From 1ff4c11ced4de0a7b8f56dba8d05c848d8d14cbc Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 16 Dec 2014 17:54:58 +0100
Subject: [PATCH] Updated documentation
---
doc/html/_modules/index.html | 4 +-
doc/html/_modules/promod3/core/argcheck.html | 4 +-
doc/html/_modules/promod3/core/helper.html | 4 +-
doc/html/_modules/promod3/rawmodel.html | 97 +++++++++
doc/html/_sources/cmake/index.txt | 83 ++++++++
doc/html/_sources/contributing.txt | 11 +-
doc/html/_sources/core/argcheck.txt | 12 +-
doc/html/_sources/core/helper.txt | 2 +-
doc/html/_sources/core/index.txt | 2 +-
doc/html/_sources/developers.txt | 1 +
doc/html/_sources/index.txt | 4 +-
doc/html/_sources/rawmodel/index.txt | 2 +-
doc/html/buildsystem.html | 12 +-
doc/html/changelog.html | 14 +-
doc/html/cmake/index.html | 201 +++++++++++++++++++
doc/html/contributing.html | 25 ++-
doc/html/core/argcheck.html | 42 ++--
doc/html/core/helper.html | 32 +--
doc/html/core/index.html | 20 +-
doc/html/developers.html | 25 ++-
doc/html/genindex.html | 35 +++-
doc/html/index.html | 19 +-
doc/html/objects.inv | 4 +-
doc/html/py-modindex.html | 4 +-
doc/html/rawmodel/index.html | 18 +-
doc/html/search.html | 4 +-
doc/html/searchindex.js | 2 +-
doc/html/users.html | 12 +-
28 files changed, 563 insertions(+), 132 deletions(-)
create mode 100644 doc/html/_modules/promod3/rawmodel.html
create mode 100644 doc/html/_sources/cmake/index.txt
create mode 100644 doc/html/cmake/index.html
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index d8763d02..ec0ee24d 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -85,8 +85,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 52e2bef8..a93ba9d3 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -192,8 +192,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 3cb6679e..ed1ae044 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -112,8 +112,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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..97ba70ba
--- /dev/null
+++ b/doc/html/_modules/promod3/rawmodel.html
@@ -0,0 +1,97 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>promod3.rawmodel — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../',
+ VERSION: '0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
+ <link rel="top" title="ProMod3 0 documentation" href="../../index.html" />
+ <link rel="up" title="Module code" href="../index.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../../genindex.html" title="General Index"
+ accesskey="I">index</a></li>
+ <li class="right" >
+ <a href="../../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li><a href="../../index.html">ProMod3 0 documentation</a> »</li>
+ <li><a href="../index.html" accesskey="U">Module code</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+ <h1>Source code for promod3.rawmodel</h1><div class="highlight"><pre>
+<span class="sd">"""</span>
+<span class="sd">Initialise the rawmodel module.</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">_rawmodel</span> <span class="kn">import</span> <span class="n">BuildRawModel</span><span class="p">,</span> <span class="n">StructuralGap</span><span class="p">,</span> <span class="n">GapExtender</span>
+</pre></div>
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar">
+ <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none">
+ <h3>Quick search</h3>
+ <form class="search" action="../../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ <p class="searchtip" style="font-size: 90%">
+ Enter search terms or a module, class or function name.
+ </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../../genindex.html" title="General Index"
+ >index</a></li>
+ <li class="right" >
+ <a href="../../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li><a href="../../index.html">ProMod3 0 documentation</a> »</li>
+ <li><a href="../index.html" >Module code</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
+ 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
new file mode 100644
index 00000000..8fb98c96
--- /dev/null
+++ b/doc/html/_sources/cmake/index.txt
@@ -0,0 +1,83 @@
+|project|'s Share Of |cmake|
+===============================================================================
+
+Introduction
+--------------------------------------------------------------------------------
+
+This section describes the set of |project|'s own set of |cmake| functions (or
+macros) fed from the :file:`cmake_support` directory. Those could be easily put
+into three categories of varying relevance for you:
+
+1. Functions used to integrate your contribution into |project|. Its all about
+ adding files to the documentation, declaring unit tests and code management.
+ Almost all of them have their home in the file :file:`PROMOD3.cmake`.
+
+2. Then there is a set of functions needed to set up |cmake| itself. Those are
+ little helpers to find tools, external packages and such. These are found in
+ :file:`Find<DEPENDENCY>.cmake` files.
+
+3. The last and probably least relevant category for you is also to be found in
+ :file:`PROMOD3.cmake`. There is a set of functions used to define more
+ |cmake| functionality. You only need to consider those if you dare to extend
+ this set up.
+
+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
+--------------------------------------------------------------------------------
+
+Unit Tests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. cmake:command:: promod3_unittest
+
+ .. code-block:: cmake
+
+ promod3_unittest(MODULE name
+ SOURCES source1 [source2 ...]
+ [LINK library1/ linker flag1 [library2/ linker flag2 ...]]
+ [DATA data1 [data2 ...]])
+
+ 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
+ :cmake:command:`promod3_unittest`. Test data also needs to be registered
+ here, since it will be copied to the build directory. That way, inside your
+ code you do not need to set a special path to your data. Additionally, since
+ it is out of the source tree, you may change test data as you like, without
+ the |git| repository noticing. Calling :cmake:command:`promod3_unittest` will
+ create a set of certain ``make`` targets for you, beside feeding ``codetest``.
+
+ The parameters are:
+
+ ``MODULE``
+ Specify the name of the module these tests are made for. Needs to be set,
+ needs to be a single word.
+
+ ``Sources``
+ 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
+ you. But the programming language makes a difference for the ``make``
+ targets produced. |C++| files will all be gathered in a single
+ ``test_suite_<MODULE>_run`` target (there is also a ``_xml`` target but
+ this is for tools for automated testing). |python| code works on a 'one
+ target per file' basis. So :file:`test_foo.py` will have own target
+ ``test_foo.py_run``.
+
+ ``LINK``
+ Add additional libraries and linker flags for |C++| source files. Has no
+ effect on |python| tests.
+
+ ``DATA``
+ Define test data. Instead of giving data directories its own
+ :file:`CMakeLists.txt`, those files are added here. Usually located
+ somewhere in a dedicated :file:`data` subtree, files need to be given with
+ a path relative to this directory. That path will then be created in the
+ build directory.
+
+.. Finding packages
+.. -----------------
+
+.. Extending |cmake|
+.. -----------------
+
+.. LocalWords: cmake PROMOD
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index ba4eef09..be7f6cf0 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -44,7 +44,14 @@ what goes into this branch:
* Your project needs documentation
* It must not break the ability of out-of-source builds
-The reason to be a bit restrictive on branches which end up in actual releases, should be mostly obvious: |project| is used by productive services as a third party toolbox. There it is not an item of active development and people probably have no insight in its internals. So messing up a new release creates a lot of extra work for a lot of people. First for the developer of a service to find out that |project| has turned malicious, then for the maintainer of this package to figure out that its your contribution messing things up and in the end for you, fixing the problems.
+The reason to be a bit restrictive on branches which end up in actual releases,
+should be mostly obvious: |project| is used by productive services as a third
+party toolbox. There it is not an item of active development and people
+probably have no insight in its internals. So messing up a new release creates
+a lot of extra work for a lot of people. First for the developer of a service
+to find out that |project| has turned malicious, then for the maintainer of
+this package to figure out that its your contribution messing things up and in
+the end for you, fixing the problems.
The place where you may get messy is your own |git| branch within the |project|
repository. This is basically where you should develop your project. Once you
@@ -258,7 +265,7 @@ install our very own |git| hook to check some coding rules on commit.
.. code-block:: console
- $ cp extras/pre-commit .git/hooks/
+ $ cp extras/pre_commit/pre-commit .git/hooks/
$
With that in place, changes which break our coding standards will abort any
diff --git a/doc/html/_sources/core/argcheck.txt b/doc/html/_sources/core/argcheck.txt
index be77ef73..53f517f1 100644
--- a/doc/html/_sources/core/argcheck.txt
+++ b/doc/html/_sources/core/argcheck.txt
@@ -1,4 +1,4 @@
-:mod:`~promod3.core.argcheck` - Standard tests for command line arguments
+:mod:`~promod3.core.argcheck` - Standard Tests For Command Line Arguments
================================================================================
.. currentmodule:: promod3.core.argcheck
@@ -9,11 +9,11 @@ Introduction
For parsing command line arguments -
:py_docs:`optional <howto/argparse.html#introducing-optional-arguments>` and
:py_docs:`positional <howto/argparse.html#introducing-positional-arguments>` -
-|project| tools should utilise Pythons own :py_docs:`argparse <library/argparse.html>`
-module. While this comes with a lot of functionality to fetch values from the
-command line comfortably, it has no means in checking/ verifying input. Some of
-the most common tests are covered here. All tests are designed to exit a script
-on failure.
+|project| tools should utilise Pythons own
+:py_docs:`argparse <library/argparse.html>` module. While this comes with a lot
+of functionality to fetch values from the command line comfortably, it has no
+means in checking/ verifying input. Some of the most common tests are covered
+here. All tests are designed to exit a script on failure.
.. testcode:: argcheck
:hide:
diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.txt
index 3108fb5c..3d9413f9 100644
--- a/doc/html/_sources/core/helper.txt
+++ b/doc/html/_sources/core/helper.txt
@@ -1,4 +1,4 @@
-:mod:`~promod3.core.helper` - Shared functionality for the everything
+:mod:`~promod3.core.helper` - Shared Functionality For the Everything
================================================================================
.. currentmodule:: promod3.core.helper
diff --git a/doc/html/_sources/core/index.txt b/doc/html/_sources/core/index.txt
index 896ac2e6..1e2eccaf 100644
--- a/doc/html/_sources/core/index.txt
+++ b/doc/html/_sources/core/index.txt
@@ -1,4 +1,4 @@
-:mod:`~promod3.core` - ProMod3 core functionality
+:mod:`~promod3.core` - ProMod3 Core Functionality
================================================================================
.. module:: promod3.core
diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.txt
index 850cac5a..0830ebc6 100644
--- a/doc/html/_sources/developers.txt
+++ b/doc/html/_sources/developers.txt
@@ -13,5 +13,6 @@ Contents:
rawmodel/index
buildsystem
contributing
+ cmake/index
.. todolist::
diff --git a/doc/html/_sources/index.txt b/doc/html/_sources/index.txt
index b0330546..102c6f13 100644
--- a/doc/html/_sources/index.txt
+++ b/doc/html/_sources/index.txt
@@ -3,7 +3,7 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-Welcome to ProMod3's documentation!
+Welcome To ProMod3's Documentation!
===================================
Contents:
@@ -17,7 +17,7 @@ Contents:
.. todolist::
-Indices and tables
+Indices And Tables
==================
* :ref:`genindex`
diff --git a/doc/html/_sources/rawmodel/index.txt b/doc/html/_sources/rawmodel/index.txt
index 6ac1a6d1..0e95c1b6 100644
--- a/doc/html/_sources/rawmodel/index.txt
+++ b/doc/html/_sources/rawmodel/index.txt
@@ -1,4 +1,4 @@
-:mod:`~promod3.rawmodel` - Coordinate modeling
+:mod:`~promod3.rawmodel` - Coordinate Modeling
================================================================================
.. module:: promod3.rawmodel
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index f37c2969..06711aeb 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.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="Contributing" href="contributing.html" />
- <link rel="prev" title="rawmodel - Coordinate modeling" href="rawmodel/index.html" />
+ <link rel="prev" title="rawmodel - Coordinate Modeling" href="rawmodel/index.html" />
</head>
<body>
<div class="related">
@@ -42,7 +42,7 @@
<a href="contributing.html" title="Contributing"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="rawmodel/index.html" title="rawmodel - Coordinate modeling"
+ <a href="rawmodel/index.html" title="rawmodel - Coordinate Modeling"
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>
@@ -165,7 +165,7 @@ builder</li>
<h4>Previous topic</h4>
<p class="topless"><a href="rawmodel/index.html"
- title="previous chapter"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a></p>
+ title="previous chapter"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate Modeling</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="contributing.html"
title="next chapter">Contributing</a></p>
@@ -204,15 +204,15 @@ builder</li>
<a href="contributing.html" title="Contributing"
>next</a> |</li>
<li class="right" >
- <a href="rawmodel/index.html" title="rawmodel - Coordinate modeling"
+ <a href="rawmodel/index.html" title="rawmodel - Coordinate Modeling"
>previous</a> |</li>
<li><a href="index.html">ProMod3 0 documentation</a> »</li>
<li><a href="developers.html" >Documentation For Developes</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 5a038a74..9296d61a 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.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="prev" title="Contributing" href="contributing.html" />
+ <link rel="prev" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
</head>
<body>
<div class="related">
@@ -37,7 +37,7 @@
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="contributing.html" title="Contributing"
+ <a href="cmake/index.html" title="ProMod3‘s Share Of CMake"
accesskey="P">previous</a> |</li>
<li><a href="index.html">ProMod3 0 documentation</a> »</li>
</ul>
@@ -87,8 +87,8 @@
</ul>
<h4>Previous topic</h4>
- <p class="topless"><a href="contributing.html"
- title="previous chapter">Contributing</a></p>
+ <p class="topless"><a href="cmake/index.html"
+ title="previous chapter">ProMod3‘s Share Of CMake</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/changelog.txt"
@@ -121,14 +121,14 @@
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="contributing.html" title="Contributing"
+ <a href="cmake/index.html" title="ProMod3‘s Share Of CMake"
>previous</a> |</li>
<li><a href="index.html">ProMod3 0 documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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
new file mode 100644
index 00000000..b37ddcc5
--- /dev/null
+++ b/doc/html/cmake/index.html
@@ -0,0 +1,201 @@
+<!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‘s Share Of CMake — ProMod3 0 documentation</title>
+
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="top" title="ProMod3 0 documentation" href="../index.html" />
+ <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="next" title="Changelog" href="../changelog.html" />
+ <link rel="prev" title="Contributing" href="../contributing.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../genindex.html" title="General Index"
+ accesskey="I">index</a></li>
+ <li class="right" >
+ <a href="../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="right" >
+ <a href="../changelog.html" title="Changelog"
+ accesskey="N">next</a> |</li>
+ <li class="right" >
+ <a href="../contributing.html" title="Contributing"
+ accesskey="P">previous</a> |</li>
+ <li><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
+ </ul>
+ </div>
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+ <div class="section" id="project-s-share-of-cmake">
+<h1>ProMod3‘s Share Of CMake<a class="headerlink" href="#project-s-share-of-cmake" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="introduction">
+<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
+<p>This section describes the set of ProMod3‘s own set of CMake functions (or
+macros) fed from the <tt class="file docutils literal"><span class="pre">cmake_support</span></tt> directory. Those could be easily put
+into three categories of varying relevance for you:</p>
+<ol class="arabic simple">
+<li>Functions used to integrate your contribution into ProMod3. Its all about
+adding files to the documentation, declaring unit tests and code management.
+Almost all of them have their home in the file <tt class="file docutils literal"><span class="pre">PROMOD3.cmake</span></tt>.</li>
+<li>Then there is a set of functions needed to set up CMake itself. Those are
+little helpers to find tools, external packages and such. These are found in
+<tt class="file docutils literal"><span class="pre">Find<DEPENDENCY>.cmake</span></tt> files.</li>
+<li>The last and probably least relevant category for you is also to be found in
+<tt class="file docutils literal"><span class="pre">PROMOD3.cmake</span></tt>. There is a set of functions used to define more
+CMake functionality. You only need to consider those if you dare to extend
+this set up.</li>
+</ol>
+<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="unit-tests">
+<h3>Unit Tests<a class="headerlink" href="#unit-tests" title="Permalink to this headline">¶</a></h3>
+<dl class="command">
+<dt id="command:promod3_unittest">
+<tt class="descname">promod3_unittest</tt><a class="headerlink" href="#command:promod3_unittest" title="Permalink to this definition">¶</a></dt>
+<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 ...]])
+</pre></div>
+</div>
+<p>Add unit tests to ProMod3. Unit tests should go in module-wise so all
+source files containing test code go by a single call of
+<span class="target" id="index-0-command:promod3_unittest"></span><a class="reference internal" href="#command:promod3_unittest" title="promod3_unittest"><tt class="xref cmake cmake-command docutils literal"><span class="pre">promod3_unittest()</span></tt></a>. Test data also needs to be registered
+here, since it will be copied to the build directory. That way, inside your
+code you do not need to set a special path to your data. Additionally, since
+it is out of the source tree, you may change test data as you like, without
+the Git repository noticing. Calling <span class="target" id="index-1-command:promod3_unittest"></span><a class="reference internal" href="#command:promod3_unittest" title="promod3_unittest"><tt class="xref cmake cmake-command docutils literal"><span class="pre">promod3_unittest()</span></tt></a> will
+create a set of certain <tt class="docutils literal"><span class="pre">make</span></tt> targets for you, beside feeding <tt class="docutils literal"><span class="pre">codetest</span></tt>.</p>
+<p>The parameters are:</p>
+<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>
+<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
+you. But the programming language makes a difference for the <tt class="docutils literal"><span class="pre">make</span></tt>
+targets produced. C++ files will all be gathered in a single
+<tt class="docutils literal"><span class="pre">test_suite_<MODULE>_run</span></tt> target (there is also a <tt class="docutils literal"><span class="pre">_xml</span></tt> target but
+this is for tools for automated testing). Python code works on a ‘one
+target per file’ basis. So <tt class="file docutils literal"><span class="pre">test_foo.py</span></tt> will have own target
+<tt class="docutils literal"><span class="pre">test_foo.py_run</span></tt>.</dd>
+<dt><tt class="docutils literal"><span class="pre">LINK</span></tt></dt>
+<dd>Add additional libraries and linker flags for C++ source files. Has no
+effect on Python tests.</dd>
+<dt><tt class="docutils literal"><span class="pre">DATA</span></tt></dt>
+<dd>Define test data. Instead of giving data directories its own
+<tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt>, those files are added here. Usually located
+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>
+</dl>
+</dd></dl>
+
+</div>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar">
+ <div class="sphinxsidebarwrapper">
+ <h3><a href="../index.html">Table Of Contents</a></h3>
+ <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="#unit-tests">Unit Tests</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="../contributing.html"
+ title="previous chapter">Contributing</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="../changelog.html"
+ title="next chapter">Changelog</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/cmake/index.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
+<div id="searchbox" style="display: none">
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ <p class="searchtip" style="font-size: 90%">
+ Enter search terms or a module, class or function name.
+ </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px">
+ <a href="../genindex.html" title="General Index"
+ >index</a></li>
+ <li class="right" >
+ <a href="../py-modindex.html" title="Python Module Index"
+ >modules</a> |</li>
+ <li class="right" >
+ <a href="../changelog.html" title="Changelog"
+ >next</a> |</li>
+ <li class="right" >
+ <a href="../contributing.html" title="Contributing"
+ >previous</a> |</li>
+ <li><a href="../index.html">ProMod3 0 documentation</a> »</li>
+ <li><a href="../developers.html" >Documentation For Developes</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
+ 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/contributing.html b/doc/html/contributing.html
index 9738ae3e..94cb4f14 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -25,7 +25,7 @@
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developes" href="developers.html" />
- <link rel="next" title="Changelog" href="changelog.html" />
+ <link rel="next" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
<link rel="prev" title="Building ProMod3" href="buildsystem.html" />
</head>
<body>
@@ -39,7 +39,7 @@
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="changelog.html" title="Changelog"
+ <a href="cmake/index.html" title="ProMod3‘s Share Of CMake"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="buildsystem.html" title="Building ProMod3"
@@ -94,7 +94,14 @@ what goes into this branch:</p>
<li>Your project needs documentation</li>
<li>It must not break the ability of out-of-source builds</li>
</ul>
-<p>The reason to be a bit restrictive on branches which end up in actual releases, should be mostly obvious: ProMod3 is used by productive services as a third party toolbox. There it is not an item of active development and people probably have no insight in its internals. So messing up a new release creates a lot of extra work for a lot of people. First for the developer of a service to find out that ProMod3 has turned malicious, then for the maintainer of this package to figure out that its your contribution messing things up and in the end for you, fixing the problems.</p>
+<p>The reason to be a bit restrictive on branches which end up in actual releases,
+should be mostly obvious: ProMod3 is used by productive services as a third
+party toolbox. There it is not an item of active development and people
+probably have no insight in its internals. So messing up a new release creates
+a lot of extra work for a lot of people. First for the developer of a service
+to find out that ProMod3 has turned malicious, then for the maintainer of
+this package to figure out that its your contribution messing things up and in
+the end for you, fixing the problems.</p>
<p>The place where you may get messy is your own Git branch within the ProMod3
repository. This is basically where you should develop your project. Once you
created something that could go into a release, tidy things up according to the
@@ -273,7 +280,7 @@ from it. As an example, your feature will go by the name of ‘sidechains
<p>This time, Git should tell you about going for <strong>a new</strong> branch.</p>
<p>Before starting to create anything for real, now is the perfect moment to
install our very own Git hook to check some coding rules on commit.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cp extras/pre-commit .git/hooks/
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
<span class="gp">$</span>
</pre></div>
</div>
@@ -750,8 +757,8 @@ contributions to web pages using ProMod3.</p>
<p class="topless"><a href="buildsystem.html"
title="previous chapter">Building ProMod3</a></p>
<h4>Next topic</h4>
- <p class="topless"><a href="changelog.html"
- title="next chapter">Changelog</a></p>
+ <p class="topless"><a href="cmake/index.html"
+ title="next chapter">ProMod3‘s Share Of CMake</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/contributing.txt"
@@ -784,7 +791,7 @@ contributions to web pages using ProMod3.</p>
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="changelog.html" title="Changelog"
+ <a href="cmake/index.html" title="ProMod3‘s Share Of CMake"
>next</a> |</li>
<li class="right" >
<a href="buildsystem.html" title="Building ProMod3"
@@ -794,8 +801,8 @@ contributions to web pages using ProMod3.</p>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 5e31b3c9..4178be9a 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>argcheck - Standard tests for command line arguments — ProMod3 0 documentation</title>
+ <title>argcheck - Standard Tests For Command Line Arguments — ProMod3 0 documentation</title>
<link rel="stylesheet" href="../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -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="next" title="helper - Shared functionality for the everything" href="helper.html" />
- <link rel="prev" title="core - ProMod3 core functionality" href="index.html" />
+ <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
+ <link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
+ <link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
</head>
<body>
<div class="related">
@@ -39,14 +39,14 @@
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="helper.html" title="helper - Shared functionality for the everything"
+ <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="core - ProMod3 Core Functionality"
accesskey="P">previous</a> |</li>
<li><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 core functionality</a> »</li>
+ <li><a href="index.html" accesskey="U"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
@@ -56,17 +56,17 @@
<div class="body">
<div class="section" id="argcheck-standard-tests-for-command-line-arguments">
-<h1><tt class="xref py py-mod docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments<a class="headerlink" href="#argcheck-standard-tests-for-command-line-arguments" title="Permalink to this headline">¶</a></h1>
+<h1><tt class="xref py py-mod docutils literal"><span class="pre">argcheck</span></tt> - Standard Tests For Command Line Arguments<a class="headerlink" href="#argcheck-standard-tests-for-command-line-arguments" title="Permalink to this headline">¶</a></h1>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
<p>For parsing command line arguments -
<a class="reference external" href="https://docs.python.org/2.7/howto/argparse.html#introducing-optional-arguments">optional</a> and
<a class="reference external" href="https://docs.python.org/2.7/howto/argparse.html#introducing-positional-arguments">positional</a> -
-ProMod3 tools should utilise Pythons own <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html">argparse</a>
-module. While this comes with a lot of functionality to fetch values from the
-command line comfortably, it has no means in checking/ verifying input. Some of
-the most common tests are covered here. All tests are designed to exit a script
-on failure.</p>
+ProMod3 tools should utilise Pythons own
+<a class="reference external" href="https://docs.python.org/2.7/library/argparse.html">argparse</a> module. While this comes with a lot
+of functionality to fetch values from the command line comfortably, it has no
+means in checking/ verifying input. Some of the most common tests are covered
+here. All tests are designed to exit a script on failure.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">argparse</span>
<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">argcheck</span>
@@ -160,7 +160,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments</a><ul>
+<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard Tests For Command Line Arguments</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#file-tests">File Tests</a></li>
</ul>
@@ -169,10 +169,10 @@ 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">core</span></tt> - ProMod3 Core Functionality</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="helper.html"
- title="next chapter"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a></p>
+ title="next chapter"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared Functionality For the Everything</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../_sources/core/argcheck.txt"
@@ -205,19 +205,19 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="helper.html" title="helper - Shared functionality for the everything"
+ <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="core - ProMod3 Core Functionality"
>previous</a> |</li>
<li><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li><a href="index.html" ><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 core functionality</a> »</li>
+ <li><a href="index.html" ><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 9bec665f..5690b18b 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>helper - Shared functionality for the everything — ProMod3 0 documentation</title>
+ <title>helper - Shared Functionality For the Everything — ProMod3 0 documentation</title>
<link rel="stylesheet" href="../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -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="next" title="rawmodel - Coordinate modeling" href="../rawmodel/index.html" />
- <link rel="prev" title="argcheck - Standard tests for command line arguments" href="argcheck.html" />
+ <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
+ <link rel="next" title="rawmodel - Coordinate Modeling" href="../rawmodel/index.html" />
+ <link rel="prev" title="argcheck - Standard Tests For Command Line Arguments" href="argcheck.html" />
</head>
<body>
<div class="related">
@@ -39,14 +39,14 @@
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="../rawmodel/index.html" title="rawmodel - Coordinate modeling"
+ <a href="../rawmodel/index.html" title="rawmodel - Coordinate Modeling"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="argcheck.html" title="argcheck - Standard tests for command line arguments"
+ <a href="argcheck.html" title="argcheck - Standard Tests For Command Line Arguments"
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">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
@@ -56,7 +56,7 @@
<div class="body">
<div class="section" id="helper-shared-functionality-for-the-everything">
-<h1><tt class="xref py py-mod docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything<a class="headerlink" href="#helper-shared-functionality-for-the-everything" title="Permalink to this headline">¶</a></h1>
+<h1><tt class="xref py py-mod docutils literal"><span class="pre">helper</span></tt> - Shared Functionality For the Everything<a class="headerlink" href="#helper-shared-functionality-for-the-everything" title="Permalink to this headline">¶</a></h1>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
<p>We collect functions here, which should be useful in many places but would make
@@ -103,7 +103,7 @@ traditionally reserved to successful commands.</li>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a><ul>
+<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared Functionality For the Everything</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#messages">Messages</a></li>
</ul>
@@ -112,10 +112,10 @@ traditionally reserved to successful commands.</li>
<h4>Previous topic</h4>
<p class="topless"><a href="argcheck.html"
- title="previous chapter"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments</a></p>
+ title="previous chapter"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard Tests For Command Line Arguments</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="../rawmodel/index.html"
- title="next chapter"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a></p>
+ title="next chapter"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate Modeling</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../_sources/core/helper.txt"
@@ -148,19 +148,19 @@ traditionally reserved to successful commands.</li>
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="../rawmodel/index.html" title="rawmodel - Coordinate modeling"
+ <a href="../rawmodel/index.html" title="rawmodel - Coordinate Modeling"
>next</a> |</li>
<li class="right" >
- <a href="argcheck.html" title="argcheck - Standard tests for command line arguments"
+ <a href="argcheck.html" title="argcheck - Standard Tests For Command Line Arguments"
>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">core</span></tt> - ProMod3 Core Functionality</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 a0238bad..b322dd3d 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>core - ProMod3 core functionality — ProMod3 0 documentation</title>
+ <title>core - ProMod3 Core Functionality — ProMod3 0 documentation</title>
<link rel="stylesheet" href="../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -25,7 +25,7 @@
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developes" href="../developers.html" />
- <link rel="next" title="argcheck - Standard tests for command line arguments" href="argcheck.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" />
</head>
<body>
@@ -39,7 +39,7 @@
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="argcheck.html" title="argcheck - Standard tests for command line arguments"
+ <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"
@@ -55,17 +55,17 @@
<div class="body">
<div class="section" id="module-promod3.core">
-<span id="core-promod3-core-functionality"></span><h1><a class="reference internal" href="#module-promod3.core" title="promod3.core: Basic functionality, supporting standard tasks in your code."><tt class="xref py py-mod docutils literal"><span class="pre">core</span></tt></a> - ProMod3 core functionality<a class="headerlink" href="#module-promod3.core" title="Permalink to this headline">¶</a></h1>
+<span id="core-promod3-core-functionality"></span><h1><a class="reference internal" href="#module-promod3.core" title="promod3.core: Basic functionality, supporting standard tasks in your code."><tt class="xref py py-mod docutils literal"><span class="pre">core</span></tt></a> - ProMod3 Core Functionality<a class="headerlink" href="#module-promod3.core" title="Permalink to this headline">¶</a></h1>
<p>This module gathers functions and classes which are not devoted to homology
modeling per se but cover standard programming issues.</p>
<div class="toctree-wrapper compound">
<ul>
-<li class="toctree-l1"><a class="reference internal" href="argcheck.html"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="argcheck.html"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard Tests For Command Line Arguments</a><ul>
<li class="toctree-l2"><a class="reference internal" href="argcheck.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="argcheck.html#file-tests">File Tests</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="helper.html"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="helper.html"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared Functionality For the Everything</a><ul>
<li class="toctree-l2"><a class="reference internal" href="helper.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="helper.html#messages">Messages</a></li>
</ul>
@@ -85,7 +85,7 @@ modeling per se but cover standard programming issues.</p>
title="previous chapter">Documentation For Developes</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>
+ title="next chapter"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard Tests For Command Line Arguments</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../_sources/core/index.txt"
@@ -118,7 +118,7 @@ modeling per se but cover standard programming issues.</p>
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="argcheck.html" title="argcheck - Standard tests for command line arguments"
+ <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"
@@ -128,8 +128,8 @@ modeling per se but cover standard programming issues.</p>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 f54f20e8..7c507c83 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="core - ProMod3 Core Functionality" href="core/index.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/index.html" title="core - ProMod3 Core Functionality"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="users.html" title="Documentation For Users"
@@ -57,12 +57,12 @@
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
-<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>
+<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>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="rawmodel/index.html"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="rawmodel/index.html"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate Modeling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
</ul>
</li>
@@ -82,6 +82,11 @@
<li class="toctree-l2"><a class="reference internal" href="contributing.html#third-party-contributions-license-issues">Third Party Contributions (License Issues)</a></li>
</ul>
</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>
+</ul>
+</li>
</ul>
</div>
</div>
@@ -97,7 +102,7 @@
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>
+ title="next chapter"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 Core Functionality</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/developers.txt"
@@ -130,7 +135,7 @@
<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/index.html" title="core - ProMod3 Core Functionality"
>next</a> |</li>
<li class="right" >
<a href="users.html" title="Documentation For Users"
@@ -139,8 +144,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 310c27eb..6f5b46d3 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -50,6 +50,7 @@
<div class="genindex-jumpbox">
<a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#M"><strong>M</strong></a>
@@ -67,6 +68,23 @@
</dl></td>
</tr></table>
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt>
+ command
+ </dt>
+
+ <dd><dl>
+
+ <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>
+
+ </dl></dd>
+ </dl></td>
+</tr></table>
+
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
@@ -140,12 +158,23 @@
<dt><a href="core/index.html#module-promod3.core">promod3.core (module)</a>
</dt>
+
+ <dt><a href="rawmodel/index.html#module-promod3.rawmodel">promod3.rawmodel (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>
+ promod3_unittest
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="cmake/index.html#command:promod3_unittest"><strong>command</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>
+ </dl></dd>
</dl></td>
</tr></table>
@@ -199,8 +228,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 e34abe04..b7e39fb3 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Welcome to ProMod3’s documentation! — ProMod3 0 documentation</title>
+ <title>Welcome To ProMod3’s Documentation! — ProMod3 0 documentation</title>
<link rel="stylesheet" href="_static/default.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -49,16 +49,17 @@
<div class="body">
<div class="section" id="welcome-to-promod3-s-documentation">
-<h1>Welcome to ProMod3’s documentation!<a class="headerlink" href="#welcome-to-promod3-s-documentation" title="Permalink to this headline">¶</a></h1>
+<h1>Welcome To ProMod3’s Documentation!<a class="headerlink" href="#welcome-to-promod3-s-documentation" title="Permalink to this headline">¶</a></h1>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<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/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="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>
<li class="toctree-l2"><a class="reference internal" href="contributing.html">Contributing</a></li>
+<li class="toctree-l2"><a class="reference internal" href="cmake/index.html">ProMod3‘s Share Of CMake</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
@@ -70,7 +71,7 @@
</div>
</div>
<div class="section" id="indices-and-tables">
-<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+<h1>Indices And Tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li>
<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li>
@@ -86,8 +87,8 @@
<div class="sphinxsidebarwrapper">
<h3><a href="#">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#">Welcome to ProMod3’s documentation!</a></li>
-<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
+<li><a class="reference internal" href="#">Welcome To ProMod3’s Documentation!</a></li>
+<li><a class="reference internal" href="#indices-and-tables">Indices And Tables</a></li>
</ul>
<h4>Next topic</h4>
@@ -131,8 +132,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 afa275d0..7fdd6319 100644
--- a/doc/html/objects.inv
+++ b/doc/html/objects.inv
@@ -2,5 +2,5 @@
# Project: ProMod3
# Version: 0.1
# The remainder of this file is compressed using zlib.
-xڝ��N�0��}
-Kp����HA� �O�ڋc��Ѯ��oO��(����l���~��+� ���Yq˪-��U7
x:{�������W���V���j��d;dëа�яk ��#î�K�Y�V�yPݲjɠ8��`��� ��� Բ�Ο��z��x��ޢ�!��dq~�� �S4V�ũ��V %� �l��5��G��������e�0N
|9��1�֕>-z�k]�����P�GZAt�����
\ No newline at end of file
+xڝ��N�0��y
+Kp�!�HE�!*�\{q��'��jx{b٩���)����5N(+`$E��4�2|Ԧ h�FߐΉ���TI��Y-�l
�<��Vl����$T�ìh��o�*DH�a'h˘4��n���UIQ�<LК�|O��4�A��xv���27�?dS=e^� ��>+
���l�{��czo2�Ź��ѧ��8�s7#-:��V4=�<��y����Q�Mq~�2c(+�Fz9C��~�u�O�!��n��*`���WP��k��O�x&�
\ No newline at end of file
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index f1d5cd03..7823911e 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -112,8 +112,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 f90af7dc..7441ae35 100644
--- a/doc/html/rawmodel/index.html
+++ b/doc/html/rawmodel/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>rawmodel - Coordinate modeling — ProMod3 0 documentation</title>
+ <title>rawmodel - Coordinate Modeling — ProMod3 0 documentation</title>
<link rel="stylesheet" href="../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -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="Building ProMod3" href="../buildsystem.html" />
- <link rel="prev" title="helper - Shared functionality for the everything" href="../core/helper.html" />
+ <link rel="prev" title="helper - Shared Functionality For the Everything" href="../core/helper.html" />
</head>
<body>
<div class="related">
@@ -42,7 +42,7 @@
<a href="../buildsystem.html" title="Building ProMod3"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="../core/helper.html" title="helper - Shared functionality for the everything"
+ <a href="../core/helper.html" title="helper - Shared Functionality For the Everything"
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>
@@ -55,7 +55,7 @@
<div class="body">
<div class="section" id="module-promod3.rawmodel">
-<span id="rawmodel-coordinate-modeling"></span><h1><a class="reference internal" href="#module-promod3.rawmodel" title="promod3.rawmodel: Raw Coordinate Model"><tt class="xref py py-mod docutils literal"><span class="pre">rawmodel</span></tt></a> - Coordinate modeling<a class="headerlink" href="#module-promod3.rawmodel" title="Permalink to this headline">¶</a></h1>
+<span id="rawmodel-coordinate-modeling"></span><h1><a class="reference internal" href="#module-promod3.rawmodel" title="promod3.rawmodel: Raw Coordinate Model"><tt class="xref py py-mod docutils literal"><span class="pre">rawmodel</span></tt></a> - Coordinate Modeling<a class="headerlink" href="#module-promod3.rawmodel" title="Permalink to this headline">¶</a></h1>
<p>Functionality to build raw (pseudo) models based on a sequence alignment.
Here is an example of how to build a model from an alignment and a structure.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
@@ -159,7 +159,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a><ul>
+<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate Modeling</a><ul>
<li><a class="reference internal" href="#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
</ul>
</li>
@@ -167,7 +167,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
<h4>Previous topic</h4>
<p class="topless"><a href="../core/helper.html"
- title="previous chapter"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a></p>
+ title="previous chapter"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared Functionality For the Everything</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="../buildsystem.html"
title="next chapter">Building ProMod3</a></p>
@@ -206,15 +206,15 @@ missing or incomplete backbone coordinates in the template structure.</p>
<a href="../buildsystem.html" title="Building ProMod3"
>next</a> |</li>
<li class="right" >
- <a href="../core/helper.html" title="helper - Shared functionality for the everything"
+ <a href="../core/helper.html" title="helper - Shared Functionality For the Everything"
>previous</a> |</li>
<li><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li><a href="../developers.html" >Documentation For Developes</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 22dc512c..2cf86f8a 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -98,8 +98,8 @@
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
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 eb581bef..e2cee77e 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:42,terms:{aln:8,all:[7,1,4,8],code:[7,1,4,5],forget:[7,4],chain:[7,8],messi:7,skip:7,forbidden:7,sidechains_unit_test:7,ost:[0,1,2,3,4,5,6,7,8,9],disable_document:[7,4],prefix:[7,1],concept:7,legal:7,abil:7,follow:[7,8],middl:7,readabl:7,send:5,init:7,program:6,under:7,introduc:7,sourc:[7,1,4,5],everi:[7,8],string:1,fals:[7,1,8],internet:7,worst:7,failur:[7,1],veri:[7,1],affect:7,solver:7,runnabl:7,tri:8,magic:7,level:[7,4],did:7,list:[7,1,4,8],assertequ:7,item:[7,8],fileextens:1,align:8,dir:7,malici:7,promod_gcc_45:7,your_modul:7,direct:7,past:7,second:8,design:1,pass:7,download:4,acid:8,even:[7,4],index:[7,3],what:[7,1,4],hide:7,sub:7,resembl:7,exot:7,"while":[7,1],find:7,current:7,delet:8,version:[7,4],"new":[7,8],boost:[0,1,2,3,4,5,6,7,8,9],meld:0,subtre:7,submodule1:7,honour:8,gener:7,never:7,here:[7,1,4,5,8],sphinx:[0,1,2,3,4,5,6,7,8,9],save:7,lib_stage_path:7,let:7,set_directory_properti:7,path:[7,1,4],along:7,modifi:[7,8,0],implicit:4,valu:[4,1,5],wait:7,headlin:7,search:[7,3,4],produc:4,executable_output_path:7,setup_boost:7,promod3_version_minor:7,gly:8,doctest:[7,4],action:7,implement:7,chanc:7,spawn:7,via:7,extra:7,activ:7,modul:0,submodul:7,put:[7,1,4],unix:7,api:[7,9],instal:[7,4],smallish:[7,4],unit:4,highli:4,yourself:[7,4],fed:7,from:[1,0,4,5,8,7],describ:1,would:[7,4,5],regist:7,two:7,next:7,everybodi:7,few:[7,4,8],live:7,call:[7,4],recommend:4,msg:5,loadalign:8,checkout:7,tell:[7,1],tightli:7,more:[7,4,8],chapter:7,peopl:7,relat:7,notic:7,warn:7,flag:[7,1],include_directori:7,particular:7,known:1,actual:7,hold:8,cach:[7,4],must:7,ost_double_precis:4,py_run:7,hous:7,setup:[7,0],work:[7,4],histori:7,paragraph:7,can:[7,1,4,8],purpos:7,root:7,fetch:[7,1],def:7,control:7,give:7,process:7,add_argu:1,indic:1,topic:7,abort:7,want:[7,4],phrase:7,unfortun:7,hydrogen:8,alwai:7,gcc:7,cours:7,end:[7,1,4,5],sit:7,rather:[7,5],comfort:1,sever:[7,4],verifi:1,config:7,updat:7,python_vers:7,product:7,entityhandl:8,rebas:7,mess:7,clone:7,after:[7,4],usabl:7,befor:7,wrong:4,attent:7,mai:[7,4,8],multipl:7,data:7,grow:8,man:[7,4],"short":7,essenti:7,practic:7,ost_doc_url:7,python_binari:7,correspond:7,stash:7,exclud:7,alias:7,"switch":7,maintain:7,environ:7,allow:7,exclus:7,origin:7,promod3_version_major:7,eigen:[7,4],over:[7,4,8],insight:7,becaus:[7,4],through:7,same:[7,4],rawmodel:[7,3,9,0],gitignor:7,still:7,pointer:4,disable_disable_doctest:7,entiti:7,perfect:7,output_vari:7,funni:4,fix:[7,1],selenium:8,structuralgaplist:8,relev:4,carri:[7,1],drawback:7,onc:7,bin:7,python_doc_url:7,therefor:7,linkcheck:[7,4],them:7,good:7,"return":[1,5,8],thei:[7,4],python:[0,1,2,3,4,5,6,7,8,9],dai:1,initi:0,"break":7,framework:7,conquer:7,instead:[7,1,4],front:[7,1,4],now:[7,8],minimalist:8,cmake_cxx_flags_releas:7,libexec_stage_path:7,name:[7,1],anyth:[7,4],drop:7,separ:7,easili:7,achiev:7,each:7,debug:7,found:7,went:7,complet:[7,8],side:[7,8],mean:[7,1,4],compil:7,everyth:7,monolith:7,cmake_module_path:7,test_sidechain:7,idea:[7,0],realli:[7,1,4],runtest:7,member:[7,8],"static":7,our:7,extract:7,special:[7,4],out:[7,4],variabl:[7,4],shown:7,goe:[7,4],promod3_unittest:7,crucial:7,content:[7,3,9],reader:7,print:4,got:4,exec_program:7,merg:7,dive:7,integr:7,runtimeerror:8,differ:[7,4],free:7,standard:[7,4],test_someth:7,reason:7,base:[1,8],latest:4,ask:7,org:7,basi:7,could:[7,8],insert:8,keep:7,thing:[7,4],place:[7,5],think:7,first:[7,0],oper:7,softwar:7,major:7,suffix:1,obviou:7,prevent:7,feel:7,sidechains_pymod:7,number:8,sometim:7,restrict:7,date:7,alreadi:7,done:7,least:[7,4],blank:7,stabl:7,miss:[1,8],straight:7,exit_statu:[1,5],given:1,script:[7,1,4,5],top:[7,4],perfectli:7,mkdir:7,system:[7,4,0],messag:[7,1],stack:7,attach:8,stori:7,master:7,too:7,which:[7,4,5,8,6],termin:1,scheme:7,"final":[7,8],store:[7,8],shell:[4,1,5],option:[7,1,4],tool:1,copi:[7,8],restrict_chain:8,openstructur:[0,1,2,3,4,5,6,7,8,9],part:7,pars:1,boost_include_dir:7,mostli:7,rst:7,off:[7,8],exactli:4,than:7,kind:7,grep:4,target:[7,4],whenev:7,provid:[7,4],seamlessli:7,tree:7,unrecognis:1,project:7,nevertheless:7,reus:8,str:[1,5],were:7,posit:1,toward:7,builder:4,pre:7,respons:7,mind:7,argument:4,packag:7,manner:7,have:[7,4,8],"__main__":7,need:[7,1,4],dedic:[7,4],turn:[7,1],tidi:7,cmake_current_source_dir:7,optimis:7,imagin:7,probabl:[7,4],built:7,advic:7,inform:8,diverg:7,self:7,also:[7,1,4,8],exampl:[7,4,8],take:[7,8],advis:7,thoroughli:7,noth:7,singl:[7,8],"_opt":7,sure:7,distribut:7,track:1,forg:7,compress:1,strict:7,wno:7,most:[7,1,8],eigen3_found:7,hotfix:7,"class":[7,8,6],charg:7,renam:0,bug:7,url:7,doc:[7,4],later:7,cover:[7,1,6],doe:[7,1,8],ext:1,declar:7,clean:[7,4],usual:[7,4],review:7,came:7,cmakelist:[7,4],show:7,test_suite_your_module_run:7,dbg:7,attachview:8,bring:7,permiss:7,cmake_support:7,fine:7,anywai:7,help:[7,4],involv:7,onli:[7,1,8],locat:4,explain:7,configur:[7,4],solut:7,figur:7,should:[7,1,5],suppos:7,templat:8,folder:7,move:7,hit:7,unus:7,variou:4,get:[7,4],watch:7,soon:7,cannot:7,loadpdb:8,report:[7,8],toolbox:7,requir:[7,4],setup_compiler_flag:7,add_changelog_to_doc:7,enabl:1,"2b1":4,"default":[7,4],common:[7,1],contain:[7,1,4,8],python_root:4,where:7,remov:4,view:7,set:[7,1,4,8],project_nam:7,seq:[7,8],frame:7,ost_include_dir:7,see:7,temporarili:7,mandatori:7,result:[7,4,8],smng:0,arg:7,testcas:7,close:7,sport:7,subject:7,awar:7,statu:7,detect:1,msgerrorandexit:5,someth:[7,5],version_great:7,enumer:7,label:7,state:[7,4],header_stage_path:7,subdir:7,simplest:7,"import":[7,1,4,5,8],awai:7,paramet:[1,5,8],approach:7,attribut:7,accord:7,extend:7,sole:7,cmake_cxx_compiler_vers:7,test_your_modul:7,recent:7,solv:7,come:[7,1],addit:[7,1],fail:[7,5],extens:1,alon:5,disable_doctest:[7,4],promod3_version_patch:7,tutori:7,grain:7,fno:7,mani:5,whole:[7,8],pdb:[1,8],comment:7,sidechains_rst:7,author:7,point:[7,4],cxx:7,overview:7,unittest:7,argumentpars:1,pop:7,walk:7,residu:8,header:[7,4],featur:7,littl:7,test_submodule1:7,assum:7,amino:8,quit:7,template_structur:8,creat:[7,4],coupl:7,rebuild:[7,4],three:7,been:7,sinc:[7,1,4],compon:7,trigger:7,besid:4,treat:[7,8],basic:[7,4,8],ost_root:[7,4],popul:[7,4],seq_alg:7,tini:7,quickli:7,life:7,fasta:8,convert:8,ani:7,coordin:[3,9],togeth:7,els:7,fileexist:1,educ:7,those:[7,4],"case":7,cmake_c_compiler_vers:7,uncertain:7,look:[7,1],raw:9,testfileexistsfals:7,disable_disable_linkcheck:7,servic:7,properti:7,commerci:7,formatt:7,invok:[7,4],boost_root:4,abov:7,error:[1,5],dost_root:[7,4],loop:[7,8],stage_dir:7,methionin:8,real:7,argpars:1,readi:4,sidechain:7,henc:7,non:7,itself:7,clutter:7,conf:[7,4],protein:8,vanish:7,calpha_onli:8,"__init__":7,reviv:7,parent:8,develop:7,fedora:7,etc:7,suggest:7,belong:7,savepdb:8,files_to_be_remov:7,promod3_version_str:7,binari:7,complex:7,admir:7,document:[4,0],start:4,conflict:7,higher:4,http:7,cmakecach:4,optim:[7,4],bienchen:7,make_directori:7,hand:4,driven:7,moment:7,rais:8,disable_linkcheck:[7,4],user:3,kic:7,tradition:[1,5],expand:7,codetest:7,task:7,conop:7,pymod:7,find_packag:7,macro:7,markup:7,well:[7,4,8],without:[7,1,8],command:7,branchnam:7,thi:[7,1,4,8,6],endif:7,gzip:1,model:[3,9,6],academ:7,spend:7,piec:7,left:5,interpret:5,add_doc_sourc:7,entri:7,just:[7,4],elabor:7,obtain:8,rest:[0,1,2,3,4,5,6,7,8,9],touch:7,web:[7,4],lapack:[7,4],restructuredtext:[0,1,2,3,4,5,6,7,8,9],makefil:[7,4],except:7,seem:7,add:7,eigen3:7,input:1,subsequ:8,match:[7,8],opt:1,around:7,format:7,handl:8,specimen:1,term:7,source2:7,source1:7,know:4,background:4,mol:7,bit:[7,4],you:[7,1,4],mod:7,eigen3_include_dir:[7,4],loss:7,like:[7,4,8],success:[1,5],incred:8,manual:[7,4],html:[7,4,0],test_:7,test_awesome_featur:7,collect:5,"boolean":1,either:[7,8],output:[7,1],hook:7,page:[7,3,4],www:7,right:[7,4],often:[7,1],acknowledg:7,some:[7,1,4],begin:7,resolv:7,intern:7,proper:7,librari:7,qmean:[7,4],thu:1,txt:[7,4],lead:1,avoid:7,definit:7,subclass:7,exit:[1,5],select:8,recognis:7,devot:6,condit:7,core:[7,1,5],plu:7,cmake_source_dir:7,backbon:8,step:7,promot:7,repositori:[7,0],"__name__":7,add_subdirectori:7,intervent:7,mmcif:1,stage:4,trustworthi:7,src:7,about:[7,8],rare:7,materi:7,manag:7,coars:7,commit:7,mol_alg:7,disabl:7,qmean_root:[7,4],within:[7,4],automat:[7,1],due:8,empti:[7,5],cmake_cxx_flag:7,strip:8,announc:7,your:4,per:[7,6],git:[4,0],log:[7,5],wai:[7,4],pictur:7,qmean_include_dir:7,support:[7,1],renumb:8,custom:7,avail:[7,4],lost:7,much:[7,8],interfac:7,includ:[7,1,0],lot:[7,1],suit:7,forward:7,parse_arg:1,"function":[7,1],headach:7,unexpect:4,enough:7,tupl:1,buildrawmodel:8,somethingtest:7,back:7,link:[7,4],atom:8,don:[7,4],line:7,inlin:7,"true":[7,1,8],setup_stag:7,pull:[7,4],tripl:1,immedi:7,consist:7,possibl:[7,8],whether:1,type:[1,8],displai:1,below:7,otherwis:7,problem:7,similar:4,eigenvector:7,testutil:7,reserv:[1,5],gather:[7,6],evalu:7,"int":[1,5],certain:4,utilis:[7,1],fellow:7,incomplet:8,exist:[7,1],file:[7,4],dqmean_root:[7,4],deuterium:8,check:[7,1,4],fill:7,echo:7,again:[7,4],calpha:8,modif:8,when:[7,8],detail:[7,8],other:[7,4,8],bool:1,test:4,cmake_compiler_is_gnucxx:7,phosphoserin:8,nice:7,additional_make_clean_fil:7,extern:7,determin:1,rawmodelingresult:8,sequenc:8,cmake_build_typ:7,cmake_minimum_requir:7,briefli:7,eigenvalu:7,consid:7,gap:8,homolog:6,doptim:7,fatal_error:7,stai:7,peptid:8,algorithm:[7,8],project_binary_dir:7,directori:4,descript:7,pseudo:8,rule:7,ignor:8,time:[7,8],push:7},objtypes:{"0":"py:module","1":"py:function","2":"py:attribute","3":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","attribute","Python attribute"],"3":["py","class","Python class"]},filenames:["changelog","core/argcheck","users","index","buildsystem","core/helper","core/index","contributing","rawmodel/index","developers"],titles:["Changelog","<tt class=\"docutils literal\"><span class=\"pre\">argcheck</span></tt> - Standard tests for command line arguments","Documentation For Users","Welcome to ProMod3’s documentation!","Building ProMod3","<tt class=\"docutils literal\"><span class=\"pre\">helper</span></tt> - Shared functionality for the everything","<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","Documentation For Developes"],objects:{"promod3.rawmodel":{BuildRawModel:[8,1,1,""],RawModelingResult:[8,3,1,""]},"promod3.core.argcheck":{FileExtension:[1,1,1,""],FileExists:[1,1,1,""]},promod3:{core:[6,0,0,"-"],rawmodel:[8,0,0,"-"]},"promod3.core.helper":{MsgErrorAndExit:[5,1,1,""]},"promod3.rawmodel.RawModelingResult":{model:[8,2,1,""],gaps:[8,2,1,""]}},titleterms:{own:7,helper:5,modul:7,share:5,argument:1,indic:3,raw:8,api:8,file:1,tabl:3,run:4,your:7,unit:7,git:7,develop:9,welcom:3,how:7,parti:7,make:4,messag:5,write:7,start:7,build:4,branch:7,test:[7,1],document:[7,3,9,2],promod3:[4,3,6],"function":[5,6],core:6,argcheck:1,contribut:7,chang:0,standard:1,coordin:8,user:2,releas:0,cmake:[7,4],line:1,everyth:5,stage:7,third:7,changelog:0,directori:7,introduct:[1,5],structur:7,issu:7,command:1,rawmodel:8,model:8,licens:7,depend:4}})
\ No newline at end of file
+Search.setIndex({envversion:42,terms:{aln:8,all:[7,0,4,10,8],code:[7,0,4,1,10],forget:[7,4],chain:[7,8],messi:7,skip:7,forbidden:7,sidechains_unit_test:7,ost:[0,1,2,3,4,5,6,7,8,9,10],disable_document:[7,4],prefix:[7,0],concept:7,legal:7,abil:7,follow:[7,8],content:[7,3,9],middl:7,test_foo:10,readabl:7,send:1,init:7,program:[10,6],under:7,introduc:7,sourc:[7,0,4,1,10],everi:[7,8],string:0,fals:[7,0,8],internet:7,worst:7,failur:[7,0],veri:[7,0],affect:7,solver:7,runnabl:7,tri:8,magic:7,level:[7,4],did:7,list:[7,0,4,8],assertequ:7,item:[7,8],fileextens:0,align:8,dir:7,malici:7,promod_gcc_45:7,your_modul:7,direct:7,past:7,second:8,design:0,pass:7,download:4,acid:8,even:[7,4],index:[7,3],what:[7,0,4],hide:7,sub:7,resembl:7,section:10,exot:7,"while":[7,0],find:[7,10],current:7,delet:8,version:[7,4],"new":[7,8],boost:[0,1,2,3,4,5,6,7,8,9,10],meld:5,subtre:[7,10],submodule1:7,honour:8,gener:7,never:7,here:[0,4,1,8,7,10],sphinx:[0,1,2,3,4,5,6,7,8,9,10],save:7,lib_stage_path:7,let:7,set_directory_properti:7,path:[7,0,4,10],along:7,modifi:[7,8,5],implicit:4,valu:[4,0,1],wait:7,headlin:7,search:[7,3,4],produc:[4,10],executable_output_path:7,setup_boost:7,host:10,promod3_version_minor:7,gly:8,doctest:[7,4],action:7,implement:7,chanc:7,spawn:7,via:7,extra:7,activ:7,modul:5,submodul:7,put:[7,0,4,10],unix:7,api:[7,9],instal:[7,4],smallish:[7,4],unit:4,highli:4,fed:[7,10],from:[0,5,4,1,8,7,10],describ:[0,10],would:[7,4,1],regist:[7,10],two:7,next:7,everybodi:7,few:[7,4,8],live:7,call:[7,4,10],recommend:4,msg:1,loadalign:8,checkout:7,tell:[7,0],tightli:7,more:[7,4,10,8],sort:10,chapter:7,peopl:7,relat:7,notic:[7,10],warn:7,flag:[7,0,10],include_directori:7,particular:7,known:0,actual:7,hold:8,cach:[7,4],must:7,ost_double_precis:4,word:10,py_run:[7,10],hous:7,setup:[7,5],work:[7,4,10],histori:7,paragraph:7,can:[7,0,4,8],purpos:7,root:7,fetch:[7,0],def:7,test_suite_:10,control:7,give:[7,10],process:7,add_argu:0,indic:0,topic:7,abort:7,want:[7,4],phrase:7,made:10,hydrogen:8,contribut:10,alwai:7,gcc:7,cours:7,end:[7,0,4,1],sit:7,rather:[7,1],comfort:0,"_xml":10,"__init__":7,verifi:0,config:7,updat:7,python_vers:7,product:7,entityhandl:8,rebas:7,mess:7,clone:7,after:[7,4],usabl:7,befor:7,wrong:4,attent:7,date:7,multipl:7,data:[7,10],grow:8,man:[7,4],"short":7,essenti:7,practic:[7,10],ost_doc_url:7,python_binari:7,correspond:7,stash:7,exclud:7,alias:7,"switch":7,maintain:7,environ:7,allow:7,exclus:7,origin:7,promod3_version_major:7,eigen:[7,4],over:[7,4,8],insight:7,becaus:[7,4],through:7,same:[7,4],rawmodel:[7,3,9,5],gitignor:7,still:7,pointer:4,disable_disable_doctest:7,paramet:[0,1,10,8],perfect:7,output_vari:7,funni:4,fix:[7,0],selenium:8,structuralgaplist:8,relev:[4,10],carri:[7,0],drawback:7,onc:7,bin:7,python_doc_url:7,therefor:7,linkcheck:[7,4],them:[7,10],good:7,"return":[0,1,8],thei:[7,4],python:[0,1,2,3,4,5,6,7,8,9,10],dai:0,initi:5,"break":7,framework:7,conquer:7,instead:[7,0,4,10],front:[7,0,4],now:[7,8],pre_commit:7,minimalist:8,cmake_cxx_flags_releas:7,libexec_stage_path:7,somewher:10,name:[7,0,10],anyth:[7,4],drop:7,separ:7,easili:[7,10],achiev:7,each:7,debug:7,found:[7,10],went:7,complet:[7,8],side:[7,8],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:[7,8],"static":7,our:[7,10],extract:7,special:[7,4,10],out:[7,4,10],variabl:[7,4],shown:7,goe:[7,4],promod3_unittest:[7,10],crucial:7,categori:10,rel:10,reader:7,print:4,got:4,exec_program:7,merg:7,dive:7,integr:[7,10],insid:10,runtimeerror:8,differ:[7,4,10],free:7,standard:[7,4],test_someth:7,reason:7,base:[0,8],latest:4,ask:7,org:7,basi:[7,10],could:[7,10,8],insert:8,keep:7,thing:[7,4],place:[7,1],think:7,first:[7,5],oper:7,softwar:7,major:7,suffix:0,obviou:7,prevent:7,feel:7,sidechains_pymod:7,number:8,yourself:[7,4],restrict:7,mai:[7,4,10,8],alreadi:7,done:7,least:[7,4,10],blank:7,stabl:7,miss:[0,8],exit_statu:[0,1],given:[0,10],script:[7,0,4,1],top:[7,4],perfectli:7,mkdir:7,system:[7,4,5],messag:[7,0],stack:7,attach:8,stori:7,master:7,too:7,"_run":10,termin:0,scheme:7,"final":[7,8],store:[7,8],shell:[4,0,1],option:[7,0,4],tool:[0,10],copi:[7,10,8],restrict_chain:8,specifi:10,openstructur:[0,1,2,3,4,5,6,7,8,9,10],part:7,pars:0,boost_include_dir:7,mostli:7,rst:7,off:[7,8],exactli:4,than:7,kind:7,grep:4,target:[7,4,10],whenev:7,provid:[7,4],seamlessli:7,tree:[7,10],unrecognis:0,project:[7,10],matter:10,reus:8,str:[0,1],were:7,posit:0,toward:7,builder:4,pre:7,linker:10,mind:7,argument:4,packag:[7,10],manner:7,have:[7,4,10,8],"__main__":7,need:[7,0,4,10],dedic:[7,4,10],turn:[7,0],tidi:7,cmake_current_source_dir:7,optimis:7,imagin:7,probabl:[7,4,10],built:7,advic:7,inform:8,diverg:7,self:7,mix:10,without:[7,0,10,8],take:[7,8],which:[7,4,1,8,6],thoroughli:7,data1:10,noth:7,singl:[7,10,8],data2:10,"_opt":7,sure:7,distribut:7,track:0,forg:7,compress:0,strict:7,wno:7,most:[7,0,8],eigen3_found:7,hotfix:7,"class":[7,8,6],charg:7,renam:5,bug:7,url:7,doc:[7,4],later:7,cover:[7,0,6],doe:[7,0,10,8],ext:0,declar:[7,10],clean:[7,4],brew:10,usual:[7,4,10],review:7,came:7,cmakelist:[7,4,10],show:7,test_suite_your_module_run:7,dbg:7,attachview:8,bring:7,permiss:7,cmake_support:[7,10],fine:7,anywai:7,help:[7,4],involv:7,onli:[7,0,10,8],locat:[4,10],nevertheless:7,explain:7,configur:[7,4],solut:7,state:[7,4],should:[7,0,1,10],suppos:7,templat:8,folder:7,move:7,hit:7,unus:7,variou:[4,10],get:[7,4],watch:7,autom:10,cannot:7,loadpdb:8,report:[7,8],toolbox:7,requir:[7,4],setup_compiler_flag:7,add_changelog_to_doc:7,enabl:0,"2b1":4,"default":[7,4],common:[7,0],contain:[7,0,4,10,8],python_root:4,where:7,remov:4,view:7,set:[7,0,4,10,8],project_nam:7,seq:[7,8],frame:7,ost_include_dir:7,see:7,temporarili:7,mandatori:7,result:[7,4,8],smng:5,arg:7,testcas:7,close:7,sport:7,servic:7,best:10,subject:7,awar:7,statu:7,detect:0,msgerrorandexit:1,vari:10,someth:[7,1],version_great:7,enumer:7,label:7,figur:7,header_stage_path:7,subdir:7,simplest:7,"import":[7,0,4,1,8],awai:7,entiti:7,approach:7,attribut:7,accord:7,extend:[7,10],sole:7,cmake_cxx_compiler_vers:7,test_your_modul:7,solv:7,come:[7,0],popul:[7,4],fail:[7,1],last:10,extens:0,alon:1,disable_doctest:[7,4],promod3_version_patch:7,tutori:7,grain:7,fno:7,mani:1,whole:[7,8],pdb:[0,8],comment:7,sidechains_rst:7,author:7,point:[7,4],cxx:7,overview:7,unittest:7,argumentpars:0,pop:7,walk:7,residu:8,header:[7,4],featur:7,littl:[7,10],codetest:[7,10],test_submodule1:7,assum:7,amino:8,sever:[7,4],quit:7,template_structur:8,creat:[7,4,10],coupl:7,addition:10,rebuild:[7,4],three:[7,10],been:7,sinc:[7,0,4,10],compon:7,trigger:7,besid:[4,10],treat:[7,8],basic:[7,4,8],ost_root:[7,4],addit:[7,0,10],seq_alg:7,tini:7,quickli:7,life:7,fasta:8,convert:8,ani:7,coordin:[3,9],togeth:7,els:7,fileexist:0,educ:7,those:[7,4,10],"case":7,cmake_c_compiler_vers:7,uncertain:7,look:[7,0],raw:9,testfileexistsfals:7,disable_disable_linkcheck:7,straight:7,properti:7,commerci:7,formatt:7,defin:10,invok:[7,4],boost_root:4,abov:7,error:[0,1],wild:10,dost_root:[7,4],loop:[7,8],stage_dir:7,methionin:8,real:7,argpars:0,helper:10,almost:10,sidechain:7,henc:7,non:7,itself:[7,10],clutter:7,conf:[7,4],protein:8,vanish:7,calpha_onli:8,feed:10,reviv:7,parent:8,develop:7,fedora:7,etc:7,suggest:7,belong:7,savepdb:8,files_to_be_remov:7,promod3_version_str:7,binari:7,complex:7,flag2:10,flag1:10,advis:7,admir:7,document:[4,10,5],start:4,conflict:7,higher:4,http:7,cmakecach:4,optim:[7,4],bienchen:7,make_directori:7,effect:10,hand:4,driven:7,moment:7,rais:8,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:[7,10],markup:7,well:[7,4,8],exampl:[7,4,8],command:7,branchnam:7,thi:[0,4,8,7,6,10],endif:7,gzip:0,model:[3,9,6],academ:7,spend:7,piec:7,left:1,interpret:1,add_doc_sourc:7,entri:7,just:[7,4],elabor:7,obtain:8,rest:[0,1,2,3,4,5,6,7,8,9,10],touch:7,languag:10,web:[7,4],also:[7,0,4,10,8],lapack:[7,4],restructuredtext:[0,1,2,3,4,5,6,7,8,9,10],makefil:[7,4],except:7,seem:7,add:[7,10],eigen3:7,input:0,subsequ:8,match:[7,8],opt:0,around:7,format:7,handl:8,specimen:0,term:7,source2:[7,10],source1:[7,10],know:4,background:4,mol:7,bit:[7,4],you:[7,0,4,10],dare:10,mod:7,eigen3_include_dir:[7,4],loss:7,like:[7,4,10,8],success:[0,1],incred:8,manual:[7,4],html:[7,4,5],test_:7,test_awesome_featur:7,collect:1,"boolean":0,either:[7,8],output:[7,0],hook:7,page:[7,3,4],www:7,right:[7,4],often:[7,0],acknowledg:7,some:[7,0,4],begin:7,resolv:7,intern:7,proper:7,home:10,librari:[7,10],qmean:[7,4],thu:0,txt:[7,4,10],lead:0,avoid:7,definit:7,subclass:7,exit:[0,1],select:8,recognis:7,devot:6,condit:7,manag:[7,10],core:[7,0,1],plu:7,cmake_source_dir:7,backbon:8,step:7,promot:7,repositori:[7,10,5],"__name__":7,add_subdirectori:7,intervent:7,mmcif:0,stage:4,trustworthi:7,src:7,about:[7,10,8],rare:7,materi:7,unfortun:7,coars:7,commit:7,mol_alg:7,disabl:7,qmean_root:[7,4],own:10,within:[7,4],automat:[7,0],due:8,empti:[7,1],cmake_cxx_flag:7,strip:8,announc:7,soon:7,your:[4,10],per:[7,10,6],git:[4,10,5],log:[7,1],wai:[7,4,10],pictur:7,qmean_include_dir:7,support:[7,0],renumb:8,custom:7,avail:[7,4],lost:7,much:[7,8],interfac:7,includ:[7,0,5],lot:[7,0],suit:7,forward:7,parse_arg:0,headach:7,unexpect:4,enough:7,tupl:0,buildrawmodel:8,somethingtest:7,back:7,link:[7,4,10],atom:8,don:[7,4],line:7,inlin:7,"true":[7,0,8],setup_stag:7,pull:[7,4],tripl:0,immedi:7,wise:10,consist:7,possibl:[7,8],whether:0,type:[0,8],displai:0,below:7,otherwis:7,problem:7,similar:4,eigenvector:7,testutil:7,reserv:[0,1],gather:[7,10,6],evalu:7,"int":[0,1],certain:[4,10],utilis:[7,0],fellow:7,incomplet:8,exist:[7,0],file:[7,4,10],dqmean_root:[7,4],deuterium:8,check:[7,0,4],fill:7,echo:7,again:[7,4],readi:4,calpha:8,modif:8,when:[7,8],detail:[7,8],other:[7,4,8],bool:0,test:4,cmake_compiler_is_gnucxx:7,phosphoserin:8,nice:7,sometim:7,additional_make_clean_fil:7,extern:[7,10],determin:0,rawmodelingresult:8,sequenc:8,cmake_build_typ:7,cmake_minimum_requir:7,briefli:7,eigenvalu:7,consid:[7,10],gap:8,homolog:6,doptim:7,fatal_error:7,stai:7,library2:10,library1:10,peptid:8,algorithm:[7,8],project_binary_dir:7,directori:[4,10],descript:7,pseudo:8,rule:7,ignor:8,time:[7,8],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","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\">rawmodel</span></tt> - Coordinate Modeling","Documentation For Developes","ProMod3‘s Share Of CMake"],objects:{"":{"command:promod3_unittest":[10,0,1,""]},"promod3.rawmodel":{BuildRawModel:[8,2,1,""],RawModelingResult:[8,4,1,""]},"promod3.core.argcheck":{FileExtension:[0,2,1,""],FileExists:[0,2,1,""]},"promod3.rawmodel.RawModelingResult":{model:[8,3,1,""],gaps:[8,3,1,""]},promod3:{core:[6,1,0,"-"],rawmodel:[8,1,0,"-"]},"promod3.core.helper":{MsgErrorAndExit:[1,2,1,""]}},titleterms:{own:7,helper:1,modul:[7,10],share:[1,10],argument:0,indic:3,raw:8,api:8,file:0,tabl:3,run:4,your:7,unit:[7,10],git:7,develop:9,welcom:3,how:7,parti:7,make:4,messag:1,write:7,start:7,build:4,branch:7,test:[7,0,10],stage:7,promod3:[4,3,10,6],"function":[1,10,6],core:6,argcheck:0,contribut:7,chang:5,standard:0,coordin:8,mainten:10,user:2,releas:5,cmake:[7,4,10],line:0,everyth:1,introduct:[0,1,10],document:[7,3,9,2],third:7,changelog:5,directori:7,structur:7,issu:7,command:0,rawmodel:8,model:8,licens:7,depend:4}})
\ No newline at end of file
diff --git a/doc/html/users.html b/doc/html/users.html
index 34a27449..26b34d4a 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -25,7 +25,7 @@
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="index.html" />
<link rel="next" title="Documentation For Developes" href="developers.html" />
- <link rel="prev" title="Welcome to ProMod3’s documentation!" href="index.html" />
+ <link rel="prev" title="Welcome To ProMod3’s Documentation!" href="index.html" />
</head>
<body>
<div class="related">
@@ -41,7 +41,7 @@
<a href="developers.html" title="Documentation For Developes"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="index.html" title="Welcome to ProMod3’s documentation!"
+ <a href="index.html" title="Welcome To ProMod3’s Documentation!"
accesskey="P">previous</a> |</li>
<li><a href="index.html">ProMod3 0 documentation</a> »</li>
</ul>
@@ -64,7 +64,7 @@
<div class="sphinxsidebarwrapper">
<h4>Previous topic</h4>
<p class="topless"><a href="index.html"
- title="previous chapter">Welcome to ProMod3’s documentation!</a></p>
+ title="previous chapter">Welcome To ProMod3’s Documentation!</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="developers.html"
title="next chapter">Documentation For Developes</a></p>
@@ -103,14 +103,14 @@
<a href="developers.html" title="Documentation For Developes"
>next</a> |</li>
<li class="right" >
- <a href="index.html" title="Welcome to ProMod3’s documentation!"
+ <a href="index.html" title="Welcome To ProMod3’s Documentation!"
>previous</a> |</li>
<li><a href="index.html">ProMod3 0 documentation</a> »</li>
</ul>
</div>
<div class="footer">
- © Copyright 2013, Bienchen.
- Last updated on Nov 04 11:22, 2014.
+ © Copyright 2014, Bienchen.
+ Last updated on Dec 16 17:54, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
--
GitLab