diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html index 2f0828e6f53e70413b75ec397afc28b321ace832..8dfb68e7be98f936de1bca25d2812928ebacc4db 100644 --- a/doc/html/_modules/index.html +++ b/doc/html/_modules/index.html @@ -45,10 +45,11 @@ <div class="body"> <h1>All modules for which code is available</h1> +<ul><li><a href="promod3.html">promod3</a></li> <ul><li><a href="promod3/core/argcheck.html">promod3.core.argcheck</a></li> <li><a href="promod3/core/helper.html">promod3.core.helper</a></li> <li><a href="promod3/rawmodel.html">promod3.rawmodel</a></li> -</ul> +</ul></ul> </div> </div> @@ -86,7 +87,7 @@ </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 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 bce1498b9cfbd2a1773c80aba740d05ef5be102d..b7a4d0195e35158835e46d3383ba8e96dc4bfd91 100644 --- a/doc/html/_modules/promod3/core/argcheck.html +++ b/doc/html/_modules/promod3/core/argcheck.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="Module code" href="../../index.html" /> + <link rel="up" title="promod3" href="../../promod3.html" /> </head> <body> <div class="related"> @@ -37,7 +37,8 @@ <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> + <li><a href="../../index.html" >Module code</a> »</li> + <li><a href="../../promod3.html" accesskey="U">promod3</a> »</li> </ul> </div> @@ -188,12 +189,13 @@ <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="../../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 Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 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 f30d4279225dd3a8efe1a554c4d46919ddcb377b..8ad36d49473b677873dcfc567bda0ab39c1e5e1f 100644 --- a/doc/html/_modules/promod3/core/helper.html +++ b/doc/html/_modules/promod3/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="Module code" href="../../index.html" /> + <link rel="up" title="promod3" href="../../promod3.html" /> </head> <body> <div class="related"> @@ -37,7 +37,8 @@ <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> + <li><a href="../../index.html" >Module code</a> »</li> + <li><a href="../../promod3.html" accesskey="U">promod3</a> »</li> </ul> </div> @@ -108,12 +109,13 @@ <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="../../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 Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 2015. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body> diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.txt index 0830ebc615e152ab515e5eb178b892ba771c5b14..a750240d77b63b5c476fcc12b03d2c08874e425d 100644 --- a/doc/html/_sources/developers.txt +++ b/doc/html/_sources/developers.txt @@ -9,6 +9,7 @@ Contents: .. toctree:: :maxdepth: 2 + core/setcompoundschemlib core/index rawmodel/index buildsystem diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html index af691cbbc98b65a50537323a40fde5c2be99bea6..32595928ad033b9c5826d3d490f1bb7d8ecee6ff 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 Jan 05 14:50, 2015. + Last updated on Feb 11 13:37, 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 231598ff1f6241b13f3a6663ff81c4f21f64a7c5..e9ce4ea18ea42181520364e2d7fc7f71b6a49215 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 Jan 05 14:50, 2015. + Last updated on Feb 11 13:37, 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 ea7c81ea28ee6b9d65e17b5ea9bced154f6349b9..7fe296a93b06ea23f2c39af1d350b558b9c44fe2 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 Jan 05 14:50, 2015. + Last updated on Feb 11 13:37, 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 dfd6cfc3200d4080a00b785b47bdfdd646e45c1a..5289e1d205e8e3a1408b448fa8ee24b9534194c6 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 Jan 05 15:48, 2015. + Last updated on Feb 11 13:37, 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 3597372c7668a439e6841989a95f614ed23ec8bf..d7268659294297e18375b230aa1fcff5bcc2944f 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="core - ProMod3 Core Functionality" href="index.html" /> + <link rel="up" title="SetCompoundsChemlib()" href="index.html" /> <link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" /> - <link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" /> + <link rel="prev" title="SetCompoundsChemlib()" 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="core - ProMod3 Core Functionality" + <a href="index.html" title="SetCompoundsChemlib()" 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">core</span></tt> - ProMod3 Core Functionality</a> »</li> + <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></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">core</span></tt> - ProMod3 Core Functionality</a></p> + title="previous chapter"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></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="core - ProMod3 Core Functionality" + <a href="index.html" title="SetCompoundsChemlib()" >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">core</span></tt> - ProMod3 Core Functionality</a> »</li> + <li><a href="index.html" ><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a> »</li> </ul> </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Jan 05 14:50, 2015. + Last updated on Feb 11 13:37, 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 ae498d5517be94c37ecbd14e94f0206f93ac1069..dc5266d5e9b2c5fcad857a89c3eef541d43e1144 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="core - ProMod3 Core Functionality" href="index.html" /> + <link rel="up" title="SetCompoundsChemlib()" 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">core</span></tt> - ProMod3 Core Functionality</a> »</li> + <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></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">core</span></tt> - ProMod3 Core Functionality</a> »</li> + <li><a href="index.html" ><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a> »</li> </ul> </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Jan 05 14:50, 2015. + Last updated on Feb 11 13:37, 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 0663e0669e8f6fa0e8702070fafcff28ce3ad32c..40b88c32dd75733e544b4fd770a083d7c5f835db 100644 --- a/doc/html/core/index.html +++ b/doc/html/core/index.html @@ -26,7 +26,7 @@ <link rel="top" title="ProMod3 0 documentation" href="../index.html" /> <link rel="up" title="Documentation For Developes" href="../developers.html" /> <link rel="next" title="argcheck - Standard Tests For Command Line Arguments" href="argcheck.html" /> - <link rel="prev" title="Documentation For Developes" href="../developers.html" /> + <link rel="prev" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" /> </head> <body> <div class="related"> @@ -42,7 +42,7 @@ <a href="argcheck.html" title="argcheck - Standard Tests For Command Line Arguments" accesskey="N">next</a> |</li> <li class="right" > - <a href="../developers.html" title="Documentation For Developes" + <a href="setcompoundschemlib.html" title="SetCompoundsChemlib()" 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> @@ -81,8 +81,8 @@ modeling per se but cover standard programming issues.</p> <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> + <p class="topless"><a href="setcompoundschemlib.html" + title="previous chapter"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a></p> <h4>Next topic</h4> <p class="topless"><a href="argcheck.html" title="next chapter"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard Tests For Command Line Arguments</a></p> @@ -121,7 +121,7 @@ modeling per se but cover standard programming issues.</p> <a href="argcheck.html" title="argcheck - Standard Tests For Command Line Arguments" >next</a> |</li> <li class="right" > - <a href="../developers.html" title="Documentation For Developes" + <a href="setcompoundschemlib.html" title="SetCompoundsChemlib()" >previous</a> |</li> <li><a href="../index.html">ProMod3 0 documentation</a> »</li> <li><a href="../developers.html" >Documentation For Developes</a> »</li> @@ -129,7 +129,7 @@ modeling per se but cover standard programming issues.</p> </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Jan 05 14:50, 2015. + Last updated on Feb 11 15:52, 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 a6ac379a5a2c306044fd26c85dd634579ab9a5e4..f914a2b2c9fc49013ecb5576a3676798f988ba57 100644 --- a/doc/html/developers.html +++ b/doc/html/developers.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="next" title="core - ProMod3 Core Functionality" href="core/index.html" /> + <link rel="next" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" /> <link rel="prev" title="Documentation For Users" href="users.html" /> </head> <body> @@ -38,7 +38,7 @@ <a href="py-modindex.html" title="Python Module Index" >modules</a> |</li> <li class="right" > - <a href="core/index.html" title="core - ProMod3 Core Functionality" + <a href="core/setcompoundschemlib.html" title="SetCompoundsChemlib()" accesskey="N">next</a> |</li> <li class="right" > <a href="users.html" title="Documentation For Users" @@ -57,6 +57,7 @@ <p>Contents:</p> <div class="toctree-wrapper compound"> <ul> +<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a></li> <li class="toctree-l1"><a class="reference internal" href="core/index.html"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a><ul> <li class="toctree-l2"><a class="reference internal" href="core/argcheck.html"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard Tests For Command Line Arguments</a></li> <li class="toctree-l2"><a class="reference internal" href="core/helper.html"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared Functionality For the Everything</a></li> @@ -102,8 +103,8 @@ <p class="topless"><a href="users.html" title="previous chapter">Documentation For Users</a></p> <h4>Next topic</h4> - <p class="topless"><a href="core/index.html" - title="next chapter"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a></p> + <p class="topless"><a href="core/setcompoundschemlib.html" + title="next chapter"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a></p> <h3>This Page</h3> <ul class="this-page-menu"> <li><a href="_sources/developers.txt" @@ -136,7 +137,7 @@ <a href="py-modindex.html" title="Python Module Index" >modules</a> |</li> <li class="right" > - <a href="core/index.html" title="core - ProMod3 Core Functionality" + <a href="core/setcompoundschemlib.html" title="SetCompoundsChemlib()" >next</a> |</li> <li class="right" > <a href="users.html" title="Documentation For Users" @@ -146,7 +147,7 @@ </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 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 46eb6c8e3591ad2348c4c212aaf0487186314efd..a72eb0ba1f4d1d535efa8d78495747760877fb85 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -56,6 +56,7 @@ | <a href="#M"><strong>M</strong></a> | <a href="#P"><strong>P</strong></a> | <a href="#R"><strong>R</strong></a> + | <a href="#S"><strong>S</strong></a> </div> <h2 id="B">B</h2> @@ -185,6 +186,16 @@ <dt><a href="rawmodel/index.html#promod3.rawmodel.RawModelingResult">RawModelingResult (class in promod3.rawmodel)</a> </dt> + </dl></td> +</tr></table> + +<h2 id="S">S</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">SetCompoundsChemlib() (in module promod3)</a> + </dt> + </dl></td> </tr></table> @@ -229,7 +240,7 @@ </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 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 1df5318c52f97ba2b451b07ddf294798d72bc505..fbdc0ab77fe1867779641dc3b5d7dbbf34c43a64 100644 --- a/doc/html/index.html +++ b/doc/html/index.html @@ -55,6 +55,7 @@ <ul> <li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li> <li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a><ul> +<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><tt class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></tt></a></li> <li class="toctree-l2"><a class="reference internal" href="core/index.html"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a></li> <li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate Modeling</a></li> <li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li> @@ -133,7 +134,7 @@ </div> <div class="footer"> © Copyright 2014, Bienchen. - Last updated on Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 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 979d022a717fd90b643a1eb7c01f740860a0ba55..0df5916267f2a0ba5f87cc88636c67d309928459 100644 Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html index faefcc62b30bc01711adbcb2f84f8ca01d39d9d3..fe4469c49e84c9852fce6fab728fd0e642844b7d 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 Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 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 fb42a2a37a380818b52bc813d92abc045d540099..fc694673a0ee181591c6c39d8b919d9263d2fde8 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 Jan 05 14:50, 2015. + Last updated on Feb 11 13:37, 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 0092fa7ff786751c875c689bb28a2f0c498b4bc5..acfa2b584c4bcdd97b0663d881ad5447fc073610 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 Jan 05 15:48, 2015. + Last updated on Feb 11 15:52, 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 4a96c0350191b59cfb1b8616d51655d2e2848514..283e672aa38ffa742a9e3df7742686c82c8834c2 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({envversion:42,terms:{aln:9,all:[8,0,4,10,9],code:[8,0,1,10,4],forget:[8,4],chain:[8,9],messi:8,skip:8,forbidden:8,sidechains_unit_test:8,ost:[0,1,2,3,4,5,6,7,8,9,10],disable_document:[8,4],prefix:[8,0],concept:8,subclass:8,abil:8,follow:[8,9],content:[8,3,6],middl:8,test_foo:10,readabl:8,send:1,init:8,program:[10,7],under:8,introduc:8,"case":8,sourc:[8,0,1,10,4],everi:[8,9],string:0,fals:[8,0,9],internet:8,worst:8,failur:[8,0],veri:[8,0],rawmodel:[],relev:[4,10],tri:9,magic:8,solver:8,did:8,list:[8,0,4,9],assertequ:8,item:[8,9],fileextens:0,straight:8,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:10,invok:[8,4],anywai:8,current:8,delet:9,version:[8,4],"new":[8,9],boost:[0,1,2,3,4,5,6,7,8,9,10],meld:5,subtre:[8,10],submodule1:8,honour:9,gener:8,never:8,here:[0,4,1,9,8,10],lib_stage_path:8,let:8,set_directory_properti:8,path:[8,0,4,10],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,extra:8,solut:8,modul:[],submodul:8,ask:8,unix:8,api:[],instal:[8,4],smallish:[8,4],unit:[],highli:4,fed:[8,10],from:[0,5,4,1,9,8,10],describ:[0,10],would:[8,4,1],regist:[8,10],two:8,next:8,everybodi:8,few:[8,4,9],live:8,call:[8,4,10],recommend:4,msg:1,loadalign:9,checkout:8,tell:[8,0],tightli:8,more:[8,4,10,9],sort:10,trustworthi:8,peopl:8,relat:8,pylint:8,notic:[8,10],warn:8,flag:[8,0,10],include_directori:8,particular:8,known:0,rare:8,hold:9,cach:[8,4],must:8,ost_double_precis:4,word:10,py_run:[8,10],hous:8,generalis:8,setup:[8,5],work:[8,4,10],histori:8,left:1,paragraph:8,can:[8,0,4,9],purpos:8,root:8,fetch:[8,0],def:8,test_suite_:10,control:8,give:[8,10],process:8,add_argu:0,indic:[],topic:8,abort:8,want:[8,4],phrase:8,hydrogen:9,unus:8,alwai:8,gcc:8,cours:8,end:[8,0,4,1],sit:8,rather:[8,1],peptid:9,comfort:0,"_xml":10,calpha_onli:9,sever:[8,4],opt:[8,0],instead:[8,0,4,10],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:[8,4,10,9],multipl:8,data:[8,10],grow:9,man:[8,4],subsequ:9,"short":8,essenti:8,practic:[8,10],mol_alg:8,python_binari:8,correspond:8,stash:8,exclud:8,caus:8,alias:8,"switch":8,maintain:8,environ:8,allow:8,exclus:8,croak:8,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,smart:8,gitignor:8,still:8,pointer:4,disable_disable_doctest:8,paramet:[0,1,10,9],perfect:8,output_vari:8,binari:8,fix:[8,0],selenium:9,structuralgaplist:9,runnabl:8,carri:[8,0],complex:8,onc:8,python_doc_url:8,therefor:8,linkcheck:[8,4],them:[8,10],good:8,"return":[0,1,9],thei:[8,4],python:[0,1,2,3,4,5,6,7,8,9,10],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:10,name:[8,0,10],anyth:[8,4],drop:8,separ:8,easili:[8,10],achiev:8,each:8,debug:8,found:[8,10],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:[8,10],extract:8,special:[8,4,10],out:[8,4,10],variabl:[8,4],shown:8,goe:[8,4],promod3_unittest:[8,10],crucial:8,categori:10,rel:10,reader:8,print:4,got:4,exec_program:8,merg:8,clone:8,common:[8,0],model:[],insid:10,make_directori:8,runtimeerror:9,given:[0,10],free:8,standard:[],headlin:8,reason:8,base:[0,9],term:8,put:[8,0,4,10],org:8,basi:[8,10],could:[8,10,9],promod3_version_patch:8,keep:8,thing:[8,4],place:[8,1],think:8,first:[8,5],oper:8,softwar:8,major:8,suffix:0,obviou:8,prevent:8,feel:8,sidechains_pymod:8,number:9,yourself:[8,4],restrict:8,date:8,alreadi:8,done:8,messag:[],blank:8,stabl:8,miss:[0,9],exit_statu:[0,1],differ:[8,4,10],level:[8,4],script:[8,0,4,1],top:[8,4],perfectli:8,mkdir:8,system:[8,4,5],least:[8,4,10],tradition:[0,1],attach:9,stori:8,master:8,too:8,"_run":10,termin:0,scheme:8,"final":[8,9],store:[8,9],shell:[4,0,1],option:[8,0,4],cope:8,tool:[0,10],copi:[8,10,9],restrict_chain:9,specifi:10,openstructur:[0,1,2,3,4,5,6,7,8,9,10],part:8,pars:0,boost_include_dir:8,mostli:8,rst:8,conop:8,exactli:4,than:8,kind:8,grep:4,target:[8,4,10],whenev:8,provid:[8,4],seamlessli:8,tree:[8,10],unrecognis:0,project:[8,10],matter:10,reus:9,str:[0,1],were:8,posit:0,toward:8,markup:8,pre:8,linker:10,mind:8,argument:[],packag:[8,10],manner:8,have:[8,4,10,9],"__main__":8,need:[8,0,4,10],dedic:[8,4,10],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:10,exampl:[8,4,9],take:[8,9],which:[8,4,1,9,7],thoroughli:8,data1:10,noth:8,singl:[8,10,9],data2:10,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,"class":[8,9,7],charg:8,renam:5,url:8,doc:[8,4],later:8,cover:[8,0,7],doe:[8,0,10,9],ext:0,declar:[8,10],clean:[8,4],brew:10,usual:[8,4,10],someth:[8,1],came:8,cmakelist:[8,4,10],show:8,enumer:8,dbg:8,attachview:9,bring:8,permiss:8,add_doc_sourc:8,fine:8,find:[8,10],help:[8,4],involv:8,onli:[8,0,10,9],locat:[4,10],explain:8,configur:[8,4],activ:8,figur:8,should:[8,0,1,10],suppos:8,templat:9,folder:8,move:8,hit:8,contribut:[],variou:[8,4,10],get:[8,4],watch:8,autom:10,cannot:8,loadpdb:9,report:[8,9],toolbox:8,requir:[8,4],setup_compiler_flag:8,add_changelog_to_doc:8,enabl:0,ever:8,"2b1":4,gather:[8,10,7],whether:0,feed:10,integr:[8,10],contain:[8,0,4,10,9],python_root:4,where:8,remov:4,view:8,user:[],set:[8,0,4,10,9],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:10,subject:8,awar:8,statu:8,detect:0,msgerrorandexit:1,inconveni:8,vari:10,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,entiti:8,approach:8,attribut:8,accord:8,extend:[8,10],sole:8,cmake_cxx_compiler_vers:8,test_your_modul:8,recent:8,solv:8,come:[8,0],popul:[8,4],fail:[8,1],last:10,extens:0,alon:1,disable_doctest:[8,4],etc:8,tutori:8,grain:8,fno:8,mani:1,whole:[8,9],pdb:[0,9],comment:8,sidechains_rst:8,point:[8,4],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:10,rebuild:[8,4],three:[8,10],been:8,sinc:[8,0,4,10],compon:8,trigger:8,besid:[4,10],treat:[8,9],basic:[8,4,9],ost_root:[8,4],addit:[8,0,10],seq_alg:8,tini:8,quickli:8,life:8,convert:9,ani:8,coordin:[],understand:8,togeth:8,input:0,"catch":[],fileexist:0,educ:8,those:[8,4,10],emploi:8,cmake_c_compiler_vers:8,uncertain:8,look:[8,0],raw:[],testfileexistsfals:8,disable_disable_linkcheck:8,align:9,properti:8,commerci:8,trick:8,defin:10,"while":[8,0],match:[8,9],abov:8,error:[0,1],wild:10,dost_root:[8,4],loop:[8,9],stage_dir:8,spawn:8,real:8,test_sidechain:8,helper:[],almost:10,sidechain:8,henc:8,non:8,itself:[8,10],clutter:8,conf:[8,4],protein:9,vanish:8,fasta:9,"__init__":8,reviv:8,parent:9,disabl:8,develop:[],fedora:8,author:8,perform:8,suggest:8,belong:8,savepdb:9,same:[8,4],member:[8,9],funni:4,drawback:8,flag2:10,flag1:10,admir:8,document:[],start:[],conflict:8,complet:[8,9],http:8,again:[8,4],optim:[8,4],bienchen:8,argpars:0,effect:10,hand:4,driven:8,moment:8,rais:9,disable_linkcheck:[8,4],initi:5,kic:8,immedi:8,respons:8,stack:8,expand:8,codetest:[8,10],task:8,off:[8,9],pymod:8,nevertheless:8,macro:[8,10],builder:4,well:[8,4,9],pep8:[],without:[8,0,10,9],command:[],branchnam:8,thi:[0,4,9,8,7,10],endif:8,gzip:0,everyth:[],academ:8,loss:8,spend:8,latest:4,interpret:1,cmake_support:[8,10],entri:8,just:[8,4],less:8,sound:8,mol:8,obtain:9,rest:[0,1,2,3,4,5,6,7,8,9,10],legal:8,touch:8,languag:10,web:[8,4],also:[8,0,4,10,9],lapack:[8,4],restructuredtext:[0,1,2,3,4,5,6,7,8,9,10],makefil:[8,4],except:8,littl:[8,10],add:[8,10],valid:8,eigen3:8,appli:8,els:8,save:8,boost_root:4,bin:8,complaint:8,advis:8,format:8,handl:9,specimen:0,setup_stag:8,piec:8,source2:[8,10],source1:[8,10],know:4,background:4,elabor:8,bit:[8,4],cmake_compiler_is_gnucxx:8,dare:10,mod:8,eigen3_include_dir:[8,4],insert:9,like:[8,4,10,9],success:[0,1],incred:9,manual:[8,4],resolv:8,test_:8,test_awesome_featur:8,collect:1,"boolean":0,either:[8,9],bunch:8,output:[8,0],hook:[],page:[8,3,4],filecheck:8,www:8,right:[8,4],often:[8,0],acknowledg:8,some:[8,0,4],begin:8,self:8,intern:8,flush:8,proper:8,home:10,librari:[8,10],qmean:[8,4],thu:0,txt:[8,4,10],lead:0,avoid:8,definit:8,per:[8,10,7],exit:[0,1],select:9,recognis:8,sequenc:9,condit:8,overli:8,core:[],plu:8,cmake_source_dir:8,backbon:9,host:[8,10],promot:8,repositori:[8,10,5],fulli:8,"__name__":8,cmake_minimum_requir:8,intervent:8,mmcif:0,stage:[],chapter:8,src:8,about:[8,10,9],pep:8,actual:8,reappear:8,materi:8,unfortun:8,coars:8,commit:8,ost_doc_url:8,produc:[4,10],qmean_root:[8,4],own:[],within:[8,4],automat:[8,0],due:9,promod3_version_str:8,empti:[8,1],cmake_cxx_flag:8,cmake_module_path:8,ensur:[],announc:8,soon:8,your:[],manag:[8,10],git:[],fill:8,log:[8,1],wai:[8,4,10],pictur:8,qmean_include_dir:8,support:[8,0],renumb:9,custom:8,avail:[8,4],lost:8,much:[8,9],interfac:8,includ:[8,0,5],lot:[8,0],suit:8,forward:8,parse_arg:0,ehi:[],headach:8,unexpect:4,enough:8,tupl:0,forg:8,wno:8,back:8,link:[8,4,10],atom:9,don:[8,4],line:[],inlin:8,"true":[8,0,9],bug:8,pull:[8,4],tripl:0,made:10,wise:10,consist:8,possibl:[8,9],"default":[8,4],type:[0,9],displai:0,below:8,otherwis:8,problem:8,similar:[8,4],eigenvector:8,testutil:8,reserv:[0,1],featur:8,creat:[8,4,10],"int":[0,1],certain:[8,4,10],utilis:[8,0],html:[8,4,5],fellow:8,incomplet:9,exist:[8,0],file:[],dqmean_root:[8,4],deuterium:9,check:[8,0,4],pylintrc:8,probabl:[8,4,10],echo:8,cmakecach:4,readi:4,calpha:9,modif:9,when:[8,9],detail:[8,9],other:[8,4,9],bool:0,seem:8,test:[],you:[8,0,4,10],phosphoserin:9,nice:8,sometim:8,additional_make_clean_fil:8,extern:[8,10],determin:0,rawmodelingresult:9,devot:7,why:8,cmake_build_typ:8,add_subdirectori:8,formatt:8,briefli:8,eigenvalu:8,consid:[8,10],gap:9,homolog:7,doptim:8,fatal_error:8,stai:8,library2:10,library1:10,sphinx:[0,1,2,3,4,5,6,7,8,9,10],algorithm:[8,9],project_binary_dir:8,directori:[],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","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","ProMod3‘s Share Of CMake"],objects:{"":{"command:promod3_unittest":[10,0,1,""]},"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,"-"],rawmodel:[9,1,0,"-"]},"promod3.core.helper":{MsgErrorAndExit:[1,2,1,""]}},titleterms:{model:9,own:8,helper:1,modul:[8,10],share:[1,10],argument:0,indic:3,hook:8,api:9,file:0,tabl:3,argcheck:0,your:8,unit:[8,10],git:8,develop:6,welcom:3,start:8,parti:8,make:4,messag:1,write:8,how:8,build:4,branch:8,test:[8,0,10],foo:[],promod3:[4,3,10,7],"function":[1,10,7],core:7,run:4,contribut:8,standard:0,coordin:9,mainten:10,user:2,releas:5,cmake:[8,4,10],line:0,everyth:1,stage:8,document:[8,3,6,2],third:8,raw:9,directori:8,changelog:5,introduct:[0,1,10],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:[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 diff --git a/doc/html/users.html b/doc/html/users.html index e28a90ef7180e6e0f3617696a8cc112d8f1d6935..bb435c90f8ccef8539bd641779d9059aa8b35d82 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 Jan 05 14:50, 2015. + Last updated on Feb 11 13:37, 2015. Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. </div> </body>