From b0a55426a7ec86d9ebea958baef0f05e7ec0e86b Mon Sep 17 00:00:00 2001 From: Stefan Bienert <stefan.bienert@unibas.ch> Date: Tue, 24 Mar 2015 17:45:08 +0100 Subject: [PATCH] Updated documentation --- doc/html/_modules/index.html | 2 +- doc/html/_modules/promod3.html | 6 +- doc/html/_modules/promod3/core/argcheck.html | 2 +- doc/html/_modules/promod3/core/helper.html | 2 +- doc/html/_modules/promod3/rawmodel.html | 99 +++++++++++++++++++ doc/html/_sources/cmake/index.txt | 39 +++++++- doc/html/buildsystem.html | 2 +- doc/html/changelog.html | 2 +- doc/html/cmake/index.html | 43 ++++++-- doc/html/contributing.html | 2 +- doc/html/core/argcheck.html | 2 +- doc/html/core/helper.html | 2 +- doc/html/core/index.html | 2 +- doc/html/core/setcompoundschemlib.html | 2 +- doc/html/developers.html | 4 +- doc/html/genindex.html | 21 +++- doc/html/index.html | 2 +- doc/html/objects.inv | Bin 450 -> 459 bytes doc/html/py-modindex.html | 2 +- doc/html/rawmodel/index.html | 2 +- doc/html/search.html | 2 +- doc/html/searchindex.js | 2 +- doc/html/users.html | 2 +- 23 files changed, 210 insertions(+), 34 deletions(-) create mode 100644 doc/html/_modules/promod3/rawmodel.html diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html index bcf62c85..dfe8a0d8 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 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 index c5edb195..ebd9347a 100644 --- a/doc/html/_modules/promod3.html +++ b/doc/html/_modules/promod3.html @@ -55,7 +55,7 @@ <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> +<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_20150306/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> @@ -72,7 +72,7 @@ <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="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_20150306"</span><span class="p">)</span> <span class="k">except</span><span class="p">:</span> <span class="k">raise</span> @@ -124,7 +124,7 @@ </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Feb 12 07:23, 2015. + Last updated on Mar 24 17:42, 2015. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html index 0b825163..dbbbd04e 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 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 82f521cd..42cd7024 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 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 new file mode 100644 index 00000000..bb31ef7e --- /dev/null +++ b/doc/html/_modules/promod3/rawmodel.html @@ -0,0 +1,99 @@ +<!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="promod3" href="../promod3.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" >Module code</a> »</li> + <li><a href="../promod3.html" accesskey="U">promod3</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> + <li><a href="../promod3.html" >promod3</a> »</li> + </ul> + </div> + <div class="footer"> + © Copyright 2014, Bienchen. + Last updated on Mar 24 17:42, 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/cmake/index.txt b/doc/html/_sources/cmake/index.txt index ca224d7d..368f4b1c 100644 --- a/doc/html/_sources/cmake/index.txt +++ b/doc/html/_sources/cmake/index.txt @@ -26,7 +26,7 @@ into three categories of varying relevance for you: Best practices for using our home-brew |cmake| functions are found in the various :file:`CMakeLists.txt` files in the project's directory tree. -Functions For Module Maintenance +Functions For Module/ Action Maintenance -------------------------------------------------------------------------------- Unit Tests @@ -38,7 +38,8 @@ Unit Tests promod3_unittest(MODULE name SOURCES source1 [source2 ...] [LINK library1/ linker flag1 [library2/ linker flag2 ...]] - [DATA data1 [data2 ...]]) + [DATA data1 [data2 ...]] + [TARGET target]) Add unit tests to |project|. Unit tests should go in module-wise so all source files containing test code go by a single call of @@ -53,7 +54,8 @@ Unit Tests ``MODULE`` Specify the name of the module these tests are made for. Needs to be set, - needs to be a single word. + needs to be a single word. Ends up in ``make help`` as a prefix, nothing + will break if it does not match the name of any existing module. ``Sources`` Describe a set of files hosting unit test code here. If its a wild mix of @@ -76,10 +78,39 @@ Unit Tests a path relative to this directory. That path will then be created in the build directory. + ``TARGET`` + This defines an additional dependency for the unit test. + +Actions +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. cmake:command:: pm_action + + .. code-block:: cmake + + pm_action(ACTION action-script + TARGET target) + + Add an action to |project|. Actions are scripts called by the ``pm`` launcher + and should all live in the :file:`actions` directory as executable files. + Adding an action means connecting its file with the given target to be copied + to the :file:`libexec` directory. No dedicated ``make`` target will be + created. + + The parameters are: + + ``ACTION`` + Name of the action to be added. Should start with ``pm-``. Needs to be an + existing file in the same directory as the invoking :file:`CMakeLists.txt`. + + ``TARGET`` + Provide a ``make`` target to trigger copying the action's script file. The + target has to be created **before** any action may be attached to it. + .. Finding packages .. ----------------- .. Extending |cmake| .. ----------------- -.. LocalWords: cmake PROMOD +.. LocalWords: cmake PROMOD CMakeLists txt promod unittest codetest xml py +.. LocalWords: libexec diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html index b0ea9d23..90d19048 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 12 07:23, 2015. + Last updated on Mar 23 14:52, 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 7ea457af..b7014472 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 12 07:23, 2015. + Last updated on Mar 23 14:52, 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 90aef323..15828bd4 100644 --- a/doc/html/cmake/index.html +++ b/doc/html/cmake/index.html @@ -76,8 +76,8 @@ this set up.</li> <p>Best practices for using our home-brew CMake functions are found in the various <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt> files in the project’s directory tree.</p> </div> -<div class="section" id="functions-for-module-maintenance"> -<h2>Functions For Module Maintenance<a class="headerlink" href="#functions-for-module-maintenance" title="Permalink to this headline">¶</a></h2> +<div class="section" id="functions-for-module-action-maintenance"> +<h2>Functions For Module/ Action Maintenance<a class="headerlink" href="#functions-for-module-action-maintenance" title="Permalink to this headline">¶</a></h2> <div class="section" id="unit-tests"> <h3>Unit Tests<a class="headerlink" href="#unit-tests" title="Permalink to this headline">¶</a></h3> <dl class="command"> @@ -86,7 +86,8 @@ various <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span <dd><div class="highlight-cmake"><div class="highlight"><pre>promod3_unittest(MODULE name SOURCES source1 [source2 ...] [LINK library1/ linker flag1 [library2/ linker flag2 ...]] - [DATA data1 [data2 ...]]) + [DATA data1 [data2 ...]] + [TARGET target]) </pre></div> </div> <p>Add unit tests to ProMod3. Unit tests should go in module-wise so all @@ -101,7 +102,8 @@ create a set of certain <tt class="docutils literal"><span class="pre">make</spa <dl class="docutils"> <dt><tt class="docutils literal"><span class="pre">MODULE</span></tt></dt> <dd>Specify the name of the module these tests are made for. Needs to be set, -needs to be a single word.</dd> +needs to be a single word. Ends up in <tt class="docutils literal"><span class="pre">make</span> <span class="pre">help</span></tt> as a prefix, nothing +will break if it does not match the name of any existing module.</dd> <dt><tt class="docutils literal"><span class="pre">Sources</span></tt></dt> <dd>Describe a set of files hosting unit test code here. If its a wild mix of C++ and Python files does not matter, CMake will sort this out for @@ -120,6 +122,34 @@ effect on Python tests.</dd> somewhere in a dedicated <tt class="file docutils literal"><span class="pre">data</span></tt> subtree, files need to be given with a path relative to this directory. That path will then be created in the build directory.</dd> +<dt><tt class="docutils literal"><span class="pre">TARGET</span></tt></dt> +<dd>This defines an additional dependency for the unit test.</dd> +</dl> +</dd></dl> + +</div> +<div class="section" id="actions"> +<h3>Actions<a class="headerlink" href="#actions" title="Permalink to this headline">¶</a></h3> +<dl class="command"> +<dt id="command:pm_action"> +<tt class="descname">pm_action</tt><a class="headerlink" href="#command:pm_action" title="Permalink to this definition">¶</a></dt> +<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">pm_action</span><span class="p">(</span><span class="s">ACTION</span> <span class="s">action-script</span> + <span class="s">TARGET</span> <span class="s">target</span><span class="p">)</span> +</pre></div> +</div> +<p>Add an action to ProMod3. Actions are scripts called by the <tt class="docutils literal"><span class="pre">pm</span></tt> launcher +and should all live in the <tt class="file docutils literal"><span class="pre">actions</span></tt> directory as executable files. +Adding an action means connecting its file with the given target to be copied +to the <tt class="file docutils literal"><span class="pre">libexec</span></tt> directory. No dedicated <tt class="docutils literal"><span class="pre">make</span></tt> target will be +created.</p> +<p>The parameters are:</p> +<dl class="docutils"> +<dt><tt class="docutils literal"><span class="pre">ACTION</span></tt></dt> +<dd>Name of the action to be added. Should start with <tt class="docutils literal"><span class="pre">pm-</span></tt>. Needs to be an +existing file in the same directory as the invoking <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt>.</dd> +<dt><tt class="docutils literal"><span class="pre">TARGET</span></tt></dt> +<dd>Provide a <tt class="docutils literal"><span class="pre">make</span></tt> target to trigger copying the action’s script file. The +target has to be created <strong>before</strong> any action may be attached to it.</dd> </dl> </dd></dl> @@ -137,8 +167,9 @@ build directory.</dd> <ul> <li><a class="reference internal" href="#">ProMod3‘s Share Of CMake</a><ul> <li><a class="reference internal" href="#introduction">Introduction</a></li> -<li><a class="reference internal" href="#functions-for-module-maintenance">Functions For Module Maintenance</a><ul> +<li><a class="reference internal" href="#functions-for-module-action-maintenance">Functions For Module/ Action Maintenance</a><ul> <li><a class="reference internal" href="#unit-tests">Unit Tests</a></li> +<li><a class="reference internal" href="#actions">Actions</a></li> </ul> </li> </ul> @@ -194,7 +225,7 @@ build directory.</dd> </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Feb 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 574a105d..8e841817 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 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 016616ad..900c80d9 100644 --- a/doc/html/core/argcheck.html +++ b/doc/html/core/argcheck.html @@ -217,7 +217,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Feb 12 07:23, 2015. + Last updated on Mar 23 14:52, 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 d7bb686a..41150221 100644 --- a/doc/html/core/helper.html +++ b/doc/html/core/helper.html @@ -160,7 +160,7 @@ traditionally reserved to successful commands.</li> </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Feb 12 07:23, 2015. + Last updated on Mar 23 14:52, 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 1b548a13..c8c1c23d 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 12 07:23, 2015. + Last updated on Mar 23 14:52, 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 index 54d249a9..715c8be3 100644 --- a/doc/html/core/setcompoundschemlib.html +++ b/doc/html/core/setcompoundschemlib.html @@ -135,7 +135,7 @@ enabled globally.</p> </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Feb 12 07:23, 2015. + Last updated on Mar 23 14:52, 2015. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/developers.html b/doc/html/developers.html index f9ecd800..1aec1d8c 100644 --- a/doc/html/developers.html +++ b/doc/html/developers.html @@ -86,7 +86,7 @@ </li> <li class="toctree-l1"><a class="reference internal" href="cmake/index.html">ProMod3‘s Share Of CMake</a><ul> <li class="toctree-l2"><a class="reference internal" href="cmake/index.html#introduction">Introduction</a></li> -<li class="toctree-l2"><a class="reference internal" href="cmake/index.html#functions-for-module-maintenance">Functions For Module Maintenance</a></li> +<li class="toctree-l2"><a class="reference internal" href="cmake/index.html#functions-for-module-action-maintenance">Functions For Module/ Action Maintenance</a></li> </ul> </li> </ul> @@ -147,7 +147,7 @@ </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Feb 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 9faafa6d..c3593cc1 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -79,6 +79,10 @@ <dd><dl> + <dt><a href="cmake/index.html#command:pm_action"><strong>pm_action</strong></a> + </dt> + + <dt><a href="cmake/index.html#command:promod3_unittest"><strong>promod3_unittest</strong></a>, <a href="cmake/index.html#index-0-command:promod3_unittest">[1]</a>, <a href="cmake/index.html#index-1-command:promod3_unittest">[2]</a> </dt> @@ -156,16 +160,27 @@ <table style="width: 100%" class="indextable genindextable"><tr> <td style="width: 33%" valign="top"><dl> - <dt><a href="core/index.html#module-promod3.core">promod3.core (module)</a> + <dt> + pm_action + </dt> + + <dd><dl> + + <dt><a href="cmake/index.html#command:pm_action"><strong>command</strong></a> </dt> + </dl></dd> - <dt><a href="rawmodel/index.html#module-promod3.rawmodel">promod3.rawmodel (module)</a> + <dt><a href="core/index.html#module-promod3.core">promod3.core (module)</a> </dt> </dl></td> <td style="width: 33%" valign="top"><dl> + <dt><a href="rawmodel/index.html#module-promod3.rawmodel">promod3.rawmodel (module)</a> + </dt> + + <dt> promod3_unittest </dt> @@ -240,7 +255,7 @@ </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Feb 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 007d58aa..91c6b3ef 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 12 07:23, 2015. + Last updated on Mar 24 17:42, 2015. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/objects.inv b/doc/html/objects.inv index 0df5916267f2a0ba5f87cc88636c67d309928459..4269956fc669eeb339789c4a5eefd4292e2490c6 100644 GIT binary patch delta 339 zcmX@ae42SeV|^u;Be!j2?uoP8&30U9&h(H|(71F=>|+1KFqO*Rr>4%ey0IkFzv=GG zi{_KIIY}|9KMH)(_10lxj^C`}WxH9|2CilgiV_r=&|hY<`hd@jUzyK6g80vT{1r7L zZEntF7VWTuYc6*8WS2GgMAW_gDQD0BN&e)in;u&$KBWX3vp*@W_n(#;a(2hnS&|dY z&m9x%&NUDcv{^P`PxR!I7v3CSyS-=emS=X+<&sa$7MVPcS<YUq_%=bquRG^O;Twtb z5hX8Px9_jGU2!VrX!Zm4UwWb<>MW0=KS*rnSDQLReL{B;%f0*V_nShJ&i1ADo1B=@ zBz5u10;z&6UqT<wDP8X-qTcBfY%;e<WHVz-)ZH5iE%DbDOugfK(^lbqs?Eu~FR!#c zgV!EpZ~gM=1<%Eku?{;HKkD7nW%_S@Veo%-+h6r{_c&Iaeb`l5-~5!@epc>$0JK!9 A_5c6? delta 330 zcmX@je295MV|^W$Be!j2?uoP8&6Zqf&h(I5pmFJ%*hTqUrk?lqm8G(?&;IgU#nAe5 z<+V+5nadv>nGlkAM2_dQxXzs7+x!*2*Y0e*wE7rB_3I^Tn9PNxuGmdn!=ZHQ*R2^_ z?rrmK>s_J1T{hEOn{R@){(9s4pB{JApEtX>eeE><6J=XF4&1Z9S-&bLcIKCBT+6!z zYIh&~w775<#{{7zFOKJk%}THB^1g3$c;|-9&+6AWlZ&OEJoXVe{w+tkzqt8_^R~mq zg4&VIHXp)s6Ka(TR_uLUFu!;5mAm3APaL(>w5#dgZ*ptJT8nAUO9hkHU0LGGtLE@T zHSD!SZB1EL?In}z%gX%>tQSmm-hR;B@8K%8>@RhCeGWw%PNwYMczwg9va4bn43FsB r#|pUa&F84w_=q=7mFb_T`S&_0&i_9vCI`v7OEp$3J}v$_H!1=E4x*xy diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html index 3d505f99..18411ab9 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 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 e9ca776e..7b46c952 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 12 07:23, 2015. + Last updated on Mar 23 14:52, 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 0379abc3..0865bb82 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 12 07:23, 2015. + Last updated on Mar 24 17:42, 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 81950fe4..f2dc9a83 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ -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 +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],secondli:[],prefix:[8,0,11],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,autotestcas:[],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:5,relev:[4,11],pm_action_init:[],tri:9,magic:8,solver:8,did:8,gui:[],list:[8,0,4,9],assertequ:8,item:[8,9],fileextens:0,setup:[8,5],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:[8,4,11,10],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],"public":[],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:[],implement:8,chanc:8,methionin:9,via:[8,10],extra:8,appli:[8,10],modul:5,submodul:8,filenam:[],unix:8,api:[],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:[8,11],call:[8,4,11,10],usr:[],recommend:4,msg:1,loadalign:9,checkout:8,tell:[8,0],tightli:8,more:[8,4,11,9],sort:11,chapter: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,prepar:[],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:[8,0,1,11,4],sit:8,rather:[8,1],peptid:9,comfort:0,"_xml":11,calpha_onli:9,snippet:[],"__init__":8,env:[],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:[8,11],wrong:4,attent:8,date:8,multipl:8,data:[8,11],grow:9,man:[8,4],subsequ:9,"short":8,essenti:8,practic:[8,11],mol_alg:8,python_binari:8,correspond:8,stash:8,pylintrc:8,caus:8,alias:8,"switch":8,maintain:8,environ:8,allow:8,exclus:8,croak:8,oper: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,carri:[8,0],complex:8,helper:[],sidechains_pymod:8,python_doc_url:8,match:[8,11,9],main:[],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":[8,11],framework:8,conquer:8,verifi:[8,0],front:[8,0,4],now:[8,9],align: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:[8,0,4,11],compil:8,monolith:8,strip:9,idea:[8,5],realli:[8,0,4],runtest:8,"static":8,connect:[8,11],our:[8,11],extract:8,special:[8,4,11],out:[8,4,11],variabl:[8,4],"try":[],shown:8,goe:[8,4],promod3_unittest:[8,11],crucial:8,categori:11,rel:11,reader:8,print:4,got:4,exec_program:8,ref:[],clone:8,common:[8,0],model:7,insid:11,make_directori:8,runtimeerror:9,given:[0,11],free:8,standard:4,headlin:8,reason:8,base:[0,9],term:8,dictionari:10,ask:8,org:8,hand:4,basi:[8,11],could:[8,11,9],put:[8,0,4,11],keep:8,thing:[8,4],place:[8,1],think:8,first:[8,5],origin:8,softwar:8,major:8,suffix:0,obviou:8,prevent:8,feel:8,onc:8,number:9,yourself:[8,4],restrict:8,mai:[8,4,11,9],alreadi:8,done:8,messag:0,blank:8,stabl:8,miss:[0,9],exit_statu:[0,1],differ:[8,4,11,10],ancient:10,level:[8,4,10],script:[8,0,1,11,4],top:[8,4,10],perfectli:8,mkdir:8,system:[8,4,5],least:[8,4,11],tradition:[0,1],attach:[11,9],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:[8,4,11],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,cmake_c_compiler_vers: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],turn:[8,0],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:[8,11],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,extern:[8,11],add_doc_sourc:8,fine:8,find:[8,11],help:[8,4,11],involv:8,onli:[8,0,11,9,10],inlin:8,locat:[4,11],execut: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:[],variou:[8,4,11],get:[8,4],watch:8,autom:11,repo:[],solut:8,cannot:8,loadpdb:9,chemic:10,report:[8,9],toolbox:8,requir:[8,4],setup_compiler_flag:8,add_changelog_to_doc:8,bar:[],enabl:[0,10],ever:8,automatis:[],"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,"import":[8,0,4,1,9],awai:8,bunch:8,approach:8,attribut:8,accord:8,extend:[8,11],sole:8,cmake_cxx_compiler_vers:8,job:[],test_your_modul:8,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],pm_action:11,load:10,sidechains_rst:8,author:8,point:[8,4,10],cxx:8,overview:8,unittest:8,argumentpars:0,chmod:[],walk:8,residu:9,header:[8,4],exclud: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:[8,11],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:[8,11,10],coordin:[],understand:8,togeth:8,input:0,fileexist:0,educ:8,those:[8,4,11],"case":8,therefor:8,uncertain:8,look:[8,0],raw:[],launcher:11,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,test_action_awesom:[],almost:11,sidechain:8,henc:8,non:8,itself:[8,11],clutter:8,conf:[8,4],protein:9,vanish:8,fasta:9,sever:[8,4],reviv:8,parent:9,disabl:8,develop:[],fedora:8,"_startmodul":[],perform:8,suggest:8,belong:8,savepdb:9,same:[8,4,11],member:[8,9],funni:4,drawback:8,flag2:11,flag1:11,admir:8,document:[4,5],start:4,conflict:8,complet:[8,9],http:8,again:[8,4],optim:[8,4],bienchen:8,argpars:0,effect:11,detour:[],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],libexec:11,task:8,off:[8,9],pymod:8,nevertheless:8,macro:[8,11],builder:4,well:[8,4,9],full:[],know:4,without:[8,0,11,9],command:[],branchnam:8,thi:[0,4,10,8,9,7,11],endif:8,entiti:8,everyth:[],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],detail:[8,9],behind:[],touch:8,languag:11,web:[8,4],easi:[],also:[8,0,4,11,9],lapack:[8,4],scenario:[],filecheck:8,makefil:[8,4],except:8,littl:[8,11],add:[8,11],valid:8,eigen3:8,els:8,save:8,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],pop:8,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,test_submodule1:8,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],mood:[],lead:0,avoid:[8,10],definit:8,legal:8,exit:[0,1],select:9,recognis:8,sequenc:9,condit:8,foo:[],overli:8,manag:[8,11],core:[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,trustworthi: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:[],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,merg:8,testfileexistsfals:8,git:[4,5],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:[],highest:10,"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,until:[],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:[8,0,11],file:4,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],add_custom_target:[],other:[8,4,9],bool:0,seem:8,test:4,you:[8,0,4,11,10],phosphoserin:9,intermedi:[],nice:8,restructuredtext:[0,1,2,3,4,5,6,7,8,9,10,11],sometim:8,additional_make_clean_fil:8,intend:[],determin:0,rawmodelingresult:9,devot:7,"class":[8,9,7],cmake_build_typ:8,add_subdirectori:8,propag:[],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,descript:8,pseudo:9,rule:8,ignor:9,awesom:[],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,""],"command:pm_action":[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,action:11,chang:5,licens:8,depend:4}}) \ No newline at end of file diff --git a/doc/html/users.html b/doc/html/users.html index 656cf5bf..c7c1665e 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 12 07:23, 2015. + Last updated on Mar 23 14:52, 2015. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> -- GitLab