diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 3915121c5c662ed729a30d8d576d1594f9cd2ff0..2f0828e6f53e70413b75ec397afc28b321ace832 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -86,7 +86,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index 8eb995432f99c3d891294134579bc0a2640fe541..bce1498b9cfbd2a1773c80aba740d05ef5be102d 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -193,7 +193,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index a60854954efb94889578b29c25accb2f7e470b1b..f30d4279225dd3a8efe1a554c4d46919ddcb377b 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -113,7 +113,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/_modules/promod3/rawmodel.html b/doc/html/_modules/promod3/rawmodel.html
index b6677afcf469cdff81f10b96c7403dfdf1378821..c6e7453f42428ddabe038387b5255f28ac2ef5c8 100644
--- a/doc/html/_modules/promod3/rawmodel.html
+++ b/doc/html/_modules/promod3/rawmodel.html
@@ -90,7 +90,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index 16a266c21bd849784f850e45349b1127ad9bc993..e22e06c668e536ce337d1eefd2e54001492a50e9 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -121,6 +121,45 @@ For branches which are available to others, do a proper merge:
 
 This may require some manual conflict solving and will end up in a merge commit.
 
+--------------------------------------------------------------------------------
+|git| Hooks
+--------------------------------------------------------------------------------
+|git| hooks are scripts invoked by |git| in connection to certain commands.
+|project| currently provides one for :command:`commit`. It is installed by
+
+.. code-block:: console
+
+   $ cp extras/pre_commit/pre-commit .git/hooks/
+   $
+
+Its task is applying coding standards and doing a bunch of other checks on the
+files involved in a commit. Everything around the script is hosted in :file:`extras/pre_commit/`.
+
+If you ever have to skip the hook,
+
+.. code-block:: console
+
+   $ git commit --no-verify
+   $
+
+does the trick. **But** checks are always run on the complete file containing
+changes, not only on the lines changed. This means if you opt out of an issue,
+it will reappear next time that very file changes.
+
+For checking |python| code, the pre-commit hook employs |pylint|_, to make sure
+we stay close to |pep8|_. If you feel the need to make changes to the |pylint|
+call, please make sure you fully understand what the complaints are. Sometimes
+|pep8| sounds overly restrictive but it may help with performance and
+compatibility with |python| 3. For |project| it is also important that the code
+looks similar throughout the various modules. So do not disable a check because
+it just seems inconvenient or you do not understand why |pylint| is croaking at
+what looks like 'working' code. But then there are also cases where |pylint| is
+not smart enough to cope with valid |pep8| code. For changes with valid cause,
+the configuration flushed into |pylint| may be found at
+:file:`extras/pre_commit/pm3_csc/filecheck/pylintrc` and
+:file:`extras/pre_commit/pm3_csc/filecheck/pylint-unittest-rc`. The latter one
+is invoked on unit test code, where we may go a little bit less restrictive.
+
 --------------------------------------------------------------------------------
 Directory Structure
 --------------------------------------------------------------------------------
@@ -635,7 +674,10 @@ contributions to web pages using |project|.
 
 .. |fedora| replace:: Fedora
 .. |nameattr| replace:: :attr:`__name__`
-
+.. |pylint| replace:: Pylint
+.. _pylint: http://www.pylint.org
+.. |pep8| replace:: PEP 8
+.. _pep8: https://www.python.org/dev/peps/pep-0008/
 ..  LocalWords:  cmake hotfix doctest linkcheck rebase BRANCHNAME rebasing py
 ..  LocalWords:  CMakeLists txt rst pymod init submodule src restructuredtext
 ..  LocalWords:  makefiles formatters Changelog codetest promod sidechains io
@@ -646,4 +688,4 @@ contributions to web pages using |project|.
 ..  LocalWords:  SomethingTests testFileExistsFalse testutils RunTests DQMEAN
 ..  LocalWords:  pre API inline CMake hh ProMod Bienchen OST OPENSTRUCTURE
 ..  LocalWords:  mol alg conop QMEAN KIC eigen eigenvectors Lapack rawmodel
-..  LocalWords:  OpenStructure ost
+..  LocalWords:  OpenStructure ost pylint
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 06711aebda183009f626c52f3f47cf90b45b71c6..af691cbbc98b65a50537323a40fde5c2be99bea6 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -212,7 +212,7 @@ builder</li>
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 16 17:54, 2014.
+      Last updated on Jan 05 14:50, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 9296d61ae2472c946c5a86c0d34d226dc7347da1..231598ff1f6241b13f3a6663ff81c4f21f64a7c5 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -128,7 +128,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 16 17:54, 2014.
+      Last updated on Jan 05 14:50, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 4d924791f6d934a511a8284ada382c9269e904d1..ea7c81ea28ee6b9d65e17b5ea9bced154f6349b9 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -194,7 +194,7 @@ build directory.</dd>
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 17 17:54, 2014.
+      Last updated on Jan 05 14:50, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index e6016eb6f5320ba157d20ea37d75392d302c5f02..dfd6cfc3200d4080a00b785b47bdfdd646e45c1a 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -155,6 +155,38 @@ case <tt class="docutils literal"><span class="pre">develop</span></tt> may be u
 </div>
 <p>This may require some manual conflict solving and will end up in a merge commit.</p>
 </div>
+<div class="section" id="git-hooks">
+<h2>Git Hooks<a class="headerlink" href="#git-hooks" title="Permalink to this headline">¶</a></h2>
+<p>Git hooks are scripts invoked by Git in connection to certain commands.
+ProMod3 currently provides one for <strong class="command">commit</strong>. It is installed by</p>
+<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>
+<p>Its task is applying coding standards and doing a bunch of other checks on the
+files involved in a commit. Everything around the script is hosted in <tt class="file docutils literal"><span class="pre">extras/pre_commit/</span></tt>.</p>
+<p>If you ever have to skip the hook,</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git commit --no-verify
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>does the trick. <strong>But</strong> checks are always run on the complete file containing
+changes, not only on the lines changed. This means if you opt out of an issue,
+it will reappear next time that very file changes.</p>
+<p>For checking Python code, the pre-commit hook employs <a class="reference external" href="http://www.pylint.org">Pylint</a>, to make sure
+we stay close to <a class="reference external" href="https://www.python.org/dev/peps/pep-0008/">PEP 8</a>. If you feel the need to make changes to the Pylint
+call, please make sure you fully understand what the complaints are. Sometimes
+PEP 8 sounds overly restrictive but it may help with performance and
+compatibility with Python 3. For ProMod3 it is also important that the code
+looks similar throughout the various modules. So do not disable a check because
+it just seems inconvenient or you do not understand why Pylint is croaking at
+what looks like &#8216;working&#8217; code. But then there are also cases where Pylint is
+not smart enough to cope with valid PEP 8 code. For changes with valid cause,
+the configuration flushed into Pylint may be found at
+<tt class="file docutils literal"><span class="pre">extras/pre_commit/pm3_csc/filecheck/pylintrc</span></tt> and
+<tt class="file docutils literal"><span class="pre">extras/pre_commit/pm3_csc/filecheck/pylint-unittest-rc</span></tt>. The latter one
+is invoked on unit test code, where we may go a little bit less restrictive.</p>
+</div>
 <div class="section" id="directory-structure">
 <h2>Directory Structure<a class="headerlink" href="#directory-structure" title="Permalink to this headline">¶</a></h2>
 <p>The directory structure of the ProMod3 repository is supposed to &#8216;keep
@@ -743,6 +775,7 @@ contributions to web pages using ProMod3.</p>
   <ul>
 <li><a class="reference internal" href="#">Contributing</a><ul>
 <li><a class="reference internal" href="#git-branches">Git Branches</a></li>
+<li><a class="reference internal" href="#git-hooks">Git Hooks</a></li>
 <li><a class="reference internal" href="#directory-structure">Directory Structure</a></li>
 <li><a class="reference internal" href="#cmake">CMake</a></li>
 <li><a class="reference internal" href="#the-stage-directory">The <tt class="file docutils literal"><span class="pre">stage</span></tt> Directory</a></li>
@@ -803,7 +836,7 @@ contributions to web pages using ProMod3.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index c10e06695d453d3826ffe7f184d46bdaf1c30fc5..3597372c7668a439e6841989a95f614ed23ec8bf 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -217,7 +217,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 17 17:01, 2014.
+      Last updated on Jan 05 14:50, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 13a1ce9a9cee584d8b30c75abbcec80df269941c..ae498d5517be94c37ecbd14e94f0206f93ac1069 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -160,7 +160,7 @@ traditionally reserved to successful commands.</li>
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 17 17:01, 2014.
+      Last updated on Jan 05 14:50, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 75d977379998d02b90ba8b61e5ec7abd9bc8d4e5..0663e0669e8f6fa0e8702070fafcff28ce3ad32c 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -129,7 +129,7 @@ modeling per se but cover standard programming issues.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 17 17:01, 2014.
+      Last updated on Jan 05 14:50, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 629ad054b6fc463b755ef515adec1df3d3b3c822..a6ac379a5a2c306044fd26c85dd634579ab9a5e4 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -73,6 +73,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="contributing.html#git-branches">Git Branches</a></li>
+<li class="toctree-l2"><a class="reference internal" href="contributing.html#git-hooks">Git Hooks</a></li>
 <li class="toctree-l2"><a class="reference internal" href="contributing.html#directory-structure">Directory Structure</a></li>
 <li class="toctree-l2"><a class="reference internal" href="contributing.html#cmake">CMake</a></li>
 <li class="toctree-l2"><a class="reference internal" href="contributing.html#the-stage-directory">The <tt class="file docutils literal"><span class="pre">stage</span></tt> Directory</a></li>
@@ -145,7 +146,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 6b7b6b1b59d69bd6d0c61c28227b63fe56043227..46eb6c8e3591ad2348c4c212aaf0487186314efd 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -229,7 +229,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/index.html b/doc/html/index.html
index f8b79481d380c9425638e7bc7ac30153947f844a..1df5318c52f97ba2b451b07ddf294798d72bc505 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -133,7 +133,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 223b8ae72de37fa85280e7ba2276cf5d46524563..faefcc62b30bc01711adbcb2f84f8ca01d39d9d3 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/rawmodel/index.html b/doc/html/rawmodel/index.html
index f49dd1d4907de4aedf996b0bc2c89f139fd725cd..fb42a2a37a380818b52bc813d92abc045d540099 100644
--- a/doc/html/rawmodel/index.html
+++ b/doc/html/rawmodel/index.html
@@ -214,7 +214,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 17 17:01, 2014.
+      Last updated on Jan 05 14:50, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/search.html b/doc/html/search.html
index 1547f040aeb54e08abe989f8fe389d03fedd7210..0092fa7ff786751c875c689bb28a2f0c498b4bc5 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2014, Bienchen.
-      Last updated on Dec 19 14:57, 2014.
+      Last updated on Jan 05 15:48, 2015.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
     </div>
   </body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 4d2fc0e8a69cef8fb56024cf7fd786c53c3adb55..4a96c0350191b59cfb1b8616d51655d2e2848514 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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diff --git a/doc/html/users.html b/doc/html/users.html
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