit_test:8,known:0,rare:8,hold:9,cach:[8,4],must:8,ost_double_precis:4,word:11,py_run:[8,11],hous:8,generalis:8,setup:[8,5],work:[8,4,11],histori:8,left:1,paragraph:8,can:[8,0,4,9,10],purpos:8,root:8,fetch:[8,0],def:8,test_suite_:11,control:8,give:[8,11],process:8,add_argu:0,indic:0,topic:8,abort:8,want:[8,4,10],phrase:8,hydrogen:9,unus:8,alwai:8,gcc:8,cours:8,end:[8,0,4,1],thing:[8,4],rather:[8,1],peptid:9,comfort:0,"_xml":11,calpha_onli:9,sever:[8,4],instead:[8,0,4,11],config:8,updat:8,python_vers:8,product:8,entityhandl:9,rebas:8,mess:8,dive:8,after:[8,4],usabl:8,befor:8,wrong:4,attent:8,mai:[8,4,11,9],multipl:8,data:[8,11],grow:9,man:[8,4],subsequ:9,"short":8,essenti:8,practic:[8,11],mol_alg:8,sit:8,correspond:8,stash:8,pylintrc:8,caus:8,alias:8,"switch":8,maintain:8,environ:8,allow:8,exclus:8,croak:8,"10_20150123":[],origin:8,promod3_version_major:8,eigen:[8,4],over:[8,4,9],insight:8,becaus:[8,4],through:8,files_to_be_remov:8,affect:8,hierarchi:10,gitignor:8,still:8,pointer:4,disable_disable_doctest:8,paramet:[0,1,11,9,10],perfect:8,output_vari:8,binari:8,fix:[8,0],selenium:9,structuralgaplist:9,runnabl:8,feel:8,complex:8,onc:8,python_doc_url:8,match:[8,9],therefor:8,linkcheck:[8,4],them:[8,11],good:8,"return":[0,1,9,10],thei:[8,4],python:[0,1,2,3,4,5,6,7,8,9,10,11],dai:0,exot:8,"break":8,framework:8,conquer:8,verifi:[8,0],front:[8,0,4],now:[8,9],pre_commit:8,minimalist:9,cmake_cxx_flags_releas:8,libexec_stage_path:8,somewher:11,name:[8,0,11],anyth:[8,4,10],drop:8,separ:8,easili:[8,11],achiev:8,each:8,debug:8,found:[8,11],went:8,higher:4,side:[8,9],mean:[8,0,4],compil:8,monolith:8,strip:9,idea:[8,5],realli:[8,0,4],runtest:8,"static":8,connect:8,our:[8,11],extract:8,special:[8,4,11],out:[8,4,11],variabl:[8,4],shown:8,goe:[8,4],promod3_unittest:[8,11],crucial:8,categori:11,rel:11,reader:8,print:4,got:4,exec_program:8,clone:8,common:[8,0],model:[],insid:11,make_directori:8,runtimeerror:9,given:[0,11],free:8,standard:[8,4],headlin:8,reason:8,base:[0,9],term:8,dictionari:10,put:[8,0,4,11],org:8,basi:[8,11],could:[8,11,9],keep:8,turn:[8,0],place:[8,1],think:8,first:[8,5],oper:8,softwar:8,major:8,suffix:0,obviou:8,prevent:8,carri:[8,0],sidechains_pymod:8,number:9,yourself:[8,4],restrict:8,date:8,alreadi:8,done:8,messag:[8,0],blank:8,stabl:8,miss:[0,9],exit_statu:[0,1],differ:[8,4,11,10],ancient:10,level:[8,4,10],script:[8,0,4,1],top:[8,4,10],perfectli:8,mkdir:8,system:[8,4,5],least:[8,4,11],tradition:[0,1],attach:9,stori:8,master:8,too:8,"_run":11,termin:0,scheme:8,"final":[8,9],store:[8,9],shell:[4,0,1],option:[8,0,4],cope:8,tool:[0,11],copi:[8,11,9],restrict_chain:9,specifi:11,openstructur:[0,1,2,3,4,5,6,7,8,9,10,11],part:8,pars:0,boost_include_dir:8,mostli:8,rst:8,conop:8,exactli:4,than:8,kind:8,grep:4,target:[8,4,11],whenev:8,provid:[8,4],seamlessli:8,tree:[8,11],unrecognis:0,project:[8,11],matter:11,reus:9,str:[0,1,10],were:8,posit:0,toward:8,markup:8,pre:8,python_binari:8,linker:11,mind:8,argument:4,packag:[8,11],manner:8,have:[8,4,11,9],"__main__":8,need:[8,0,4,11,10],dedic:[8,4,11],exclud:8,tidi:8,cmake_current_source_dir:8,optimis:8,imagin:8,built:8,advic:8,inform:9,diverg:8,latter:8,mix:11,exampl:[8,4,9],take:[8,9],which:[8,4,1,9,7],thoroughli:8,data1:11,noth:8,singl:[8,11,9],data2:11,compat:8,"_opt":8,sure:8,distribut:8,track:0,buildrawmodel:9,compress:0,strict:8,somethingtest:8,most:[8,0,9],eigen3_found:8,hotfix:8,why:8,charg:8,renam:5,url:8,doc:[8,4],later:8,cover:[8,0,7],doe:[8,0,11,9,10],ext:0,declar:[8,11],clean:[8,4],brew:11,usual:[8,4,11],someth:[8,1],came:8,cmakelist:[8,4,11],show:8,enumer:8,dbg:8,attachview:9,bring:8,permiss:8,add_doc_sourc:8,fine:8,find:[8,11],help:[8,4],involv:8,onli:[8,0,11,9,10],highest:10,locat:[4,11],explain:8,configur:[8,4],activ:8,figur:8,should:[8,0,1,11],suppos:8,templat:9,folder:8,move:8,hit:8,contribut:11,variou:[8,4,11],get:[8,4],watch:8,autom:11,solut:8,cannot:8,loadpdb:9,"import":[8,0,4,1,9],report:[8,9],toolbox:8,requir:[8,4],setup_compiler_flag:8,add_changelog_to_doc:8,enabl:[0,10],ever:8,"2b1":4,gather:[8,11,7],whether:0,feed:11,integr:[8,11],contain:[8,0,4,11,9],python_root:4,where:8,remov:4,view:8,user:[],set:[0,4,9,8,10,11],project_nam:8,seq:[8,9],frame:8,around:8,ost_include_dir:8,see:8,temporarili:8,mandatori:8,result:[8,4,9],smng:5,arg:8,testcas:8,close:8,sport:8,servic:8,best:11,subject:8,awar:8,statu:8,detect:0,msgerrorandexit:1,inconveni:8,vari:11,review:8,version_great:8,test_suite_your_module_run:8,label:8,state:[8,4],header_stage_path:8,subdir:8,simplest:8,chemic:10,awai:8,bunch:8,approach:8,attribut:8,accord:8,extend:[8,11],sole:8,cmake_cxx_compiler_vers:8,test_your_modul:8,goolf:[],recent:8,solv:8,come:[8,0],popul:[8,4],fail:[8,1],last:11,extens:0,alon:1,disable_doctest:[8,4],promod3_version_patch:8,tutori:8,grain:8,fno:8,mani:1,whole:[8,9],pdb:[0,9],load:10,sidechains_rst:8,point:[8,4,10],cxx:8,overview:8,unittest:8,argumentpars:0,pop:8,walk:8,residu:9,header:[8,4],test_submodule1:8,throughout:8,assum:8,amino:9,quit:8,template_structur:9,evalu:8,coupl:8,addition:11,decent:10,rebuild:[8,4],three:[8,11],been:8,sinc:[8,0,4,11],compon:[8,10],trigger:8,besid:[4,11],treat:[8,9],basic:[8,4,9],ost_root:[8,4],addit:[8,0,11],seq_alg:8,tini:8,quickli:8,life:8,immed:[],convert:9,ani:[8,10],coordin:[],understand:8,togeth:8,input:0,fileexist:0,educ:8,those:[8,4,11],"case":8,cmake_c_compiler_vers:8,uncertain:8,look:[8,0],raw:[],testfileexistsfals:8,disable_disable_linkcheck:8,straight:8,properti:8,commerci:8,trick:8,defin:[11,10],"while":[8,0],smart:8,abov:8,error:[0,1],wild:11,dost_root:[8,4],loop:[8,9],stage_dir:8,spawn:8,bin:8,test_sidechain:8,helper:11,almost:11,sidechain:8,chemlib:[],henc:8,non:8,itself:[8,11],clutter:8,conf:[8,4],protein:9,vanish:8,fasta:9,"__init__":8,reviv:8,parent:9,disabl:8,develop:8,fedora:8,author:8,perform:8,suggest:8,belong:8,savepdb:9,same:[8,4],member:[8,9],funni:4,drawback:8,flag2:11,flag1:11,admir:8,document:[4,11,5],start:4,conflict:8,complet:[8,9],http:8,again:[8,4],optim:[8,4],bienchen:8,argpars:0,effect:11,hand:4,driven:8,moment:8,rais:9,disable_linkcheck:[8,4],initi:5,kic:8,immedi:[8,10],respons:8,stack:8,expand:8,codetest:[8,11],task:8,off:[8,9],pymod:8,nevertheless:8,macro:[8,11],builder:4,well:[8,4,9],without:[8,0,11,9],command:8,branchnam:8,thi:[0,4,10,8,9,7,11],endif:8,entiti:8,everyth:8,academ:8,loss:8,spend:8,latest:4,comment:8,cmake_support:[8,11],entri:8,just:[8,4,10],less:8,sound:8,compound:10,obtain:9,rest:[0,1,2,3,4,5,6,7,8,9,10,11],touch:8,languag:11,web:[8,4],also:[8,0,4,11,9],lapack:[8,4],filecheck:8,makefil:[8,4],except:8,littl:[8,11],add:[8,11],valid:8,eigen3:8,els:8,save:8,app:[],boost_root:4,opt:[8,0],complaint:8,advis:8,format:8,handl:9,specimen:0,setup_stag:8,piec:8,source2:[8,11],source1:[8,11],know:4,background:4,elabor:8,bit:[8,4],cmake_compiler_is_gnucxx:8,dare:11,mod:8,eigen3_include_dir:[8,4],insert:9,like:[8,4,11,9],success:[0,1],incred:9,manual:[8,4],resolv:8,test_:8,test_awesome_featur:8,collect:1,"boolean":0,either:[8,9],output:[8,0],per:[8,11,7],page:[8,3,4],www:8,right:[8,4],often:[8,0],acknowledg:8,some:[8,0,4],begin:8,self:8,global:10,intern:8,flush:8,proper:8,home:11,librari:[8,11,10],qmean:[8,4],thu:0,txt:[8,4,11],lead:0,avoid:[8,10],definit:8,legal:8,exit:[0,1],select:9,recognis:8,sequenc:9,condit:8,overli:8,manag:[8,11],core:[8,0,1],plu:[8,10],cmake_source_dir:8,backbon:9,host:[8,11],promot:8,repositori:[8,11,5],fulli:8,"__name__":8,cmake_minimum_requir:8,intervent:8,mmcif:0,stage:4,chapter:8,src:8,about:[8,11,9],pep:8,actual:8,reappear:8,materi:8,unfortun:8,interpret:1,coars:8,commit:8,ost_doc_url:8,produc:[4,11],qmean_root:[8,4],own:11,real:8,within:[8,4],automat:[8,0],due:9,promod3_version_str:8,empti:[8,1],cmake_cxx_flag:8,cmake_module_path:8,announc:8,soon:8,your:[4,11],merg:8,git:[4,11,5],fill:8,log:[8,1],wai:[8,4,11],pictur:8,qmean_include_dir:8,support:[8,0],renumb:9,custom:8,avail:[8,4,10],lost:8,much:[8,9],interfac:8,includ:[8,0,5],lot:[8,0],suit:8,forward:8,parse_arg:0,headach:8,gzip:0,unexpect:4,enough:8,tupl:0,forg:8,wno:8,back:8,link:[8,4,11],atom:9,don:[8,4],line:8,inlin:8,"true":[8,0,9],bug:8,pull:[8,4],tripl:0,made:11,wise:11,consist:8,possibl:[8,9],"default":[8,4,10],type:[0,9],displai:0,below:8,otherwis:8,problem:8,similar:[8,4],eigenvector:8,testutil:8,reserv:[0,1],featur:8,creat:[8,4,11],"int":[0,1],certain:[8,4,11],utilis:[8,0],html:[8,4,5],fellow:8,incomplet:9,exist:[8,0],file:[8,4,11],dqmean_root:[8,4],deuterium:9,check:[8,0,4],probabl:[8,4,11],echo:8,cmakecach:4,readi:4,calpha:9,modif:9,path_to_chemlib:10,when:[8,9],detail:[8,9],other:[8,4,9],bool:0,seem:8,test:4,you:[8,0,4,11,10],phosphoserin:9,bc2:[],nice:8,restructuredtext:[0,1,2,3,4,5,6,7,8,9,10,11],sometim:8,additional_make_clean_fil:8,extern:[8,11],determin:0,rawmodelingresult:9,devot:7,"class":[8,9,7],cmake_build_typ:8,add_subdirectori:8,formatt:8,briefli:8,eigenvalu:8,consid:[8,11],gap:9,homolog:7,doptim:8,fatal_error:8,stai:8,library2:11,library1:11,sphinx:[0,1,2,3,4,5,6,7,8,9,10,11],algorithm:[8,9],project_binary_dir:8,directori:[4,11],descript:8,pseudo:9,rule:8,ignor:9,time:[8,9],push:8},objtypes:{"0":"cmake:command","1":"py:module","2":"py:function","3":"py:attribute","4":"py:class"},objnames:{"0":["cmake","command","CMake command"],"1":["py","module","Python module"],"2":["py","function","Python function"],"3":["py","attribute","Python attribute"],"4":["py","class","Python class"]},filenames:["core/argcheck","core/helper","users","index","buildsystem","changelog","developers","core/index","contributing","rawmodel/index","core/setcompoundschemlib","cmake/index"],titles:["<tt class=\"docutils literal\"><span class=\"pre\">argcheck</span></tt> - Standard Tests For Command Line Arguments","<tt class=\"docutils literal\"><span class=\"pre\">helper</span></tt> - Shared Functionality For the Everything","Documentation For Users","Welcome To ProMod3’s Documentation!","Building ProMod3","Changelog","Documentation For Developes","<tt class=\"docutils literal\"><span class=\"pre\">core</span></tt> - ProMod3 Core Functionality","Contributing","<tt class=\"docutils literal\"><span class=\"pre\">rawmodel</span></tt> - Coordinate Modeling","<tt class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></tt>","ProMod3‘s Share Of CMake"],objects:{"":{"command:promod3_unittest":[11,0,1,""]},"promod3.rawmodel":{BuildRawModel:[9,2,1,""],RawModelingResult:[9,4,1,""]},"promod3.core.argcheck":{FileExtension:[0,2,1,""],FileExists:[0,2,1,""]},"promod3.rawmodel.RawModelingResult":{model:[9,3,1,""],gaps:[9,3,1,""]},promod3:{core:[7,1,0,"-"],SetCompoundsChemlib:[10,2,1,""],rawmodel:[9,1,0,"-"]},"promod3.core.helper":{MsgErrorAndExit:[1,2,1,""]}},titleterms:{model:9,own:8,helper:1,modul:[8,11],share:[1,11],argument:0,indic:3,raw:9,api:9,file:0,tabl:3,argcheck:0,your:8,unit:[8,11],setcompoundschemlib:10,git:8,cmake:[8,4,11],welcom:3,start:8,parti:8,make:4,messag:1,write:8,how:8,build:4,branch:8,test:[8,0,11],stage:8,promod3:[4,3,11,7],"function":[1,11,7],core:7,run:4,contribut:8,standard:0,coordin:9,mainten:11,user:2,releas:5,develop:6,line:0,everyth:1,introduct:[0,1,11],document:[8,3,6,2],third:8,hook:8,directori:8,changelog:5,structur:8,issu:8,command:0,rawmodel:9,chang:5,licens:8,depend:4}})
\ No newline at end of file
+Search.setIndex({envversion:42,terms:{aln:9,all:[7,0,4,11,9],code:[0,4,1,8,7,11],forget:[7,4],chain:[7,9],messi:7,skip:7,forbidden:7,sidechains_unit_test:7,ost:[0,1,2,3,4,5,6,7,8,9,10,11],disable_document:[7,4],prefix:[7,0],concept:7,legal:7,abil:7,follow:[7,9],content:[7,3,10],middl:7,test_foo:11,readabl:7,send:1,init:7,program:[11,6],under:7,introduc:7,"case":7,sourc:[0,4,1,8,7,11],everi:[7,9],string:0,fals:[7,0,9],internet:7,worst:7,failur:[7,0],veri:[7,0],affect:7,solver:7,runnabl:7,tri:9,magic:7,level:[7,4,8],did:7,list:[7,0,4,9],assertequ:7,item:[7,9],fileextens:0,align:9,dir:7,pleas:7,malici:7,promod_gcc_45:7,your_modul:7,direct:7,past:7,second:9,pm3_csc:7,design:0,pass:7,download:4,acid:9,even:[7,4],index:[7,3],what:[7,0,4],hide:7,sub:7,resembl:7,section:11,exot:7,"while":[7,0],find:[7,11],current:7,delet:9,version:[7,4],"new":[7,9],boost:[0,1,2,3,4,5,6,7,8,9,10,11],meld:5,subtre:[7,11],submodule1:7,honour:9,gener:7,never:7,here:[0,4,1,9,7,11],sphinx:[0,1,2,3,4,5,6,7,8,9,10,11],save:7,lib_stage_path:7,let:7,set_directory_properti:7,path:[7,0,4,11],along:7,modifi:[7,9,5],implicit:4,valu:[4,0,1],wait:7,headlin:7,search:[7,3,4],produc:[4,11],executable_output_path:7,setup_boost:7,host:[7,11],promod3_version_minor:7,gly:9,doctest:[7,4],action:7,implement:7,chanc:7,spawn:7,via:[7,8],extra:7,appli:[7,8],modul:5,submodul:7,put:[7,0,4,11],unix:7,api:[7,10],instal:[7,4],smallish:[7,4],unit:4,highli:4,fed:[7,11],from:[0,5,4,1,9,7,11],describ:[0,11],would:[7,4,1],regist:[7,11],two:7,next:7,everybodi:7,few:[7,4,9],live:7,call:[7,4,11,8],recommend:4,msg:1,loadalign:9,checkout:7,tell:[7,0],tightli:7,more:[7,4,11,9],sort:11,chapter:7,peopl:7,relat:7,pylint:7,notic:[7,11],warn:7,flag:[7,0,11],include_directori:7,particular:7,known:0,actual:7,hold:9,cach:[7,4],must:7,ost_double_precis:4,word:11,py_run:[7,11],hous:7,generalis:7,setup:[7,5],work:[7,4,11],histori:7,paragraph:7,can:[7,0,4,8,9],purpos:7,root:7,fetch:[7,0],def:7,test_suite_:11,control:7,give:[7,11],process:7,add_argu:0,indic:0,topic:7,abort:7,want:[7,4,8],phrase:7,made:11,hydrogen:9,contribut:11,alwai:7,gcc:7,cours:7,end:[7,0,4,1],sit:7,rather:[7,1],comfort:0,"_xml":11,sever:[7,4],opt:[7,0],verifi:[7,0],config:7,updat:7,python_vers:7,product:7,entityhandl:9,rebas:7,mess:7,clone:7,after:[7,4],usabl:7,befor:7,wrong:4,attent:7,mai:[7,4,11,9],multipl:7,data:[7,11],grow:9,man:[7,4],"short":7,essenti:7,practic:[7,11],ost_doc_url:7,python_binari:7,correspond:7,stash:7,pylintrc:7,caus:7,alias:7,"switch":7,maintain:7,environ:7,allow:7,exclus:7,qmean_root:[7,4],origin:7,least:[7,4,11],promod3_version_major:7,eigen:[7,4],over:[7,4,9],insight:7,becaus:[7,4],through:7,same:[7,4],rawmodel:[7,3,10,5],hierarchi:8,gitignor:7,still:7,pointer:4,disable_disable_doctest:7,paramet:[11,0,1,8,9],perfect:7,output_vari:7,funni:4,fix:[7,0],selenium:9,structuralgaplist:9,relev:[4,11],feel:7,drawback:7,onc:7,python_doc_url:7,therefor:7,linkcheck:[7,4],them:[7,11],good:7,"return":[0,1,8,9],thei:[7,4],python:[0,1,2,3,4,5,6,7,8,9,10,11],dai:0,initi:5,"break":7,framework:7,conquer:7,instead:[7,0,4,11],front:[7,0,4],now:[7,9],pre_commit:7,minimalist:9,cmake_cxx_flags_releas:7,libexec_stage_path:7,somewher:11,name:[7,0,11],anyth:[7,4,8],drop:7,separ:7,easili:[7,11],achiev:7,each:7,debug:7,found:[7,11],went:7,complet:[7,9],side:[7,9],mean:[7,0,4],compil:7,everyth:7,monolith:7,cmake_module_path:7,test_sidechain:7,idea:[7,5],realli:[7,0,4],runtest:7,member:[7,9],"static":7,connect:7,our:[7,11],thing:[7,4],extract:7,special:[7,4,11],out:[7,4,11],variabl:[7,4],shown:7,goe:[7,4],promod3_unittest:[7,11],crucial:7,categori:11,rel:11,reader:7,print:4,got:4,exec_program:7,merg:7,dive:7,integr:[7,11],insid:11,runtimeerror:9,differ:[7,4,11,8],free:7,standard:[7,4],test_someth:7,reason:7,base:[0,9],dictionari:8,latest:4,ask:7,org:7,hand:4,basi:[7,11],could:[7,11,9],insert:9,keep:7,turn:[7,0],place:[7,1],think:7,first:[7,5],oper:7,softwar:7,major:7,suffix:0,obviou:7,prevent:7,carri:[7,0],sidechains_pymod:7,number:9,yourself:[7,4],restrict:7,date:7,alreadi:7,done:7,messag:[7,0],blank:7,stabl:7,miss:[0,9],exit_statu:[0,1],given:[0,11],ancient:8,script:[7,0,4,1],top:[7,4,8],perfectli:7,mkdir:7,system:[7,4,5],wrapper:8,stack:7,attach:9,stori:7,master:7,too:7,"_run":11,termin:0,scheme:7,"final":[7,9],store:[7,9],shell:[4,0,1],option:[7,0,4],cope:7,tool:[0,11],copi:[7,11,9],restrict_chain:9,specifi:11,openstructur:[0,1,2,3,4,5,6,7,8,9,10,11],part:7,pars:0,boost_include_dir:7,mostli:7,rst:7,off:[7,9],exactli:4,than:7,kind:7,grep:4,target:[7,4,11],whenev:7,provid:[7,4],seamlessli:7,tree:[7,11],unrecognis:0,project:[7,11],matter:11,reus:9,str:[0,1,8],were:7,posit:0,toward:7,builder:4,pre:7,linker:11,mind:7,argument:4,packag:[7,11],manner:7,have:[7,4,11,9],"__main__":7,need:[7,0,4,11,8],dedic:[7,4,11],exclud:7,tidi:7,cmake_current_source_dir:7,optimis:7,imagin:7,probabl:[7,4,11],built:7,advic:7,inform:9,diverg:7,latter:7,mix:11,without:[7,0,11,9],take:[7,9],which:[7,4,1,9,6],thoroughli:7,data1:11,noth:7,singl:[7,11,9],data2:11,compat:7,"_opt":7,sure:7,distribut:7,track:0,forg:7,compress:0,strict:7,wno:7,most:[7,0,9],eigen3_found:7,hotfix:7,why:7,charg:7,renam:5,bug:7,url:7,doc:[7,4],later:7,cover:[7,0,6],doe:[7,0,11,8,9],ext:0,declar:[7,11],clean:[7,4],brew:11,usual:[7,4,11],review:7,came:7,cmakelist:[7,4,11],show:7,test_suite_your_module_run:7,dbg:7,attachview:9,bring:7,permiss:7,cmake_support:[7,11],fine:7,anywai:7,help:[7,4],involv:7,onli:[7,0,11,8,9],inlin:7,locat:[4,11],nevertheless:7,explain:7,configur:[7,4],activ:7,state:[7,4],should:[7,0,1,11],suppos:7,templat:9,folder:7,move:7,hit:7,unus:7,variou:[7,4,11],get:[7,4],watch:7,autom:11,self:7,cannot:7,loadpdb:9,"import":[7,0,4,1,9],report:[7,9],toolbox:7,requir:[7,4],setup_compiler_flag:7,add_changelog_to_doc:7,enabl:[0,8],ever:7,elabor:7,"2b1":4,"default":[7,4,8],feed:11,common:[7,0],contain:[7,0,4,11,9],python_root:4,where:7,remov:4,view:7,set:[0,4,8,7,9,11],project_nam:7,seq:[7,9],frame:7,ost_include_dir:7,trick:7,see:7,temporarili:7,mandatori:7,result:[7,4,9],smng:5,arg:7,testcas:7,close:7,sport:7,servic:7,best:11,subject:7,awar:7,statu:7,detect:0,msgerrorandexit:1,inconveni:7,vari:11,someth:[7,1],version_great:7,enumer:7,label:7,figur:7,header_stage_path:7,subdir:7,simplest:7,chemic:8,awai:7,bunch:7,approach:7,attribut:7,accord:7,extend:[7,11],sole:7,cmake_cxx_compiler_vers:7,test_your_modul:7,solv:7,come:[7,0],popul:[7,4],fail:[7,1],last:11,extens:0,alon:1,disable_doctest:[7,4],promod3_version_patch:7,tutori:7,grain:7,fno:7,mani:1,whole:[7,9],pdb:[0,9],load:8,sidechains_rst:7,author:7,point:[7,4,8],cxx:7,overview:7,unittest:7,argumentpars:0,pop:7,walk:7,residu:9,header:[7,4],featur:7,littl:[7,11],codetest:[7,11],test_submodule1:7,throughout:7,assum:7,amino:9,quit:7,template_structur:9,creat:[7,4,11],coupl:7,addition:11,decent:8,rebuild:[7,4],three:[7,11],been:7,sinc:[7,0,4,11],compon:[7,8],trigger:7,besid:[4,11],treat:[7,9],basic:[7,4,9],ost_root:[7,4],addit:[7,0,11],seq_alg:7,tini:7,quickli:7,life:7,fasta:9,convert:9,ani:[7,8],coordin:[3,10],understand:7,togeth:7,els:7,boost_root:4,fileexist:0,educ:7,those:[7,4,11],emploi:7,cmake_c_compiler_vers:7,uncertain:7,look:[7,0],raw:10,testfileexistsfals:7,disable_disable_linkcheck:7,straight:7,properti:7,commerci:7,formatt:7,defin:[11,8],invok:[7,4,8],smart:7,abov:7,error:[0,1],wild:11,dost_root:[7,4],loop:[7,9],stage_dir:7,methionin:9,bin:7,argpars:0,helper:11,almost:11,sidechain:7,henc:7,non:7,itself:[7,11],clutter:7,conf:[7,4],protein:9,vanish:7,calpha_onli:9,"__init__":7,reviv:7,parent:9,develop:7,fedora:7,etc:7,perform:7,suggest:7,belong:7,savepdb:9,files_to_be_remov:7,promod3_version_str:7,binari:7,complex:7,flag2:11,flag1:11,advis:7,admir:7,document:[4,11,5],start:4,conflict:7,higher:4,http:7,cmakecach:4,optim:[7,4],bienchen:7,make_directori:7,effect:11,solut:7,driven:7,moment:7,rais:9,disable_linkcheck:[7,4],user:3,kic:7,respons:7,tradition:[0,1],expand:7,recent:7,task:7,conop:7,pymod:7,find_packag:7,macro:[7,11],markup:7,well:[7,4,9],exampl:[7,4,9],command:7,branchnam:7,thi:[0,4,8,7,9,11,6],endif:7,entiti:7,model:[3,10,6],academ:7,spend:7,piec:7,left:1,comment:7,add_doc_sourc:7,entri:7,just:[7,4,8],less:7,sound:7,compound:8,obtain:9,rest:[0,1,2,3,4,5,6,7,8,9,10,11],touch:7,languag:11,web:[7,4],also:[7,0,4,11,9],lapack:[7,4],filecheck:7,makefil:[7,4],except:7,seem:7,add:[7,11],other:[7,4,9],eigen3:7,input:0,subsequ:9,match:[7,9],real:7,complaint:7,around:7,format:7,handl:9,specimen:0,term:7,source2:[7,11],source1:[7,11],know:4,background:4,mol:7,bit:[7,4],you:[7,0,4,11,8],dare:11,mod:7,eigen3_include_dir:[7,4],loss:7,like:[7,4,11,9],success:[0,1],incred:9,manual:[7,4],html:[7,4,5],test_:7,test_awesome_featur:7,collect:1,"boolean":0,either:[7,9],output:[7,0],page:[7,3,4],www:7,right:[7,4],often:[7,0],acknowledg:7,some:[7,0,4],begin:7,resolv:7,global:8,intern:7,flush:7,proper:7,home:11,librari:[7,11,8],qmean:[7,4],thu:0,txt:[7,4,11],lead:0,avoid:[7,8],definit:7,subclass:7,exit:[0,1],select:9,recognis:7,devot:6,condit:7,overli:7,manag:[7,11],core:[7,0,1],plu:[7,8],cmake_source_dir:7,backbon:9,step:7,promot:7,repositori:[7,11,5],fulli:7,"__name__":7,add_subdirectori:7,intervent:7,mmcif:0,stage:4,trustworthi:7,src:7,about:[7,11,9],pep:7,rare:7,reappear:7,materi:7,unfortun:7,interpret:1,coars:7,commit:7,mol_alg:7,disabl:7,croak:7,own:11,within:[7,4],automat:[7,0],due:9,empti:[7,1],cmake_cxx_flag:7,strip:9,announc:7,soon:7,your:[4,11],per:[7,11,6],git:[4,11,5],log:[7,1],wai:[7,4,11],pictur:7,qmean_include_dir:7,support:[7,0],renumb:9,custom:7,avail:[7,4,8],lost:7,much:[7,9],interfac:7,includ:[7,0,5],lot:[7,0],suit:7,forward:7,parse_arg:0,headach:7,gzip:0,unexpect:4,enough:7,tupl:0,buildrawmodel:9,somethingtest:7,back:7,link:[7,4,11],atom:9,don:[7,4],line:7,highest:8,"true":[7,0,9],setup_stag:7,pull:[7,4],tripl:0,immedi:[7,8],wise:11,consist:7,possibl:[7,9],whether:0,type:[0,9],displai:0,below:7,otherwis:7,problem:7,similar:[7,4],eigenvector:7,testutil:7,reserv:[0,1],gather:[7,11,6],evalu:7,"int":[0,1],certain:[7,4,11],utilis:[7,0],fellow:7,incomplet:9,exist:[7,0],file:[7,4,11],dqmean_root:[7,4],deuterium:9,check:[7,0,4],fill:7,echo:7,again:[7,4],readi:4,calpha:9,modif:9,path_to_chemlib:8,when:[7,9],detail:[7,9],valid:7,bool:0,test:4,cmake_compiler_is_gnucxx:7,phosphoserin:9,nice:7,restructuredtext:[0,1,2,3,4,5,6,7,8,9,10,11],sometim:7,additional_make_clean_fil:7,extern:[7,11],determin:0,rawmodelingresult:9,sequenc:9,"class":[7,9,6],cmake_build_typ:7,cmake_minimum_requir:7,briefli:7,eigenvalu:7,consid:[7,11],gap:9,homolog:6,doptim:7,fatal_error:7,stai:7,library2:11,library1:11,peptid:9,algorithm:[7,9],project_binary_dir:7,directori:[4,11],descript:7,pseudo:9,rule:7,ignor:9,time:[7,9],push:7},objtypes:{"0":"cmake:command","1":"py:module","2":"py:function","3":"py:attribute","4":"py:class"},objnames:{"0":["cmake","command","CMake command"],"1":["py","module","Python module"],"2":["py","function","Python function"],"3":["py","attribute","Python attribute"],"4":["py","class","Python class"]},filenames:["core/argcheck","core/helper","users","index","buildsystem","changelog","core/index","contributing","core/setcompoundschemlib","rawmodel/index","developers","cmake/index"],titles:["<tt class=\"docutils literal\"><span class=\"pre\">argcheck</span></tt> - Standard Tests For Command Line Arguments","<tt class=\"docutils literal\"><span class=\"pre\">helper</span></tt> - Shared Functionality For the Everything","Documentation For Users","Welcome To ProMod3’s Documentation!","Building ProMod3","Changelog","<tt class=\"docutils literal\"><span class=\"pre\">core</span></tt> - ProMod3 Core Functionality","Contributing","<tt class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></tt>","<tt class=\"docutils literal\"><span class=\"pre\">rawmodel</span></tt> - Coordinate Modeling","Documentation For Developes","ProMod3‘s Share Of CMake"],objects:{"":{"command:promod3_unittest":[11,0,1,""]},"promod3.rawmodel":{BuildRawModel:[9,2,1,""],RawModelingResult:[9,4,1,""]},"promod3.core.argcheck":{FileExtension:[0,2,1,""],FileExists:[0,2,1,""]},"promod3.rawmodel.RawModelingResult":{model:[9,3,1,""],gaps:[9,3,1,""]},promod3:{core:[6,1,0,"-"],SetCompoundsChemlib:[8,2,1,""],rawmodel:[9,1,0,"-"]},"promod3.core.helper":{MsgErrorAndExit:[1,2,1,""]}},titleterms:{own:7,helper:1,modul:[7,11],share:[1,11],argument:0,indic:3,raw:9,api:9,file:0,tabl:3,run:4,your:7,unit:[7,11],contribut:7,git:7,cmake:[7,4,11],welcom:3,how:7,parti:7,make:4,messag:1,write:7,start:7,build:4,branch:7,test:[7,0,11],introduct:[0,1,11],promod3:[4,3,11,6],"function":[1,11,6],core:6,argcheck:0,setcompoundschemlib:8,chang:5,standard:0,coordin:9,mainten:11,user:2,releas:5,develop:10,line:0,everyth:1,stage:7,document:[7,3,10,2],third:7,hook:7,directori:7,changelog:5,structur:7,issu:7,command:0,rawmodel:9,model:9,licens:7,depend:4}})
\ No newline at end of file
diff --git a/doc/html/users.html b/doc/html/users.html
index bb435c90f8ccef8539bd641779d9059aa8b35d82..656cf5bfc6f621089861d1d090481f5851fdf316 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -110,7 +110,7 @@
</div>
<div class="footer">
© Copyright 2014, Bienchen.
- Last updated on Feb 11 13:37, 2015.
+ Last updated on Feb 12 07:23, 2015.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>