diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 6964cf96734a79a1c9de4932da5588a9924935da..138cf9cd9ad3d9260b28565a0b1c44e7f811bc8f 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -23,15 +23,14 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -58,7 +57,9 @@
 <li><a href="CBetaScorer.html">CBetaScorer</a></li>
 <li><a href="CCD.html">CCD</a></li>
 <li><a href="CCDCloser.html">CCDCloser</a></li>
+<li><a href="CTerminalCloser.html">CTerminalCloser</a></li>
 <li><a href="ClashScorer.html">ClashScorer</a></li>
+<li><a href="DeNovoCloser.html">DeNovoCloser</a></li>
 <li><a href="DirtyCCDCloser.html">DirtyCCDCloser</a></li>
 <li><a href="DiscoContainer.html">DiscoContainer</a></li>
 <li><a href="ExponentialCooler.html">ExponentialCooler</a></li>
@@ -76,9 +77,11 @@
 <li><a href="HBondScorer.html">HBondScorer</a></li>
 <li><a href="KIC.html">KIC</a></li>
 <li><a href="KICCloser.html">KICCloser</a></li>
+<li><a href="LinearScorer.html">LinearScorer</a></li>
 <li><a href="LoopCandidates.html">LoopCandidates</a></li>
 <li><a href="MmSystemCreator.html">MmSystemCreator</a></li>
 <li><a href="ModellingHandle.html">ModellingHandle</a></li>
+<li><a href="NTerminalCloser.html">NTerminalCloser</a></li>
 <li><a href="PairwiseScorer.html">PairwiseScorer</a></li>
 <li><a href="Particle.html">Particle</a></li>
 <li><a href="PhiPsiSampler.html">PhiPsiSampler</a></li>
@@ -112,6 +115,7 @@
 <li><a href="promod3/modelling/_fragger_handle.html">promod3.modelling._fragger_handle</a></li>
 <li><a href="promod3/modelling/_modelling.html">promod3.modelling._modelling</a></li>
 <li><a href="promod3/modelling/_molprobity.html">promod3.modelling._molprobity</a></li>
+<li><a href="promod3/modelling/_monte_carlo.html">promod3.modelling._monte_carlo</a></li>
 <li><a href="promod3/modelling/_pipeline.html">promod3.modelling._pipeline</a></li>
 <li><a href="promod3/modelling/_reconstruct_sidechains.html">promod3.modelling._reconstruct_sidechains</a></li>
 <li><a href="promod3/modelling/_ring_punches.html">promod3.modelling._ring_punches</a></li>
@@ -139,6 +143,9 @@
       <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>
@@ -146,11 +153,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
index 140c70b9d3e7b6edc1001cd57344d3a21c5babd7..da882aa23e3de411d7e8fbb6c3fb46fa21315fd4 100644
--- a/doc/html/_modules/promod3.html
+++ b/doc/html/_modules/promod3.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Module code" href="index.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,22 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3</h1><div class="highlight"><pre>
-<span></span><span class="c1"># enable access to loop and modelling via &quot;import promod3&quot;</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+<span class="c1"># enable access to loop and modelling via &quot;import promod3&quot;</span>
 <span class="kn">import</span> <span class="nn">promod3.core</span>
 <span class="kn">import</span> <span class="nn">promod3.sidechain</span>
 <span class="kn">import</span> <span class="nn">promod3.loop</span>
@@ -55,7 +69,7 @@
 <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
 <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
 
-<div class="viewcode-block" id="SetCompoundsChemlib"><a class="viewcode-back" href="../core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">[docs]</a><span class="k">def</span> <span class="nf">SetCompoundsChemlib</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="o">=</span><span class="s2">&quot;/home/taurielg/GT/Code/ost/build/stage/share/openstructure/compounds.chemlib&quot;</span><span class="p">):</span>
+<div class="viewcode-block" id="SetCompoundsChemlib"><a class="viewcode-back" href="../core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">[docs]</a><span class="k">def</span> <span class="nf">SetCompoundsChemlib</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="o">=</span><span class="s2">&quot;/home/schdaude/prog/ost/build/stage/share/openstructure/compounds.chemlib&quot;</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;SetCompoundsChemlib(path_to_chemlib)</span>
 <span class="sd">    Load a compounds library. Does not return anything, the library is just</span>
 <span class="sd">    enabled globally.</span>
@@ -89,7 +103,7 @@
 <span class="k">try</span><span class="p">:</span>
     <span class="n">ost</span><span class="o">.</span><span class="n">GetSharedDataPath</span><span class="p">()</span>
 <span class="k">except</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">rt_err</span><span class="p">:</span>
-    <span class="n">ost</span><span class="o">.</span><span class="n">SetPrefixPath</span><span class="p">(</span><span class="s2">&quot;/home/taurielg/GT/Code/ost/build/stage&quot;</span><span class="p">)</span>
+    <span class="n">ost</span><span class="o">.</span><span class="n">SetPrefixPath</span><span class="p">(</span><span class="s2">&quot;/home/schdaude/prog/ost/build/stage&quot;</span><span class="p">)</span>
 <span class="k">except</span><span class="p">:</span>
     <span class="k">raise</span>
 
@@ -108,7 +122,7 @@
 
 <span class="c1"># set version</span>
 <span class="n">__version__</span> <span class="o">=</span> <span class="s2">&quot;1.2.0&quot;</span>
-<span class="n">__version_extended__</span> <span class="o">=</span> <span class="s2">&quot;1.2.0 (release-1.2.0|d086aed)&quot;</span>
+<span class="n">__version_extended__</span> <span class="o">=</span> <span class="s2">&quot;1.2.0 (develop|58db1e5)&quot;</span>
 
 <span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;SetCompoundsChemlib&#39;</span><span class="p">,</span> <span class="s1">&#39;GetProMod3SharedDataPath&#39;</span><span class="p">,</span>
            <span class="s1">&#39;SetProMod3SharedDataPath&#39;</span><span class="p">)</span>
@@ -139,6 +153,9 @@
       <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>
@@ -146,11 +163,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 2266f1a35bc7f1a3cb8be03cbadf869949896d0b..a9658001355b4127932e124593c4be027f98d3ec 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.core.helper</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">Uncategorised functions which may come handy at several places.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
@@ -224,6 +239,9 @@
       <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>
@@ -231,11 +249,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index e10fff03f913d8b7779021287b59d397b5f58634..0905f2cac4fde0ed41726507223b0e94fc89657e 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.core.pm3argparse</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">Extensions for the argparse module.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
@@ -274,6 +289,17 @@
                                    <span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">33</span><span class="p">)</span>
     <span class="k">return</span> <span class="n">ent</span>
 
+<span class="k">def</span> <span class="nf">_FetchProfileFromFile</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot;Load generic profile file from filename and return it.&quot;&quot;&quot;</span>
+    <span class="n">argstr</span> <span class="o">=</span> <span class="s2">&quot;&#39;--seqprof &quot;</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> <span class="s2">&quot;&#39;&quot;</span>
+    <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s2">&quot;Profile&quot;</span><span class="p">,</span> <span class="mi">51</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+    <span class="k">try</span><span class="p">:</span>
+        <span class="n">prof</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadSequenceProfile</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+    <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span>
+        <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">&quot;: failure to parse profile file: &quot;</span> <span class="o">+</span>
+                               <span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">52</span><span class="p">)</span>        
+    <span class="k">return</span> <span class="n">prof</span>
+
 <span class="k">def</span> <span class="nf">_GetChains</span><span class="p">(</span><span class="n">structures</span><span class="p">,</span> <span class="n">structure_sources</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;Get chain id to entity view (single chain) mapping (dict).&quot;&quot;&quot;</span>
     <span class="c1"># IDs: (file_base = base file name with no extensions)</span>
@@ -439,7 +465,9 @@
         <span class="k">if</span> <span class="s1">&#39;ALIGNMENT&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleAlignment</span><span class="p">()</span>
         <span class="k">if</span> <span class="s1">&#39;STRUCTURE&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleStructure</span><span class="p">()</span></div>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleStructure</span><span class="p">()</span>
+        <span class="k">if</span> <span class="s1">&#39;PROFILE&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleProfile</span><span class="p">()</span></div>
 
 <div class="viewcode-block" id="PM3ArgumentParser.AddAlignment"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">[docs]</a>    <span class="k">def</span> <span class="nf">AddAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">allow_multitemplate</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Commandline options for alignments.</span>
@@ -516,7 +544,7 @@
 <div class="viewcode-block" id="PM3ArgumentParser.AddStructure"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">[docs]</a>    <span class="k">def</span> <span class="nf">AddStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attach_views</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Commandline options for structures.</span>
 
-<span class="sd">        Activate everything needed to load alignments to the argument parser.</span>
+<span class="sd">        Activate everything needed to load structures to the argument parser.</span>
 <span class="sd">        Command line arguments are then added in :meth:`AssembleParser` and the</span>
 <span class="sd">        input is post processed and checked in :meth:`Parse`.</span>
 
@@ -574,6 +602,48 @@
         <span class="k">if</span> <span class="n">attach_views</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">&#39;ATTACH_VIEWS&#39;</span><span class="p">)</span></div>
 
+<div class="viewcode-block" id="PM3ArgumentParser.AddProfile"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">[docs]</a>    <span class="k">def</span> <span class="nf">AddProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Commandline options for profiles</span>
+
+<span class="sd">        Activate everything needed to load profiles to the argument parser.</span>
+<span class="sd">        Command line arguments are then added in :meth:`AssembleParser` and the</span>
+<span class="sd">        input is post processed and checked in :meth:`Parse`.</span>
+
+<span class="sd">        Options/arguments added:</span>
+
+<span class="sd">        * ``-s/--seqprof &lt;FILE&gt;`` - Sequence profile in any format readable</span>
+<span class="sd">          by the :meth:`ost.io.LoadSequenceProfile` method. Format is chosen by </span>
+<span class="sd">          file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm, </span>
+<span class="sd">          .pssm.gz. Consider to use </span>
+<span class="sd">          :meth:`ost.bindings.hhblits.HHblits.A3MToProfile` if you have a file </span>
+<span class="sd">          in a3m format at hand. </span>
+
+<span class="sd">        Notes:</span>
+
+<span class="sd">        * the profiles are mapped based on exact matches towards the gapless</span>
+<span class="sd">          target sequences, i.e. one profile is mapped to several chains in</span>
+<span class="sd">          case of homo-oligomers</span>
+
+<span class="sd">        * every profile must have a unique sequence to avoid ambiguities</span>
+
+<span class="sd">        * all or nothing - you cannot provide profiles for only a subset of</span>
+<span class="sd">          target sequences</span>
+
+<span class="sd">        Attributes added to the namespace returned by :meth:`Parse`:</span>
+
+<span class="sd">        * :attr:`profiles` - :class:`list` of :class:`ost.seq.ProfileHandle`, </span>
+<span class="sd">          ordered to match the target sequences.</span>
+
+<span class="sd">        Exit codes related to profile input:</span>
+
+<span class="sd">        * 51 - a given profile file does not exist</span>
+<span class="sd">        * 52 - failure to read a given profile file </span>
+<span class="sd">        * 53 - a profile cannot be mapped to any target sequence</span>
+<span class="sd">        * 54 - profile sequences are not unique</span>
+<span class="sd">        * 55 - only subset of target sequences is covered by profile</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">&#39;PROFILE&#39;</span><span class="p">)</span></div>
+
     <span class="k">def</span> <span class="nf">_AssembleAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Actually add alignment arguments/options.&quot;&quot;&quot;</span>
         <span class="n">aln_grp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_mutually_exclusive_group</span><span class="p">(</span><span class="n">required</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
@@ -611,7 +681,15 @@
                              <span class="s2">&quot;io.LoadEntity method. Format is chosen by file &quot;</span><span class="o">+</span>
                              <span class="s2">&quot;ending. Recognized File Extensions: .ent, .pdb, &quot;</span><span class="o">+</span>
                              <span class="s2">&quot;.ent.gz, .pdb.gz, .cif, .cif.gz.&quot;</span><span class="p">,</span>
-                             <span class="n">action</span><span class="o">=</span><span class="s1">&#39;append&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span></div>
+                             <span class="n">action</span><span class="o">=</span><span class="s1">&#39;append&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="nf">_AssembleProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-s&#39;</span><span class="p">,</span> <span class="s1">&#39;--seqprof&#39;</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;&lt;FILE&gt;&#39;</span><span class="p">),</span>
+                          <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Sequence profile in any format readable by &quot;</span><span class="o">+</span>
+                          <span class="s2">&quot;OST&#39;s io.LoadSequenceProfile method. Format is &quot;</span><span class="o">+</span>
+                          <span class="s2">&quot;chosen by file ending. Recognized File Extensions: &quot;</span><span class="o">+</span>
+                          <span class="s2">&quot;.hhm, .hhm.gz, .pssm, .pssm.gz&quot;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;append&#39;</span><span class="p">,</span>
+                          <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span></div>
 
 <span class="k">class</span> <span class="nc">PM3OptionsNamespace</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
     <span class="c1"># class will grow, so for the moment pylint is ignored</span>
@@ -633,6 +711,8 @@
             <span class="bp">self</span><span class="o">.</span><span class="n">_PostProcessStructure</span><span class="p">()</span>
         <span class="k">if</span> <span class="s1">&#39;ATTACH_VIEWS&#39;</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_AttachViews</span><span class="p">()</span>
+        <span class="k">if</span> <span class="s1">&#39;PROFILE&#39;</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_PostProcessProfile</span><span class="p">()</span>
 
     <span class="k">def</span> <span class="nf">_PostProcessAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="c1">#pylint: disable=no-member</span>
@@ -682,6 +762,42 @@
         <span class="k">for</span> <span class="n">aln</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="p">:</span>
             <span class="n">_AttachViewsToAln</span><span class="p">(</span><span class="n">aln</span><span class="p">,</span> <span class="n">chain_entities</span><span class="p">)</span>
 
+    <span class="k">def</span> <span class="nf">_PostProcessProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="sd">&quot;&quot;&quot;Get Profiles from command line input.&quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">profiles</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqprof</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="c1"># no profiles provided, remember the all or nothing principle</span>
+            <span class="c1"># so not having any profile is fine</span>
+            <span class="k">return</span>
+
+        <span class="n">loaded_profiles</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqprof</span><span class="p">:</span>
+            <span class="n">loaded_profiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_FetchProfileFromFile</span><span class="p">(</span><span class="n">src</span><span class="p">))</span>
+
+        <span class="n">prof_sequences</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">sequence</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">loaded_profiles</span><span class="p">]</span>
+
+        <span class="c1"># check uniqueness of loaded profiles</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">prof_sequences</span><span class="p">))</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">prof_sequences</span><span class="p">):</span>
+            <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">&quot;All sequence profiles must have unique &quot;</span> <span class="o">+</span>
+                                   <span class="s2">&quot;sequence.&quot;</span><span class="p">,</span> <span class="mi">54</span><span class="p">)</span>
+
+        <span class="c1"># map onto alignment target sequences</span>
+        <span class="n">trg_sequences</span> <span class="o">=</span> <span class="p">[</span><span class="n">aln</span><span class="o">.</span><span class="n">GetSequence</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">GetGaplessString</span><span class="p">()</span> \
+                         <span class="k">for</span> <span class="n">aln</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="p">]</span>
+        <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">trg_sequences</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">profiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">loaded_profiles</span><span class="p">[</span><span class="n">prof_sequences</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">s</span><span class="p">)])</span>
+            <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span>
+                <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">&quot;Could not find profile with sequence &quot;</span> <span class="o">+</span>
+                                       <span class="s2">&quot;that exactly matches trg seq: &quot;</span> <span class="o">+</span> <span class="n">s</span><span class="p">,</span> <span class="mi">55</span><span class="p">)</span>
+
+        <span class="c1"># We found a profile for every target sequence. So if the size of unique </span>
+        <span class="c1"># target sequences is not the same as for unique profile sequences, </span>
+        <span class="c1"># we know that we have additional profiles that never got mapped</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">trg_sequences</span><span class="p">))</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">prof_sequences</span><span class="p">)):</span>
+            <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">&quot;Could not map every profile to a target &quot;</span> <span class="o">+</span>
+                                   <span class="s2">&quot;sequence&quot;</span><span class="p">,</span> <span class="mi">53</span><span class="p">)</span>
 
 <span class="c1">#  LocalWords:  param attr prog argparse ArgumentParser bool sys os init str</span>
 <span class="c1">#  LocalWords:  progattr descattr argpinit argv formatter meth args namespace</span>
@@ -718,6 +834,9 @@
       <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>
@@ -725,11 +844,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/modelling/_closegaps.html b/doc/html/_modules/promod3/modelling/_closegaps.html
index 85c8c033bdc62ac51dc8c0529b0e2ca2ad5f1f0f..88a45e1319ee0189f38ed1af2a7450e08d9460c0 100644
--- a/doc/html/_modules/promod3/modelling/_closegaps.html
+++ b/doc/html/_modules/promod3/modelling/_closegaps.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.modelling._closegaps</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;High-level functionality for modelling module to close gaps. Added in the</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&#39;&#39;&#39;High-level functionality for modelling module to close gaps. Added in the</span>
 <span class="sd">__init__.py file. To be used directly by passing a ModellingHandle instance</span>
 <span class="sd">as argument.</span>
 <span class="sd">&#39;&#39;&#39;</span>
@@ -1620,6 +1635,9 @@
       <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>
@@ -1627,11 +1645,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/modelling/_denovo.html b/doc/html/_modules/promod3/modelling/_denovo.html
index b2100964e66fb6ebbc6d9f4a3a710767ffecfc50..8c1bfe5ec00919724558f5d36f82f80f97a47468 100644
--- a/doc/html/_modules/promod3/modelling/_denovo.html
+++ b/doc/html/_modules/promod3/modelling/_denovo.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.modelling._denovo</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">loop</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">loop</span>
 <span class="kn">from</span> <span class="nn">_modelling</span> <span class="kn">import</span> <span class="o">*</span>
 
 <div class="viewcode-block" id="GenerateDeNovoTrajectories"><a class="viewcode-back" href="../../../modelling/algorithms.html#promod3.modelling.GenerateDeNovoTrajectories">[docs]</a><span class="k">def</span> <span class="nf">GenerateDeNovoTrajectories</span><span class="p">(</span><span class="n">sequence</span><span class="p">,</span> 
@@ -193,6 +208,9 @@
       <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>
@@ -200,11 +218,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/modelling/_fragger_handle.html b/doc/html/_modules/promod3/modelling/_fragger_handle.html
index 0ef683b33454d388f4ec6354c16ddeef42fc101d..2ffd9280d32a1ae555f18f0382003ad67fda76dc 100644
--- a/doc/html/_modules/promod3/modelling/_fragger_handle.html
+++ b/doc/html/_modules/promod3/modelling/_fragger_handle.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.modelling._fragger_handle</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;Python functionality to generate fraggers.&#39;&#39;&#39;</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&#39;&#39;&#39;Python functionality to generate fraggers.&#39;&#39;&#39;</span>
 
 <span class="kn">from</span> <span class="nn">promod3.loop</span> <span class="kn">import</span> <span class="o">*</span>
 <span class="kn">from</span> <span class="nn">ost.conop</span> <span class="kn">import</span> <span class="n">OneLetterCodeToResidueName</span>
@@ -416,6 +431,9 @@
       <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>
@@ -423,11 +441,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/modelling/_molprobity.html b/doc/html/_modules/promod3/modelling/_molprobity.html
index b9441021b1cca2bd98ef90666bf96c15f20509f6..bd5ebc586d49902e856fa23bc93fb0cc51fe6208 100644
--- a/doc/html/_modules/promod3/modelling/_molprobity.html
+++ b/doc/html/_modules/promod3/modelling/_molprobity.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.modelling._molprobity</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;Binding to external MolProbity tool to get scores.&#39;&#39;&#39;</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&#39;&#39;&#39;Binding to external MolProbity tool to get scores.&#39;&#39;&#39;</span>
 
 <span class="kn">import</span> <span class="nn">ost</span>
 <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">settings</span>
@@ -182,6 +197,9 @@
       <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>
@@ -189,11 +207,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/modelling/_monte_carlo.html b/doc/html/_modules/promod3/modelling/_monte_carlo.html
new file mode 100644
index 0000000000000000000000000000000000000000..a49d8de76ecdab7061a1d7e21130995dcdddd7c3
--- /dev/null
+++ b/doc/html/_modules/promod3/modelling/_monte_carlo.html
@@ -0,0 +1,195 @@
+<!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.modelling._monte_carlo &mdash; ProMod3 1.2.0 documentation</title>
+    
+    <link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../../../',
+        VERSION:     '1.2.0',
+        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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+    <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
+    <link rel="up" title="promod3" href="../../promod3.html" />
+   
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head>
+  <body role="document">  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <h1>Source code for promod3.modelling._monte_carlo</h1><div class="highlight"><pre>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="kn">import</span> <span class="nn">random</span>
+<span class="kn">import</span> <span class="nn">math</span>
+
+
+<div class="viewcode-block" id="SampleMonteCarlo"><a class="viewcode-back" href="../../../modelling/monte_carlo.html#promod3.modelling.SampleMonteCarlo">[docs]</a><span class="k">def</span> <span class="nf">SampleMonteCarlo</span><span class="p">(</span><span class="n">sampler</span><span class="p">,</span> <span class="n">closer</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span> <span class="n">cooler</span><span class="p">,</span> <span class="n">steps</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> 
+                     <span class="n">initialize</span><span class="p">,</span> <span class="n">seed</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">lowest_energy_conformation</span> <span class="o">=</span> <span class="bp">True</span><span class="p">):</span>
+    <span class="sd">&#39;&#39;&#39;  A convenient function to perform Monte Carlo sampling using a simulated</span>
+<span class="sd">    annealing scheme. In every iteration, a new loop conformation gets proposed </span>
+<span class="sd">    by the provided *sampler* and closed by the *closer*. Upon scoring, this new</span>
+<span class="sd">    conformation gets accepted/rejected using a metropolis criterion based on </span>
+<span class="sd">    the temperature given by the *cooler* </span>
+<span class="sd">    =&gt; acceptance probability: exp(-delta_score/T).</span>
+<span class="sd">    The result is stored in *bb_list* (passed by reference, so NO return value) </span>
+<span class="sd">    and is either the lowest energy conformation ever encountered or the last </span>
+<span class="sd">    accepted proposal.</span>
+
+<span class="sd">    :param sampler:       Sampler object capable of initializing and altering</span>
+<span class="sd">                          conformations.</span>
+<span class="sd">    :param closer:        Closer object to adapt a new conformation to</span>
+<span class="sd">                          the environment.</span>
+<span class="sd">    :param scorer:        Scorer object to score new loop conformations.</span>
+<span class="sd">    :param cooler:        Cooler object to control the temperature of the </span>
+<span class="sd">                          Monte Carlo trajectory.</span>
+<span class="sd">    :param steps:         Number of Monte Carlo iterations to be performed.</span>
+<span class="sd">    :param bb_list:       The chosen conformation gets stored here.</span>
+<span class="sd">    :param initialize:    Whether a new bb_list should be generated as starting</span>
+<span class="sd">                          point, based on the samplers Initialize function.</span>
+<span class="sd">                          The input *bb_list* gets used otherwise.</span>
+<span class="sd">    :param seed:          Seed for internal random number generator.</span>
+<span class="sd">    :param lowest_energy_conformation:  If True, we choose the lowest scoring</span>
+<span class="sd">                                        conformation of the trajectory. </span>
+<span class="sd">                                        Otherwise, the last accepted proposal.</span>
+
+<span class="sd">    :type sampler:        :ref:`mc-sampler-object`</span>
+<span class="sd">    :type closer:         :ref:`mc-closer-object`</span>
+<span class="sd">    :type scorer:         :ref:`mc-scorer-object`</span>
+<span class="sd">    :type cooler:         :ref:`mc-cooler-object`</span>
+<span class="sd">    :type steps:          :class:`int`</span>
+<span class="sd">    :type bb_list:        :class:`~promod3.loop.BackboneList`</span>
+<span class="sd">    :type initialize:     :class:`bool`</span>
+<span class="sd">    :type seed:           :class:`int`</span>
+<span class="sd">    :type lowest_energy_conformation: :class:`bool`</span>
+<span class="sd">    &#39;&#39;&#39;</span>
+
+    <span class="c1"># Initialize from scratch if necessary</span>
+    <span class="k">if</span> <span class="n">initialize</span><span class="p">:</span>
+        <span class="n">initialized</span> <span class="o">=</span> <span class="bp">False</span>
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span>
+            <span class="n">sampler</span><span class="o">.</span><span class="n">Initialize</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">closer</span><span class="o">.</span><span class="n">Close</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">):</span>
+                <span class="n">initialized</span> <span class="o">=</span> <span class="bp">True</span>
+                <span class="k">break</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">initialized</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;Failed to initialize monte carlo protocol!&quot;</span><span class="p">)</span>
+
+    <span class="c1"># setup</span>
+    <span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span>
+    <span class="n">score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">GetScore</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span>
+    <span class="n">closed</span> <span class="o">=</span> <span class="bp">False</span>
+    <span class="n">min_score</span> <span class="o">=</span> <span class="n">score</span>
+    <span class="n">min_score_bb_list</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+    <span class="n">proposed_bb_list</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">steps</span><span class="p">):</span>
+
+        <span class="c1"># try several proposals (we might not be able to close at first attempt)</span>
+        <span class="n">closed</span> <span class="o">=</span> <span class="bp">False</span>
+        <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
+            <span class="n">sampler</span><span class="o">.</span><span class="n">ProposeStep</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">proposed_bb_list</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">closer</span><span class="o">.</span><span class="n">Close</span><span class="p">(</span><span class="n">proposed_bb_list</span><span class="p">,</span> <span class="n">proposed_bb_list</span><span class="p">):</span>
+                <span class="n">closed</span> <span class="o">=</span> <span class="bp">True</span>
+                <span class="k">break</span>
+
+        <span class="c1"># check for success, try again in next step in case of failure</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">closed</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="c1"># accept / reject based on Metropolis criterion</span>
+        <span class="n">temperature</span> <span class="o">=</span> <span class="n">cooler</span><span class="o">.</span><span class="n">GetTemperature</span><span class="p">()</span>
+        <span class="n">new_score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">GetScore</span><span class="p">(</span><span class="n">proposed_bb_list</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">math</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="p">(</span><span class="n">new_score</span><span class="o">-</span><span class="n">score</span><span class="p">)</span><span class="o">/</span><span class="n">temperature</span><span class="p">)</span> <span class="o">&gt;</span> <span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">():</span>
+            <span class="n">positions</span> <span class="o">=</span> <span class="n">proposed_bb_list</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+            <span class="n">score</span> <span class="o">=</span> <span class="n">new_score</span>
+            <span class="k">if</span> <span class="n">lowest_energy_conformation</span> <span class="ow">and</span> <span class="n">score</span> <span class="o">&lt;</span> <span class="n">min_score</span><span class="p">:</span>
+                <span class="n">min_score</span> <span class="o">=</span> <span class="n">score</span>
+                <span class="n">min_score_bb_list</span> <span class="o">=</span> <span class="n">positions</span>
+
+    <span class="k">if</span> <span class="n">lowest_energy_conformation</span><span class="p">:</span>
+        <span class="n">bb_list</span> <span class="o">=</span> <span class="n">min_score_bb_list</span></div>
+</pre></div>
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../../../index.html">Documentation overview</a><ul>
+  <li><a href="../../index.html">Module code</a><ul>
+  <li><a href="../../promod3.html">promod3</a><ul>
+  </ul></li>
+  </ul></li>
+  </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <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="footer">
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
+      
+    </div>
+
+    
+
+    
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/_modules/promod3/modelling/_pipeline.html b/doc/html/_modules/promod3/modelling/_pipeline.html
index 3ea48e01d1e4a82180c71d72adbae5297ad85c69..97fed14bf067ece46d239d9cb16c83deadc3cc17 100644
--- a/doc/html/_modules/promod3/modelling/_pipeline.html
+++ b/doc/html/_modules/promod3/modelling/_pipeline.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.modelling._pipeline</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;High-level functionality for modelling module to build pipelines. Added in </span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&#39;&#39;&#39;High-level functionality for modelling module to build pipelines. Added in </span>
 <span class="sd">the __init__.py file. To be used directly by passing a ModellingHandle instance</span>
 <span class="sd">as argument.</span>
 <span class="sd">&#39;&#39;&#39;</span>
@@ -206,7 +221,8 @@
 
 
 <div class="viewcode-block" id="BuildSidechains"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.BuildSidechains">[docs]</a><span class="k">def</span> <span class="nf">BuildSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="n">fragment_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
-                    <span class="n">structure_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+                    <span class="n">structure_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
+                    <span class="n">rotamer_library</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
     <span class="sd">&#39;&#39;&#39;Build sidechains for model.</span>
 
 <span class="sd">    This is a wrapper for :func:`promod3.modelling.ReconstructSidechains`, </span>
@@ -232,10 +248,16 @@
 <span class="sd">                            if ring punches are found. A default one is loaded</span>
 <span class="sd">                            if None.</span>
 <span class="sd">    :type torsion_sampler:  :class:`~promod3.loop.TorsionSampler`</span>
+<span class="sd">    :param rotamer_library: Used as parameter for </span>
+<span class="sd">                            :func:`modelling.ReconstructSidechains`, a default </span>
+<span class="sd">                            one is loaded if None.</span>
+<span class="sd">    :type rotamer_library:  :class:`~promod3.sidechain.RotamerLib` or</span>
+<span class="sd">                            :class:`~promod3.sidechain.BBDepRotamerLib` </span>
 <span class="sd">    &#39;&#39;&#39;</span>
     <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s1">&#39;pipeline::BuildSidechains&#39;</span><span class="p">)</span>
     <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">&quot;Rebuilding sidechains.&quot;</span><span class="p">)</span>
-    <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+    <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> 
+                          <span class="n">rotamer_library</span><span class="o">=</span><span class="n">rotamer_library</span><span class="p">)</span>
     <span class="c1"># check for ring punches</span>
     <span class="n">rings</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
     <span class="n">ring_punches</span> <span class="o">=</span> <span class="n">GetRingPunches</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
@@ -263,7 +285,8 @@
         <span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
                             <span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">ring_punch_detection</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
         <span class="c1"># re-build sidechains</span>
-        <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+        <span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
+                              <span class="n">rotamer_library</span><span class="o">=</span><span class="n">rotamer_library</span><span class="p">)</span>
         <span class="c1"># restore gaps</span>
         <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span> <span class="o">=</span> <span class="n">StructuralGapList</span><span class="p">()</span>
         <span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">old_gaps</span><span class="p">:</span>
@@ -501,6 +524,7 @@
     <span class="n">fragment_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
     <span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
     <span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
+    <span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadBBDepLib</span><span class="p">()</span>
     <span class="n">merge_distance</span> <span class="o">=</span> <span class="mi">4</span>
 
     <span class="c1"># remove terminal gaps</span>
@@ -513,7 +537,7 @@
 
     <span class="c1"># build sidechains</span>
     <span class="n">BuildSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span>
-                    <span class="n">structure_db</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">)</span>
+                    <span class="n">structure_db</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">rotamer_library</span><span class="p">)</span>
 
     <span class="c1"># minimize energy of final model using molecular mechanics</span>
     <span class="n">MinimizeModelEnergy</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">use_amber_ff</span><span class="o">=</span><span class="n">use_amber_ff</span><span class="p">,</span>
@@ -553,6 +577,9 @@
       <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>
@@ -560,11 +587,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
index a8840922170b8f1448c05531aba3a51c444ff34e..22bbfa1a611d6aba5c0e1090a09bffa066d9fbdc 100644
--- a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
+++ b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.modelling._reconstruct_sidechains</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">conop</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">conop</span>
 <span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">core</span><span class="p">,</span> <span class="n">sidechain</span>
 <span class="kn">import</span> <span class="nn">traceback</span>
 
@@ -438,8 +453,7 @@
 <span class="sd">    :type consider_ligands:  :class:`bool`</span>
 
 <span class="sd">    :param rotamer_library: A rotamer library to extract the rotamers from. The</span>
-<span class="sd">                            default is the :meth:`Dunbrack &lt;LoadDunbrackLib&gt;`</span>
-<span class="sd">                            library.</span>
+<span class="sd">                            default is to call :meth:`&lt;LoadBBDepLib&gt;`.</span>
 <span class="sd">    :type rotamer_library:  :class:`BBDepRotamerLib` / :class:`RotamerLib`</span>
 
 <span class="sd">    :param optimize_subrotamers: Only considered when *rotamer_model*</span>
@@ -469,7 +483,7 @@
         <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">&quot;Only </span><span class="se">\&quot;</span><span class="s2">rrm</span><span class="se">\&quot;</span><span class="s2"> and </span><span class="se">\&quot;</span><span class="s2">frm</span><span class="se">\&quot;</span><span class="s2"> allowed for rotamer_model!&quot;</span><span class="p">)</span>
 
     <span class="k">if</span> <span class="n">rotamer_library</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> 
-        <span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
+        <span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadBBDepLib</span><span class="p">()</span>
     <span class="n">bbdep</span> <span class="o">=</span> <span class="bp">False</span>
     <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">rotamer_library</span><span class="p">)</span> <span class="ow">is</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">BBDepRotamerLib</span><span class="p">:</span>
         <span class="n">bbdep</span> <span class="o">=</span> <span class="bp">True</span>
@@ -587,6 +601,9 @@
       <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>
@@ -594,11 +611,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/promod3/modelling/_ring_punches.html b/doc/html/_modules/promod3/modelling/_ring_punches.html
index a443928984846cc8360ea5a3b7339d0c45757d85..8c31c33b3571fde047814ebc30f4a2953b7f35c1 100644
--- a/doc/html/_modules/promod3/modelling/_ring_punches.html
+++ b/doc/html/_modules/promod3/modelling/_ring_punches.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
     <link rel="up" title="promod3" href="../../promod3.html" />
    
-  <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for promod3.modelling._ring_punches</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;Helper functions to deal with ring punchings.&#39;&#39;&#39;</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&#39;&#39;&#39;Helper functions to deal with ring punchings.&#39;&#39;&#39;</span>
 <span class="kn">import</span> <span class="nn">ost</span>
 <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span>
 <span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">core</span>
@@ -301,6 +316,9 @@
       <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>
@@ -308,11 +326,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_modules/test_actions.html b/doc/html/_modules/test_actions.html
index f9739b382679bc7bfe2aafe0e47bace71563dd75..ea2f10de4d087d81a180cdce3e1dea62448324f8 100644
--- a/doc/html/_modules/test_actions.html
+++ b/doc/html/_modules/test_actions.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Module code" href="index.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -40,7 +39,23 @@
           <div class="body" role="main">
             
   <h1>Source code for test_actions</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;</span>
+<span class="c1"># Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and </span>
+<span class="c1">#                          Biozentrum - University of Basel</span>
+<span class="c1"># </span>
+<span class="c1"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span>
+<span class="c1"># you may not use this file except in compliance with the License.</span>
+<span class="c1"># You may obtain a copy of the License at</span>
+<span class="c1"># </span>
+<span class="c1">#   http://www.apache.org/licenses/LICENSE-2.0</span>
+<span class="c1"># </span>
+<span class="c1"># Unless required by applicable law or agreed to in writing, software</span>
+<span class="c1"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span>
+<span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>
+<span class="c1"># See the License for the specific language governing permissions and</span>
+<span class="c1"># limitations under the License.</span>
+
+
+<span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">unittest.TestCase class providing common functionality for testing actions.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">import</span> <span class="nn">unittest</span>
@@ -190,6 +205,9 @@
       <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>
@@ -197,11 +215,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/_sources/actions/index.txt b/doc/html/_sources/actions/index.txt
index 4820610c7519c44d285f2b8e76ce9fb87c6f667a..450ffa57d28ef1f491876e3f468880a55741713d 100644
--- a/doc/html/_sources/actions/index.txt
+++ b/doc/html/_sources/actions/index.txt
@@ -20,7 +20,7 @@ with
 .. code-block:: console
 
   $ pm build-model [-h] (-f <FILE> | -c <FILE> | -j <OBJECT>|<FILE>)
-                   (-p <FILE> | -e <FILE>) [-o <FILENAME>]
+                   (-p <FILE> | -e <FILE>) [-s <FILE>] [-o <FILENAME>]
 
 Example usage:
 
@@ -105,6 +105,30 @@ sequence names are:
 Example: ``... -p data/2jlp.pdb.gz``, where the pdb file has chains ``A``,
 ``B``, ``C`` and the template sequence is named ``2jlp.A|55``.
 
+
+You can optionally specify sequence profiles to be added (``-s``) and linked 
+to the corresponding target sequences. This has an impact on loop scoring with 
+the database approach. 
+The profiles can be provided as plain files or gzipped. Following file 
+extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
+Consider to use :meth:`ost.bindings.hhblits.HHblits.A3MToProfile` if you have a 
+file in a3m format at hand. 
+
+* The profiles are mapped based on exact matches towards the gapless
+  target sequences from the provided alignment files, 
+  i.e. one profile is mapped to several chains in case of homo-oligomers
+
+* Every profile must have a unique sequence to avoid ambiguities
+
+* All or nothing - You cannot provide profiles for only a subset of
+  target sequences
+
+Example usage:
+
+.. code-block:: console
+
+  $ pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
+
 Possible exit codes of the action:
 
 - 0: all went well
@@ -113,4 +137,56 @@ Possible exit codes of the action:
 - 3: failed to perform modelling (internal error)
 - 4: failed to write results to file
 - other non-zero: failure in argument checking
-  (see :class:`promod3.core.pm3argparse.PM3ArgumentParser`)
\ No newline at end of file
+  (see :class:`promod3.core.pm3argparse.PM3ArgumentParser`)
+
+
+Sidechain Modelling
+--------------------------------------------------------------------------------
+
+You can (re-)construct the sidechains in a model from the command line.
+
+.. code-block:: console
+
+  $ usage: build-sidechains [-h] (-p <FILE> | -e <FILE>) [-o <FILENAME>] [-k] [-n]
+                            [-r] [-i] [-s]
+
+Example usage:
+
+.. code-block:: console
+
+  $ pm build-sidechains -p input.pdb
+
+This reads a structure stored in in.pdb, strips all sidechains, 
+detects and models disulfid bonds and reconstructs all sidechains with the 
+flexible rotamer model. The result is stored as :file:`out.pdb`. 
+The output filename can be controlled with the ``-o`` flag.
+
+A structure can be provided in PDB (``-p``) or in any format readable by the
+:func:`ost.io.LoadEntity` method (``-e``). In the latter case, the format is
+chosen by file ending. Recognized File Extensions: ``.ent``, ``.pdb``,
+``.ent.gz``, ``.pdb.gz``, ``.cif``, ``.cif.gz``. 
+
+Several flags control the modelling behaviour:
+
+.. option:: -k, --keep-sidechains 
+
+  Keep existing sidechains.
+
+.. option:: -n, --no-disulfids
+
+  Do not build disulfid bonds before sidechain optimization
+
+.. option:: -r, --rigid-rotamers 
+
+  Do not use rotamers with subrotamers
+
+.. option:: -i, --backbone-independent
+
+  Use backbone independent rotamer library 
+  (from :meth:`promod3.sidechain.LoadLib`) instead of the default backbone 
+  dependent one (from :meth:`promod3.sidechain.LoadBBDepLib`)
+
+.. option:: -s, --no-subrotamer-optimization
+
+  Dont do subrotamer optimization if flexible rotamer model is used
+
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index a601d619b695a46a2f15352e312e4bdaf91ab90f..1143070094fc23525a08ced74fe8f91915e7d27c 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 .. _building-promod:
 
 Building |project|
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
index 20e7a36a38c83e77511d058c8e9f459732964672..879c3a6ca5fe7c62c2a0760b5352336420d6fea9 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.txt
@@ -5,6 +5,26 @@
 Changelog
 ================================================================================
 
+Release 1.3.0
+--------------------------------------------------------------------------------
+
+* Apply Apache Version 2.0 License to the project
+* 2010 Dunbrack rotamer library has been replaced by an own backbone dependent 
+  rotamer library. All scripts required to reproduce the data are in 
+  extras/data_generation/rotamer_library
+* Penultimate rotamer library has been replaced by an own backbone independent
+  rotamer library. All scripts required to reproduce the data are in
+  extras/data_generation/rotamer_library
+* SampleMonteCarlo function moved to Python. This makes it possible to provide 
+  sampler/closer/scorer/cooler objects implemented in both, Python and C++
+* Action script for sidechain modelling
+* Allow sequence profiles as input for build-model action script.
+* Recipe for Docker / Singularity container 
+* Check peptide bonds when building a RawModel. Treat as gap if bond is 
+  stereochemically problematic despite being in sequence.
+* Several minor bug fixes, improvements, and speed-ups  
+
+
 Release 1.2.0
 --------------------------------------------------------------------------------
 
diff --git a/doc/html/_sources/container/docker.txt b/doc/html/_sources/container/docker.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc5faaa095f903fc4f5a68ba776b5b8b144874ff
--- /dev/null
+++ b/doc/html/_sources/container/docker.txt
@@ -0,0 +1,116 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Docker
+======
+
+Build Docker Image
+------------------
+
+In order to build the image:
+
+.. code-block:: bash
+
+  sudo docker build --tag <IMAGE_NAME> -f Dockerfile <PATH_TO_DOCKERFILE_DIR>
+
+You can chose any image name (tag) eg. promod. 
+
+
+Run scripts and actions with OST/PM
+-----------------------------------
+
+If script or action requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
+path. Eg. assuming that we have a struc.pdb file in /home/<USER>/pdbs directory and
+a script.py in /home/<USER> we could mount the /home/<USER> to /home in docker as
+above by specifying -v /home/<USER>:/home. To run the script we thus need to
+provide the (relative) path to the script and (relative) path to the file eg:
+
+.. code-block:: bash
+
+  sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+or with absolute paths:
+
+.. code-block:: bash
+
+  sudo docker run --rm -v /home/<USER>:/home <IMAGE_NAME> pm /home/script.py /home/pdbs/struct.pdb
+
+An alternative is to mount the current working directory into the docker home:
+
+.. code-block:: bash
+
+  sudo docker run --rm -v $(pwd):/home <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+
+.. _docker_compound_lib:
+
+The Compound Library
+--------------------
+
+At build time of the container, a :class:`~ost.conop.CompoundLib` is generated.
+Compound libraries contain information on chemical compounds, such as their 
+connectivity, chemical class and one-letter-code. The compound library has 
+several uses, but the most important one is to provide the connectivy 
+information for the rule-based processor.
+
+The compound library is generated with the components.cif dictionary provided by 
+the PDB. As the PDB updates regularly, the compound library shipped with the 
+container is quickly outdated. For most use cases, this is not problematic. 
+However, if you rely on correct connectivity information of the latest and 
+greatest compounds, you have to keep the compound library up to date manually.
+
+The suggested way of doing this is to generate your own compound library and
+mount it into the container where the original compound lib resides to 
+override it.
+
+The simplest way to create a compound library is to use the 
+:program:`chemdict_tool` available in the container. The program allows you 
+to import the chemical description of the compounds from a MMCIF dictionary, 
+e.g. the components.cif dictionary provided by the PDB. 
+The latest dictionary can be downloaded from the 
+`wwPDB site <http://www.wwpdb.org/ccd.html>`_. 
+The files are rather large, it is therefore recommended to download the 
+gzipped version. 
+
+After downloading the file use :program:`chemdict_tool` in the container to 
+convert the MMCIF  dictionary into our internal format: 
+
+.. code-block:: bash
+
+  sudo docker run --rm -v $(pwd):/home <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+
+To run a script with the upated compound library, use the -v option for mounting/overriding:
+
+.. code-block:: bash
+
+  sudo docker run --rm -v /home/<USER>:/home -v <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm script.py pdbs/struct.pdb
+
+with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated 
+compound library with name compounds.chemlib and COMPLIB_DIR_CONTAINER the 
+according path in the container.
+If you didnt change anything in the Dockerfile, the latter should be
+/usr/local/share/ost_complib
+  
+You can check whether the default lib is successfully overriden by looking at the
+output when running a Python script with following code in the container:
+
+.. code-block:: python
+
+  import promod3 # required to setup default lib
+  from ost import conop
+  lib = conop.GetDefaultLib()
+  print lib.GetCreationDate()
diff --git a/doc/html/_sources/container/index.txt b/doc/html/_sources/container/index.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cf79e23f891def49bfd42346f0e31c027838b79
--- /dev/null
+++ b/doc/html/_sources/container/index.txt
@@ -0,0 +1,36 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+ProMod3 and Containers
+======================
+
+
+ProMod3 offers build recipes for Docker and Singularity in 
+<PATH_TO_PROMOD3_CHECKOUT>/container. To avoid code duplication, 
+the Singularity container bootstraps from the Docker one and adds 
+some sugar on top.
+
+.. toctree::
+  :maxdepth: 1
+
+  Docker <docker>
+  Singularity <singularity>
+
+
+
+
+
+
diff --git a/doc/html/_sources/container/singularity.txt b/doc/html/_sources/container/singularity.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ede88ddb3845154c24ea1534d96ebc6bb964b02a
--- /dev/null
+++ b/doc/html/_sources/container/singularity.txt
@@ -0,0 +1,120 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+Singularity
+===========
+
+We do not provide a "standalone" Singularity image, but rather bootstrap from a 
+Docker image.
+
+Build Singularity Image
+-----------------------
+
+You can pull the Docker image to start with from two different sources. 
+
+Option One:
+
+You built the Docker image locally and want to use it as a starting point. For 
+this we have to fire up a local Docker registry and pull from there. Let's 
+assume you built the Docker image with tag promod.
+
+Fire the local Registry and push the promod image to it:
+
+.. code-block:: bash
+
+  sudo docker run -d -p 5000:5000 --restart=always --name registry registry:2
+  sudo docker tag promod localhost:5000/promod
+  sudo docker push localhost:5000/promod
+
+Make sure, that on top of your Singularity recipe you have something like:
+
+.. code-block:: bash
+
+  BootStrap: docker
+  Registry: http://localhost:5000
+  Namespace:
+  From: promod:latest
+
+and build the image with:
+
+.. code-block:: bash
+
+  sudo SINGULARITY_NOHTTPS=1 singularity build promod.img Singularity
+
+
+Option Two:
+
+You pull a Docker image from an external Docker registry. 
+Fill in a lot of words as soon as its on Dockerhub. Many words. The best words.
+
+and build the image with:
+
+.. code-block:: bash
+
+  sudo singularity build promod.img Singularity
+
+
+Run scripts and actions with OST/PM
+-----------------------------------
+
+The created container can run the ost, pm or chemdict_tool executables. 
+For convenience, a jupyter notebook playground with OST, ProMod3 and nglview is 
+available.
+
+To run ost, pm or chemdict_tool executables, use the exec command.
+E.g. to run scripts with pm:
+
+.. code-block:: bash
+
+  singularity exec <IMAGE> pm my_script.py [options]
+
+The jupyter notebook is setup as an app in the container. 
+To get help on how to run it:
+
+.. code-block:: bash
+
+  singularity run --app Notebook <IMAGE> --help
+
+
+The Compound Library
+--------------------
+
+You'll have the exact same problem with outdated compound libraries as in the 
+raw Docker image. You can find more information on that matter in the Docker 
+section of the documentation: :ref:`docker_compound_lib`. 
+
+The same trick of mounting an up to date compound library from the local host into
+the container applies. The two relevant commands for Singularity are building 
+a new library and mount it.
+
+Build a new library:
+
+.. code-block:: bash
+
+  singularity exec <IMAGE_NAME> chemdict_tool create components.cif.gz compounds.chemlib
+
+Run some script with an updated compound library from localhost:
+
+.. code-block:: bash
+
+  singularity exec -B <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> <IMAGE_NAME> pm my_script.py 
+
+Same as for the Docker, if you didn't meddle with the original Dockerfile, 
+<COMPLIB_DIR_CONTAINER> should be /usr/local/share/ost_complib. 
+<COMPLIB_DIR_LOCALHOST> is the directory that contains the compound lib with the 
+name compounds.chemlib that you created before. Make sure that everything works
+as expected by executing the exact same lines of Python code as described 
+in the Docker documentation: :ref:`docker_compound_lib`. 
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index ae3c842c641522624e55d208c51e6a146773a033..3a261b411ab249a578a79cf8c0760ef1deb68150 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Contributing
 ================================================================================
 
@@ -475,23 +491,19 @@ Hence, the :file:`CMakeLists.txt` of the :file:`doc` directory of a module is
 crucial. For documentation which does not relate to a particular module, the
 repository comes with a top-level :file:`doc` directory.
 
-While you should not spend to much time thinking about how to format
-documentation, here is a helpful list of standard formatters:
-http://sphinx-doc.org/en/stable/markup/inline.html
-
 If you write new functionality for |project|, or fix bugs, feel free to extend
 the :file:`CHANGELOG` file. It will be automatically pulled into the
 documentation.
 
 It is highly recommended to add code examples with your documentation. For that
-purpose, you should write a fully runnable script, which is to be placed in the
+purpose, you should write a fully runnable script which is to be placed in the
 :file:`doc/tests/scripts` directory. The script is to be runnable from within
 the :file:`doc/tests` directory as ``pm SCRIPTPATH`` and may use data stored in
 the :file:`doc/tests/data` directory. The script and any data needed by it, must
 then be referenced in the :file:`doc/tests/CMakeLists.txt` file. Afterwards,
-they can be included in the documentation using the
-`literalinclude <http://www.sphinx-doc.org/en/stable/markup/code.html#includes>`_
-directive. For instance, if you add a new example code :file:`loop_main.py`,
+they can be included in the documentation using the literalinclude
+directive.
+For instance, if you add a new example code :file:`loop_main.py`,
 you would add it in your module documentation as follows:
 
 .. code-block:: rest
diff --git a/doc/html/_sources/core/geometry.txt b/doc/html/_sources/core/geometry.txt
index 3d36b1bd13c2506eb51fad21c9bd61712a9ad5c8..1ac82fac9c1ecc650be29cd7a099f122ed7a6a5a 100644
--- a/doc/html/_sources/core/geometry.txt
+++ b/doc/html/_sources/core/geometry.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Geometry functions
 ================================================================================
 
@@ -53,7 +69,7 @@ Geometry functions
 .. function:: ConstructCBetaPos(n_pos, ca_pos, c_pos)
 
   Constructs position of C-beta atom given the positions of the backbone nitrogen,
-  C-alpha and c atoms.
+  C-alpha and C atoms.
 
   :param n_pos: Position of nitrogen atom
   :type n_pos:  :class:`~ost.geom.Vec3`
diff --git a/doc/html/_sources/core/graph_minimizer.txt b/doc/html/_sources/core/graph_minimizer.txt
index a1ddb9639f2816086ee62f64861e5e2e5b9dacb2..a38bca5895963caf439339bf5e57af6459d10847 100644
--- a/doc/html/_sources/core/graph_minimizer.txt
+++ b/doc/html/_sources/core/graph_minimizer.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Graph Minimizer
 ================================================================================
 
@@ -228,8 +244,3 @@ a set :math:`X=[x_1, x_2, ..., x_n]` that minimizes:
                         representing the single solutions minimizing
                         the overall energy function.
                         The second element is the according energy value.          
-
-
-.. [goldstein1994] Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.
-
-.. [leach1998] Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.
diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.txt
index 03d2cef127c61cb16af4680f5580673c34dae2e7..6684d1247ae7c8a53785187b4dd24a4b38737ac0 100644
--- a/doc/html/_sources/core/helper.txt
+++ b/doc/html/_sources/core/helper.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :mod:`~promod3.core.helper` - Shared Functionality For the Everything
 ================================================================================
 
diff --git a/doc/html/_sources/core/index.txt b/doc/html/_sources/core/index.txt
index 2af5fca9cace92deef375d4857a1c9b55f9ec0d5..91b0d9c39c77212b3747e804b1a12191f422a213 100644
--- a/doc/html/_sources/core/index.txt
+++ b/doc/html/_sources/core/index.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :mod:`~promod3.core` - ProMod3 Core Functionality
 ================================================================================
 
diff --git a/doc/html/_sources/core/pm3argparse.txt b/doc/html/_sources/core/pm3argparse.txt
index 927faf547e89cc54e508fa38abfbf18b39fb217b..f6a048252ec82ce7dabbb48da87a242e26d82aa4 100644
--- a/doc/html/_sources/core/pm3argparse.txt
+++ b/doc/html/_sources/core/pm3argparse.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :mod:`~promod3.core.pm3argparse` - Parsing Command Lines
 ================================================================================
 
diff --git a/doc/html/_sources/core/runtime_profiling.txt b/doc/html/_sources/core/runtime_profiling.txt
index 07c51ad5bb447b99aaf0335a1cd5f8e48d4a5c75..44bd8621a4ad7a5b77b185f5a9be069afbc9440c 100644
--- a/doc/html/_sources/core/runtime_profiling.txt
+++ b/doc/html/_sources/core/runtime_profiling.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Runtime profiling
 ================================================================================
 
diff --git a/doc/html/_sources/core/setcompoundschemlib.txt b/doc/html/_sources/core/setcompoundschemlib.txt
index fb0223432967ffc2ed53d542191c52fce4fb770b..2c6e660ffb8e1cf6d4d3df93a7f16fda04340724 100644
--- a/doc/html/_sources/core/setcompoundschemlib.txt
+++ b/doc/html/_sources/core/setcompoundschemlib.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :func:`~promod3.SetCompoundsChemlib`
 ================================================================================
 
diff --git a/doc/html/_sources/dev_setup.txt b/doc/html/_sources/dev_setup.txt
index 3b450accf0a5cb18ada95e2e7b1ab6d0e35799dd..91909c30154907dcbb269a4d5cb805ef6af9d1bf 100644
--- a/doc/html/_sources/dev_setup.txt
+++ b/doc/html/_sources/dev_setup.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 |project| Setup
 ================================================================================
 
diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.txt
index 3955c47c1cab44e3274e54919b0b0d949299c0f6..f15f85db820e896de015b614c871d0317030dc38 100644
--- a/doc/html/_sources/developers.txt
+++ b/doc/html/_sources/developers.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Documentation For Developers
 ===============================================================================
 
diff --git a/doc/html/_sources/gettingstarted.txt b/doc/html/_sources/gettingstarted.txt
index 9b2b8024b6cb6e7cd2e98aa10c3c86df5754f645..2bed4049fe4de07f7fafe0994c1867fd40f5be61 100644
--- a/doc/html/_sources/gettingstarted.txt
+++ b/doc/html/_sources/gettingstarted.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Getting Started
 ================================================================================
 
diff --git a/doc/html/_sources/index.txt b/doc/html/_sources/index.txt
index 0699c60545cfc1014f4753e6f9a6b8647e822cc7..74cb15e8f60d131996ed5d81cc1b0950b4abf718 100644
--- a/doc/html/_sources/index.txt
+++ b/doc/html/_sources/index.txt
@@ -1,28 +1,41 @@
-.. ProMod3 documentation master file, created by
-   sphinx-quickstart on Thu Oct 10 23:17:00 2013.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome To ProMod3's Documentation!
-===================================
-
-Contents:
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+ProMod3
+=======
+
+ProMod3 is a modelling engine based on the OpenStructure [biasini2013]_ 
+computational structural biology framework that can perform all steps required 
+to generate a protein model by homology. Its modular design aims at 
+implementing flexible modelling pipelines and fast prototyping of novel 
+algorithms.
+
+
+Documentation
+=============
 
 .. toctree::
-   :maxdepth: 2
+  :maxdepth: 2
 
-   Users <users>
-   Developers <developers>
+  Users <users>
 
 .. toctree::
-   :maxdepth: 1
-
-   changelog
-   
-
-Indices And Tables
-==================
+  :maxdepth: 1  
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+  Developers <developers>
+  License <license>
+  References <references>
+  Changelog <changelog>
diff --git a/doc/html/_sources/license.txt b/doc/html/_sources/license.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ff0971e35f8e7c9fdf99a1e6191409ae2a7e375
--- /dev/null
+++ b/doc/html/_sources/license.txt
@@ -0,0 +1,22 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+License
+=======
+
+
+
+.. literalinclude:: license.txt
diff --git a/doc/html/_sources/loop/all_atom.txt b/doc/html/_sources/loop/all_atom.txt
index b2f19a81997933e3ac1815f2a7759cb0f8b06613..eaeb294774c88c8f4c239fc493e2eb641ee7408f 100644
--- a/doc/html/_sources/loop/all_atom.txt
+++ b/doc/html/_sources/loop/all_atom.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Handling All Atom Positions
 ================================================================================
 
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.txt
index 15288fb3c55e5af3ff5a698fc8fc41a9223778a4..3acc2f8e1a2b74a97e559c050e71eb97c777802e 100644
--- a/doc/html/_sources/loop/backbone.txt
+++ b/doc/html/_sources/loop/backbone.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Representing Loops
 ================================================================================
 
@@ -143,7 +159,8 @@ The BackboneList class
     :type sequence:  :class:`str`
 
     :raises: :exc:`~exceptions.RuntimeError` if *sequence* contains a one letter
-             code which is not one of the 20 default amino acids.
+             code which is not one of the 20 default amino acids or size of 
+             *sequence* does not match.
 
 
   .. method:: Extract(from, to)
@@ -450,8 +467,8 @@ The BackboneList class
 
   .. method:: SetBackrub(index, primary_rot_angle, flanking_rot_angle_one, flanking_rot_angle_two)
 
-    Applies a backrub motion at residue defined by **index**. The first
-    rotation axis is defined by the CA positions from residues at
+    Applies a backrub motion [davis2006]_ at residue defined by **index**. 
+    The first rotation axis is defined by the CA positions from residues at
     **index** -1 and **index** +1. All atoms in between get rotated around this
     axis by **primary_rot_angle**. To restore the the hydrogen bond network
     of the two transformed oxygens, the backrub motion gets completed by
diff --git a/doc/html/_sources/loop/index.txt b/doc/html/_sources/loop/index.txt
index f60393092beaea6d8315036c82ee7dfb02b267d7..1b4199c068f6532d019465b011fb112ef140443f 100644
--- a/doc/html/_sources/loop/index.txt
+++ b/doc/html/_sources/loop/index.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :mod:`~promod3.loop` - Loop Handling
 ================================================================================
 
diff --git a/doc/html/_sources/loop/load_loop_objects.txt b/doc/html/_sources/loop/load_loop_objects.txt
index 00365ca9dcbf02c832bd8ea7c018b31f5e99a78f..a8410bea4fa9ec2f5a7ff3ac96ed26d06f707aea 100644
--- a/doc/html/_sources/loop/load_loop_objects.txt
+++ b/doc/html/_sources/loop/load_loop_objects.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Loading Precomputed Objects
 ================================================================================
 
@@ -10,7 +26,7 @@ Several data objects are used throughout the loop module.
 .. method:: LoadTorsionSampler(seed=0)
 
   Loads and returns a torsion sampler with an amino acid grouping
-  as defined by Solis & Rachovsky [1] that has been trained on 
+  as defined by [solis2006]_ that has been trained on 
   non-redundant protein structures.
 
   :param seed:          Seed for internal random number generator
@@ -24,7 +40,7 @@ Several data objects are used throughout the loop module.
 .. method:: LoadTorsionSamplerCoil(seed=0)
 
   Loads and returns a torsion sampler with an amino acid grouping
-  as defined by Solis & Rachovsky [1] that has been trained on coil
+  as defined by [solis2006]_ that has been trained on coil
   residues of  non-redundant protein structures.
 
   :param seed:          Seed for internal random number generator
@@ -38,7 +54,7 @@ Several data objects are used throughout the loop module.
 .. method:: LoadTorsionSamplerHelical(seed=0)
 
   Loads and returns a torsion sampler with an amino acid grouping
-  as defined by Solis & Rachovsky [1] that has been trained on helical
+  as defined by [solis2006]_ that has been trained on helical
   residues of  non-redundant protein structures.
 
   :param seed:          Seed for internal random number generator
@@ -52,7 +68,7 @@ Several data objects are used throughout the loop module.
 .. method:: LoadTorsionSamplerExtended(seed=0)
 
   Loads and returns a torsion sampler with an amino acid grouping
-  as defined by Solis & Rachovsky [1] that has been trained on extended
+  as defined by [solis2006]_ that has been trained on extended
   residues of  non-redundant protein structures.
 
   :param seed:          Seed for internal random number generator
@@ -63,28 +79,22 @@ Several data objects are used throughout the loop module.
   :rtype:               :class:`TorsionSampler`
 
 
-.. method:: LoadFragDB()
-
-  Loads and returns a FragDB containing fragments up to the length of 14,
-  therefore capable of bridging gaps up to the length of 12.
+.. method:: LoadStructureDB()
 
-  :returns:             The Fragment database
-  :rtype:               :class:`FragDB`
+  Loads and returns a structure db containing roughly 21000 chains form the
+  PDB with seqid redundancy cutoff of 60%
 
-.. method:: LoadStructureDB(load_frequencies=True)
+  :returns:             The structure db
+  :rtype:               :class:`StructureDB`
 
-  Loads and returns a structure db containing roughly 24000 chains form the
-  PDB with redundancy cutoff of 90%
 
-  :param load_frequencies: If True, the full database including profile
-                           information gets loaded (see
-                           :meth:`StructureDB.Load`).
-  :type load_frequencies:  :class:`bool`
+.. method:: LoadFragDB()
 
-  :returns:             The structure db
-  :rtype:               :class:`StructureDB`
-  
+  Loads and returns a FragDB containing fragments up to the length of 14,
+  therefore capable of bridging gaps up to the length of 12. The returned
+  databases contains the location of fragments in the :class:`StructureDB`
+  returned by :meth:`LoadStructureDB`.
 
-[1] A. D. Solis and S. Rackovsky. Improvement of statistical potentials and     
-    threading score functions using information maximization. 
-    Proteins, 62(4):892–908, Mar 2006.
+  :returns:             The Fragment database
+  :rtype:               :class:`FragDB`
+  
\ No newline at end of file
diff --git a/doc/html/_sources/loop/mm_system_creation.txt b/doc/html/_sources/loop/mm_system_creation.txt
index 7ad0c03a88e75d071685fbee47a3d5f88dcc6530..87b6fb05808a9d70e5e489638d087cd99d95c46c 100644
--- a/doc/html/_sources/loop/mm_system_creation.txt
+++ b/doc/html/_sources/loop/mm_system_creation.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Generate :mod:`ost.mol.mm` systems
 ================================================================================
 
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.txt
index a967d08a3823e6ae0eba26410ba7bdfa313ba358..b3089c7248bc40d5f4bd292125795b2edde82204 100644
--- a/doc/html/_sources/loop/structure_db.txt
+++ b/doc/html/_sources/loop/structure_db.txt
@@ -1,9 +1,25 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Structural Data
 ================================================================================
 
 .. currentmodule:: promod3.loop
 
-The structural database serves as a container for structural backbone and 
+The :class:`StructureDB` serves as a container for structural backbone and 
 sequence data. Custom accessor objects can be implemented that relate
 arbitrary features to structural data. Examples provided by ProMod3 include
 accession using matching stem geometry (see: :class:`FragDB`) or sequence
@@ -41,7 +57,7 @@ Defining Chains and Fragments
 .. class:: CoordInfo()
 
   The CoordInfo gets automatically generated when new chains are added to
-  the structural database. It contains internal information of how a 
+  a :class:`StructureDB`. It contains internal information of how a 
   connected stretch of residues is stored in the database.
 
   .. attribute:: id
@@ -68,17 +84,17 @@ Defining Chains and Fragments
 
     Residue number of first residue in the added stretch. The residue number
     is relative to the SEQRES provided in the input profile when adding the 
-    stuff to the structure db.
+    stuff to the structure db. (:class:`int`)
 
   .. attribute:: shift
 
     Translation from original coordinates that has been applied before storing
-    structural information in db.
+    structural information in db. (:class:`ost.geom.Vec3`)
 
 
 .. class:: FragmentInfo(chain_index, offset, length)
 
-  The FragmentInfo defines any fragment in the structural database. If you 
+  The FragmentInfo defines any fragment in the :class:`StructureDB`. If you 
   implement your own accessor object, thats the information you want to store.
 
   :param chain_index:   Fills :attr:`chain_index`
@@ -89,8 +105,8 @@ Defining Chains and Fragments
 
   .. attribute:: chain_index
     
-    The index of the chain (defined by :class:`CoordInfo`) in the structure db 
-    this particle belongs to. (:class:`int`)
+    The index of the chain (defined by :class:`CoordInfo`) in the 
+    :class:`StructureDB` this particle belongs to. (:class:`int`)
 
   .. attribute:: offset
 
@@ -127,7 +143,7 @@ database, you might want to consider two things:
   to backbone coordinates and sequence.
   If you want to store all data possible, use All. If you only want a subset,
   you can combine some of the datatypes with a bitwise or operation 
-  (see example script for StructureDB). One important note:
+  (see example script for :class:`StructureDB`). One important note:
   If you enable AAFrequenciesStruct, the actual information is not automatically
   assigned. Only the according memory is allocated and set to zero, the actual 
   information must be assigned manually (see example script again...).
@@ -138,8 +154,8 @@ database, you might want to consider two things:
 
 .. class:: StructureDB(data_to_store)
 
-  Generates an empty StructureDB that can be filled with content through
-  :func:`AddCoordinates`. The information extracted there is defined by
+  Generates an empty :class:`StructureDB` that can be filled with content 
+  through :func:`AddCoordinates`. The information extracted there is defined by
   *data_to_store*. Have a look at the :class:`StructureDBDataType` 
   documentation and at the example script...
 
@@ -263,7 +279,7 @@ database, you might want to consider two things:
 
   .. method:: GetCoordIdx(id, chain_name)
 
-    :returns: The StructureDB indices (in [0, :meth:`GetNumCoords`-1]) of 
+    :returns: The :class:`StructureDB` indices (in [0, :meth:`GetNumCoords`-1]) 
               of all coords (connected stretches) with matching 
               *id* / *chain_name*.
     :rtype:   :class:`list` of :class:`int`
@@ -281,7 +297,7 @@ database, you might want to consider two things:
               index *idx*.
     :rtype:   :class:`CoordInfo`
 
-    :param idx: The StructureDB index (in [0, :meth:`GetNumCoords`-1])
+    :param idx: The :class:`StructureDB` index (in [0, :meth:`GetNumCoords`-1])
     :type idx:  :class:`int`
 
 
@@ -379,7 +395,8 @@ database, you might want to consider two things:
   .. method:: GetSolventAccessibilitites(fragment)
 
     :returns: Solvent accessibility for each residue of *fragment* in square A
-              as calculated by dssp.
+              as calculated by :meth:`~ost.mol.alg.Accessibility` when adding
+              the structure to the database.
     :rtype:   :class:`list` of :class:`float`
 
     :param fragment: Fragment definition from which to extract the solvent
@@ -472,7 +489,7 @@ database, you might want to consider two things:
              to make sure that you have no close homologue in the database.
     :rtype:  :class:`StructureDB`
 
-    :param indices: StructureDB indices to be added to the sub database (in [0,
+    :param indices: Indices of chains to be added to the sub database (in [0,
                     :meth:`GetNumCoords`-1])
     :type indices:  :class:`list`
 
@@ -532,14 +549,16 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
 
   .. method:: GetAngularBinSize()
 
-    The size of the bins for the 4 angles describing the stem geometry and used to organize the fragments in the database.
+    The size of the bins for the 4 angles describing the stem geometry and used 
+    to organize the fragments in the database.
 
     :return:    The bin size in degrees
     :rtype:     :class:`int`
 
   .. method:: GetDistBinSize()
 
-    The size of the bins for the distance describing the stem geometry and used to organize the fragments in the database.
+    The size of the bins for the distance describing the stem geometry and used 
+    to organize the fragments in the database.
 
     :return:    The bin size
     :rtype:     :class:`float`
@@ -547,8 +566,13 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
 
   .. method:: AddFragments(fragment_length, rmsd_cutoff, structure_db)
 
-    Iterates over all fragments of length **fragment_length** in the given structural database and adds them to the fragment database. Fragments will be skipped if there is already a fragment in the database that has an RMSD to the one being added smaller than **rmsd_cutoff**.
-    As the fragments are added they are organized in bins described by their length and the geometry of their N and C stem.
+    Iterates over all fragments of length **fragment_length** in 
+    **structure_db** and adds them to the fragment database. 
+    Fragments will be skipped if there is already a fragment in the database 
+    that has an RMSD smaller than **rmsd_cutoff**, where RMSD is calculated 
+    upon superposing the stem residues.
+    As the fragments are added they are organized in bins described by their 
+    length and the geometry of their N and C stem.
 
     :param fragment_length:    The length of the fragments that should be added to the databse
     :param rmsd_cutoff:        The minimal RMSD between two fragments in the fragment database
@@ -560,7 +584,7 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
 
   .. method:: PrintStatistics()
 
-    Prints statistics about the fragment databse, notably:
+    Prints statistics about the fragment database, notably:
 
     1. the number of different stem groups (number of bins used to group the
        fragments according to the geometry of their stem residues)
@@ -598,12 +622,12 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
     :param loop_length:   The length of the fragments
     :type loop_length:    :class:`int`
 
-    :returns: True if fragments of given length exist. This function is quick.
+    :returns: True if fragments of given length exist.
     :rtype:   :class:`bool`
 
   .. method:: MaxFragLength()
 
-    :returns: Maximal fragment length contained in db. This function is quick.
+    :returns: Maximal fragment length contained in db.
     :rtype:   :class:`int`
 
   .. method:: SearchDB(n_stem, c_stem, frag_size, extra_bins=0)
@@ -635,7 +659,7 @@ In some cases you might want to use the :class:`StructureDB` to search
 for fragments that possibly represent the structural conformation of interest.
 The :class:`Fragger` searches a :class:`StructureDB` for n fragments, 
 that maximize a certain score and gathers a set of fragments with a guaranteed 
-structural diversity based on an rmsd_threshold. You can use the :class:`Fragger`
+structural diversity based on an rmsd threshold. You can use the :class:`Fragger`
 wrapped in a full fletched pipeline implemented in 
 :class:`~promod3.modelling.FraggerHandle` or search for fragments from scratch 
 using an arbitrary linear combination of scores:
@@ -882,7 +906,7 @@ The PsipredPrediction class
 
 .. class:: PsipredPrediction
 
-  A container for the secondary structure prediction by Psipred.
+  A container for the secondary structure prediction by PSIPRED [Jones1999]_.
 
   .. method:: PsipredPrediction()
     
@@ -974,11 +998,3 @@ The PsipredPrediction class
   .. method:: __len__()
 
     :returns:           Number of elements in container
-
-
-
-.. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
-.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.
-.. [zhou2005] Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.
-.. [Jones1999] Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202. 
-.. [kabsch1983] Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.
diff --git a/doc/html/_sources/loop/torsion_sampler.txt b/doc/html/_sources/loop/torsion_sampler.txt
index 0962c3563d62638c5948f7d6f08189b2fcf6a95b..8344079a5065f12c19e844f50be70636032ba365 100644
--- a/doc/html/_sources/loop/torsion_sampler.txt
+++ b/doc/html/_sources/loop/torsion_sampler.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Sampling Dihedral Angles
 ================================================================================
 
diff --git a/doc/html/_sources/modelling/algorithms.txt b/doc/html/_sources/modelling/algorithms.txt
index 7ff5ae3a33e08ccccdf6d98f87abe2748e1d0d19..51357bc0615a49e58f2ef12f3efad67eeb3b003d 100644
--- a/doc/html/_sources/modelling/algorithms.txt
+++ b/doc/html/_sources/modelling/algorithms.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Modelling Algorithms
 ================================================================================
 
diff --git a/doc/html/_sources/modelling/gap_handling.txt b/doc/html/_sources/modelling/gap_handling.txt
index e939f9f60fa779b43bfdb196e0649ebd28306a08..b70d39a57558559a9ee4f6240384ffdbeb4df34c 100644
--- a/doc/html/_sources/modelling/gap_handling.txt
+++ b/doc/html/_sources/modelling/gap_handling.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Handling Gaps
 ================================================================================
 
diff --git a/doc/html/_sources/modelling/index.txt b/doc/html/_sources/modelling/index.txt
index 27ed61013a17190ebef7f0afb0027241c0e19294..ce9be313f8c26c747a5e1d711c9bf44751ac8587 100644
--- a/doc/html/_sources/modelling/index.txt
+++ b/doc/html/_sources/modelling/index.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :mod:`~promod3.modelling` - Protein Modelling
 ================================================================================
 
diff --git a/doc/html/_sources/modelling/loop_candidates.txt b/doc/html/_sources/modelling/loop_candidates.txt
index d0711c5a7c89292a61e3f1547ed28af62841382b..927107a0ddaa78b2bb6efe78b80c0f1dbc5aae1e 100644
--- a/doc/html/_sources/modelling/loop_candidates.txt
+++ b/doc/html/_sources/modelling/loop_candidates.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Handling Loop Candidates
 ================================================================================
 
diff --git a/doc/html/_sources/modelling/loop_closing.txt b/doc/html/_sources/modelling/loop_closing.txt
index 7ec7230b20a4e32fd9cc1f15a9e84ea7b549c113..21b842f5d1e25b00dc2f2cb863bf8124ccfb8f81 100644
--- a/doc/html/_sources/modelling/loop_closing.txt
+++ b/doc/html/_sources/modelling/loop_closing.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Fitting Loops Into Gaps
 ================================================================================
 
@@ -7,7 +23,7 @@ Loops often need to undergo conformational changes to fit into gaps defined by
 stem residues. |project| implements two algorithms performing this task:
 
   * Cyclic coordinate descent (CCD) [canutescu2003]_
-  * Kinematic closure (KIC) [mandell2009]_
+  * Kinematic closure (KIC) [coutsias2005]_
 
 In case of small gaps or small issues in the loop you might also consider the
 :class:`BackboneRelaxer`.
@@ -374,8 +390,4 @@ Example usage:
     :rtype:  :class:`~promod3.loop.MmSystemCreator`
 
 
-.. rubric:: Citations
-
-.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.
 
-.. [mandell2009] Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.
diff --git a/doc/html/_sources/modelling/model_checking.txt b/doc/html/_sources/modelling/model_checking.txt
index 97d7f69a83735d2757ede0afee224f181afdd6d5..03763e178971929ce13573f5ac8d72dc6624434d 100644
--- a/doc/html/_sources/modelling/model_checking.txt
+++ b/doc/html/_sources/modelling/model_checking.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Model Checking
 ================================================================================
 
diff --git a/doc/html/_sources/modelling/monte_carlo.txt b/doc/html/_sources/modelling/monte_carlo.txt
index 56e572a8788749bde35c415893a964126c5e67b9..1cb924b406ab017598f909d34872c0394697cb72 100644
--- a/doc/html/_sources/modelling/monte_carlo.txt
+++ b/doc/html/_sources/modelling/monte_carlo.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Generating Loops De Novo
 ================================================================================
 
@@ -21,46 +37,7 @@ Carlo sampling to the N-terminal part of crambin:
 
 .. literalinclude:: ../../../tests/doc/scripts/modelling_monte_carlo.py
 
-.. method:: SampleMonteCarlo(sampler, closer, scorer, cooler, steps,\
-                             bb_list, initialize=True, seed=0,\
-                             lowest_energy_conformation=True)
-
-  A convenient function to perform Monte Carlo sampling using a simulated
-  annealing scheme. In every iteration, a new loop conformation gets proposed by
-  the provided *sampler* and closed by the *closer*. Upon scoring, this new
-  conformation gets accepted/rejected using a metropolis criterion based on the
-  temperature given by the *cooler* 
-  => acceptance probability: exp(-delta_score/T).
-  The result is stored in *bb_list* and is either the lowest energy conformation
-  ever encountered or the last accepted proposal.
-
-  :param sampler:       Sampler object capable of initializing and altering
-                        conformations.
-  :param closer:        Closer object to adapt a new conformation to
-                        the environment.
-  :param scorer:        Scorer object to score new loop conformations.
-  :param cooler:        Cooler object to control the temperature of the 
-                        Monte Carlo trajectory.
-  :param steps:         Number of Monte Carlo iterations to be performed.
-  :param bb_list:       The chosen conformation gets stored here.
-  :param initialize:    Whether a new bb_list should be generated as starting
-                        point, based on the samplers Initialize function.
-                        The input *bb_list* gets used otherwise.
-  :param seed:          Seed for internal random number generator.
-  :param lowest_energy_conformation:  If True, we choose the lowest scoring
-                                      conformation of the trajectory. Otherwise,
-                                      the last accepted proposal.
-
-  :type sampler:        :ref:`mc-sampler-object`
-  :type closer:         :ref:`mc-closer-object`
-  :type scorer:         :ref:`mc-scorer-object`
-  :type cooler:         :ref:`mc-cooler-object`
-  :type steps:          :class:`int`
-  :type bb_list:        :class:`~promod3.loop.BackboneList`
-  :type initialize:     :class:`bool`
-  :type seed:           :class:`int`
-  :type lowest_energy_conformation: :class:`bool`
-
+.. autofunction:: SampleMonteCarlo
 
 .. _mc-sampler-object:
 
@@ -69,7 +46,46 @@ Sampler Object
 
 The sampler objects can be used to generate initial conformations and
 propose new conformations for a sequence of interest. They build the basis
-for any Monte Carlo sampling pipeline.
+for any Monte Carlo sampling pipeline. You can either use one of the 
+provided samplers or any object that implements the functionality of
+:class:`SamplerBase`.
+
+
+.. class:: SamplerBase
+
+  Abstract base class defining the functions that must be implemented by any 
+  sampler.
+
+  .. method:: Initialize(bb_list)
+
+    Supposed to initialize structural information from scratch. The sequence
+    of the generated :class:`promod3.loop.BackboneList` is taken from *bb_list*.
+
+    :param bb_list:     Passed by reference, so the resulting 
+                        :class:`promod3.loop.BackboneList` is assigned to this 
+                        parameter. Sequence / length stay the same.
+
+    :type bb_list:      :class:`promod3.loop.BackboneList`
+
+    :returns:           None
+
+  .. method:: ProposeStep(actual_positions, proposed_positions)
+
+    Takes current positions and proposes a new conformation. There is no 
+    guarantee on maintining any special RT state. The :ref:`mc-closer-object`
+    is supposed to sort that out. 
+
+    :param actual_positions: Starting point, must not change when calling this
+                             function.
+    :param proposed_positions: Passed by reference, so the resulting 
+                               :class:`promod3.loop.BackboneList` is assigned to 
+                               this parameter.
+
+    :type actual_positions: :class:`promod3.loop.BackboneList`
+    :type proposed_positions: :class:`promod3.loop.BackboneList`
+
+    :returns:           None
+
 
 .. class:: PhiPsiSampler(sequence, torsion_sampler, n_stem_phi=-1.0472,\
                          c_stem_psi=-0.78540, prev_aa='A', next_aa='A', seed=0)
@@ -237,9 +253,9 @@ for any Monte Carlo sampling pipeline.
   :param seed:          Seed for the internal random number generators
 
   :type sequence:       :class:`str`
-  :type fraggers:       :class:`str`
+  :type fraggers:       :class:`list`
   :type init_bb_list:   :class:`~promod3.loop.BackboneList`
-  :type samplint_start_index: :class:`int`
+  :type sampling_start_index: :class:`int`
   :type init_fragments: :class:`int`
   :type seed:           :class:`int`
 
@@ -276,7 +292,32 @@ After the proposal of new conformations by the sampler objects, the
 conformations typically have to undergo some structural changes, so they
 fit to a given environment. This can either be structural changes, that
 the stems of the sampled conformation overlap with given stem residues or
-or simple stem superposition in case of terminal sampling.
+or simple stem superposition in case of terminal sampling. You can either
+use any of the provided closers or any object that implements the 
+functionality of :class:`CloserBase`.
+
+.. class:: CloserBase
+
+  Abstract base class defining the functions that must be implemented by any 
+  closer.
+
+  .. method:: Close(actual_positions, closed_positions)
+
+    Takes current positions and proposes a new conformation that fits to a
+    given environment.
+
+    :param actual_positions: Starting point, must not change when calling this
+                             function.
+    :param closed_positions: Passed by reference, so the resulting 
+                             :class:`promod3.loop.BackboneList` is assigned to 
+                             this parameter.
+
+    :type actual_positions: :class:`promod3.loop.BackboneList`
+    :type closed_positions: :class:`promod3.loop.BackboneList`
+
+    :returns:           Whether closing procedure was successful
+    :rtype:             :class:`bool`
+
 
 .. class:: CCDCloser(n_stem, c_stem, sequence, torsion_sampler, seed)
 
@@ -305,7 +346,7 @@ or simple stem superposition in case of terminal sampling.
                          of :class:`~promod3.loop.TorsionSampler`
   :type seed:           :class:`int`
 
-  .. method:: Close(actual_positions,closed_positions)
+  .. method:: Close(actual_positions, closed_positions)
     
     :param actual_positions: Conformation to be closed.
     :param closed_positions: Closed conformation gets stored in here.
@@ -320,7 +361,8 @@ or simple stem superposition in case of terminal sampling.
 
   The DirtyCCDCloser applies the CCD algorithm to the sampled conformation 
   to enforce the match between the conformations stem residue and
-  the stems given by the closer. 
+  the stems given by the closer. There is no check for reasonable backbone
+  dihedral angles as it is the case for the :class:`CCDCloser`.
 
   :param n_stem:        Defining stem positions the closed conformation
                         should adapt.
@@ -331,7 +373,7 @@ or simple stem superposition in case of terminal sampling.
   :type n_stem:         :class:`ost.mol.ResidueHandle`
   :type c_stem:         :class:`ost.mol.ResidueHandle`
 
-  .. method:: Close(actual_positions,closed_positions)
+  .. method:: Close(actual_positions, closed_positions)
     
     :param actual_positions: Conformation to be closed.
     :param closed_positions: Closed conformation gets stored in here.
@@ -355,10 +397,10 @@ or simple stem superposition in case of terminal sampling.
   :param seed:          Seed for internal random generators.
 
   :type n_stem:         :class:`ost.mol.ResidueHandle`
-  :type n_stem:         :class:`ost.mol.ResidueHandle`
+  :type c_stem:         :class:`ost.mol.ResidueHandle`
   :type seed:           :class:`int`
 
-  .. method:: Close(actual_positions,closed_positions)
+  .. method:: Close(actual_positions, closed_positions)
     
     :param actual_positions: Conformation to be closed.
     :param closed_positions: Closed conformation gets stored in here.
@@ -371,26 +413,60 @@ or simple stem superposition in case of terminal sampling.
 
 .. class:: NTerminalCloser(c_stem)
 
-  The NTerminalCloser simply takes the conformation and closes by superposing
-  the c_stem with the desired positions.
+  The :class:`NTerminalCloser` simply takes the conformation and closes by 
+  superposing the c_stem with the desired positions.
 
   :param c_stem:        Defining stem positions the closed conformation should
                         adapt.
   :type c_stem:         :class:`ost.mol.ResidueHandle`
 
-  :returns:             Whether closing was successful
+
+  .. method:: Close(actual_positions, closed_positions)
+
+    :param actual_positions: Conformation to be closed (or in this case
+                             transformed in space).
+    :param closed_positions: Closed (transformed) conformation gets stored in 
+                             here.
+
+    :type actual_positions: :class:`~promod3.loop.BackboneList`
+    :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+    :returns:           Whether closing was successful
 
 
 .. class:: CTerminalCloser(n_stem)
 
-  The CTerminalCloser simply takes the conformation and closes by superposing
-  the n_stem with the desired positions.
+  The :class:`CTerminalCloser` simply takes the conformation and closes by 
+  superposing the n_stem with the desired positions.
 
   :param n_stem:        Defining stem positions the closed conformation should
                         adapt.
   :type n_stem:         :class:`ost.mol.ResidueHandle`
 
-  :returns:             Whether closing was successful
+  .. method:: Close(actual_positions,closed_positions)
+
+    :param actual_positions: Conformation to be closed (or in this case
+                             transformed in space).
+    :param closed_positions: Closed (transformed) conformation gets stored in 
+                             here.
+
+    :type actual_positions: :class:`~promod3.loop.BackboneList`
+    :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+    :returns:           Whether closing was successful
+
+
+.. class:: DeNovoCloser
+
+  In case of sampling a full stretch, you dont have external constraints. The 
+  closer has a rather boring job in this case.
+
+  .. method:: Close(actual_positions,closed_positions)
+
+    Does absolutely nothing, except copying over the coordinates from
+    *actual_positions* to *closed_positions* and return true.
+
+
 
         
 .. _mc-scorer-object:
@@ -399,10 +475,27 @@ Scorer Object
 --------------------------------------------------------------------------------
 
 The scorer asses a proposed conformation and are intended to return a pseudo
-energy, the lower the better.
+energy, the lower the better. You can either use the provided scorer or any
+object implementing the functionality defined in :class:`ScorerBase`. 
+
+
+.. class:: ScorerBase
 
+  Abstract base class defining the functions that must be implemented by any 
+  scorer.
+
+  .. method:: GetScore(bb_list)
 
-.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,
+    Takes coordinates and spits out a score given some internal structural 
+    environment.
+
+    :param bb_list:     Coordinates to be scored     
+    :type bb_list: :class:`promod3.loop.BackboneList`
+
+    :returns:           The score
+    :rtype:             :class:`float`
+
+.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,\
                         chain_idx, linear_weights)
 
   The LinearScorer allows to combine the scores available from
@@ -450,13 +543,31 @@ Cooler Object
 
 The cooler objects control the temperature of the Monte Carlo trajectory.
 They're intended to deliver steadily decreasing temperatures with calls
-to their GetTemperature function.
+to their GetTemperature function. You can either use the provided cooler
+or any object implementing the functionality defined in 
+:class:`CoolerBase`.
+
+.. class:: CoolerBase
+
+  Abstract base class defining the functions that must be implemented by any 
+  cooler.
+
+  .. method:: GetTemperature()
+
+    :returns:           The Temperature
+    :rtype:             :class:`float`
+
+  .. method:: Reset()
+
+    Resets to original state, so a new Monte Carlo trajectory can be generated
+
 
 .. class:: ExponentialCooler(change_frequency, start_temperature, cooling_factor)
 
   The exponential cooler starts with a given *start_temperature* and counts the
-  calls to its GetTemperature function. According to the *change_frequency*, 
-  the returned temperature gets multiplied by the *cooling_factor*.
+  calls to its :meth:`GetTemperature` function. According to the 
+  *change_frequency*, the returned temperature gets multiplied by the 
+  *cooling_factor*.
 
   :param change_frequency: Frequency to change temperature
   :param start_temperature: temperature to start with
@@ -472,4 +583,5 @@ to their GetTemperature function.
 
   .. method:: Reset()
 
-    Sets current temperature back to *start_temperature*
+    Sets current temperature back to *start_temperature* and the 
+    internal counter to 0
diff --git a/doc/html/_sources/modelling/pipeline.txt b/doc/html/_sources/modelling/pipeline.txt
index 175b65c5d6554d15f76076e3bd3c530595a7cf64..54d86037d316ed87434fea7ae1cca2e3a2ae11d0 100644
--- a/doc/html/_sources/modelling/pipeline.txt
+++ b/doc/html/_sources/modelling/pipeline.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Modelling Pipeline
 ================================================================================
 
diff --git a/doc/html/_sources/modelling/sidechain_reconstruction.txt b/doc/html/_sources/modelling/sidechain_reconstruction.txt
index 72e93a0a96a3f793542c32062748295655c010b7..f6a076c6b780c809d729bf52882d7e7e1fc04cb0 100644
--- a/doc/html/_sources/modelling/sidechain_reconstruction.txt
+++ b/doc/html/_sources/modelling/sidechain_reconstruction.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Sidechain Reconstruction
 ================================================================================
 
@@ -144,9 +160,9 @@ SidechainReconstructor Class
     :param use_frm: If True, use flexible rotamer model, else rigid.
     :type use_frm:  :class:`bool`
     :param use_bbdep_lib: If True, use default backbone dependent rot. library
-                          (:meth:`Dunbrack <LoadDunbrackLib>`), else use
+                          (:meth:`LoadBBDepLib`), else use
                           backbone independent one
-                          (:meth:`Penultimate <LoadPenultimateLib>`).
+                          (:meth:`LoadLib`).
     :type use_bbdep_lib:  :class:`bool`
     :param rotamer_library: Custom rotamer library to be used.
     :type rotamer_library:  :class:`BBDepRotamerLib` / :class:`RotamerLib`
diff --git a/doc/html/_sources/portableIO.txt b/doc/html/_sources/portableIO.txt
index d7122a208d30e34f4f4e47ce1e0890fe0f1454ef..a548e3c86400f7e09a9c7cc65c9c2fd7de19e8ce 100644
--- a/doc/html/_sources/portableIO.txt
+++ b/doc/html/_sources/portableIO.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 .. _portableIO:
 
 Using Binary Files In |project|
@@ -387,9 +403,9 @@ The following binary files are currently in |project|:
 
 - module ``sidechain``:
 
-  - :file:`2010DunbrackLib.dat`
+  - :file:`bb_dep_lib.dat`
     (:class:`~promod3.sidechain.BBDepRotamerLib`)
-  - :file:`PenultimateLib.dat`
+  - :file:`lib.dat`
     (:class:`~promod3.sidechain.RotamerLib`)
 
 During the ``make`` process, portable versions of the files (stored in the
diff --git a/doc/html/_sources/references.txt b/doc/html/_sources/references.txt
new file mode 100644
index 0000000000000000000000000000000000000000..927de6ddbad6c032f0f760c17384e977d1ed31e9
--- /dev/null
+++ b/doc/html/_sources/references.txt
@@ -0,0 +1,82 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
+References
+==========
+
+.. [biasini2013] Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J, 
+                 Johner N, Schenk AD, Philippsen A and Schwede T (2013). 
+                 OpenStructure: an integrated software framework for 
+                 computational structural biology. Acta Cryst.
+
+.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). 
+                   Cyclic coordinate descent: A robotics algorithm for protein 
+                   loop closure. Protein Sci.
+
+.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). 
+                    A graph-theory algorithm for rapid protein side-chain 
+                    prediction. Protein Sci.
+
+.. [coutsias2005] Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+                  Resultants and loop closure. International Journal of Quantum 
+                  Chemistry. 
+
+.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). 
+                     Residue depth: a novel parameter for the analysis of 
+                     protein structure and stability. Structure.
+
+.. [davis2006] Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+               The backrub motion: how protein backbone shrugs when a sidechain 
+               dances. Structure.
+
+.. [goldstein1994] Goldstein RF (1994). 
+                   Efficient rotamer elimination applied to protein side-chains 
+                   and related spin glasses. Biophys J.
+
+.. [Jones1999] Jones DT (1999). 
+               Protein secondary structure prediction based on position-specific 
+               scoring matrices. J. Mol. Biol. 
+
+.. [kabsch1983] Kabsch W, Sander C (1983). 
+                Dictionary of protein secondary structure: pattern recognition of 
+                hydrogen-bonded and geometrical features. Biopolymers.
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). 
+                Improved prediction of protein side-chain conformations with 
+                SCWRL4. Proteins.
+
+.. [leach1998] Leach AR, Lemon AP (1998). 
+               Exploring the conformational space of protein side chains using 
+               dead-end elimination and the A* algorithm. Proteins.
+
+.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). 
+                    A smoothed backbone-dependent rotamer library for proteins 
+                    derived from adaptive kernel density estimates and 
+                    regressions. Structure.
+
+.. [soding2005] Söding J (2005). 
+                Protein homology detection by HMM-HMM comparison. 
+                Bioinformatics.
+
+.. [solis2006] Solis AD, Rackovsky S (2006). Improvement of statistical 
+               potentials and threading score functions using information 
+               maximization. Proteins. 
+
+.. [zhou2005] Zhou H, Zhou Y (2005). 
+              Fold Recognition by Combining Sequence Profiles Derived From 
+              Evolution and From Depth-Dependent Structural Alignment of 
+              Fragments. Proteins.
+
diff --git a/doc/html/_sources/scoring/all_atom_scorers.txt b/doc/html/_sources/scoring/all_atom_scorers.txt
index 0a1b39b1613522dd671df0b73b32e98dcaac55eb..bcb3cdc43ed0e78becf8a07467928571d60bf604 100644
--- a/doc/html/_sources/scoring/all_atom_scorers.txt
+++ b/doc/html/_sources/scoring/all_atom_scorers.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 All Atom Scorers
 ================================================================================
 
diff --git a/doc/html/_sources/scoring/backbone_score_env.txt b/doc/html/_sources/scoring/backbone_score_env.txt
index 25980a4d34ba90890e7686c87838fa8dcd0f1679..11ea33ce9e947a60b120cc82e658231249e48082 100644
--- a/doc/html/_sources/scoring/backbone_score_env.txt
+++ b/doc/html/_sources/scoring/backbone_score_env.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Backbone Score Environment
 ================================================================================
 
@@ -187,9 +203,9 @@ Pairwise function classes
 
   Inherits all functionality of :class:`PairwiseFunction`.
   Defines a constraint function. The score for a distance between *min_dist* and
-  *max_dist* is determined by liner interpolation assuming the first and last 
-  value exactly lying on *min_dist* ang *max_dist*. For distances outside the 
-  range defined by *min_dist* and *max_dist*, the score is 0.0.
+  *max_dist* is determined by linear interpolation assuming the first and last 
+  value exactly lying on *min_dist* and *max_dist*. For distances outside the 
+  range defined by *min_dist* and *max_dist*, the returned score is 0.0.
 
   :param min_dist:    Minimal distance to be considered
   :param max_dist:    Maximal distance to be considered
@@ -200,9 +216,6 @@ Pairwise function classes
   :type max_dist:     :class:`float`
   :type values:       :class:`list` of :class:`float`
 
-
-  :returns:           Index of added constraint definition
-
   :raises: :exc:`~exceptions.RuntimeError` if *min_dist* >= *max_dist* or when
            *min_dist* or *max_dist* are negative or when *values* contains no
            elements
@@ -211,7 +224,7 @@ Pairwise function classes
 
   Inherits all functionality of :class:`PairwiseFunction`.
   Defines a simple contact function. The score value is *score* if
-  distance < *max_dist* and 0 otherwise.
+  distance < *max_dist* and 0.0 otherwise.
 
   :param max_dist:    Maximal distance to be in contact
   :param score:       Value that gets returned if in contact
diff --git a/doc/html/_sources/scoring/backbone_scorers.txt b/doc/html/_sources/scoring/backbone_scorers.txt
index 55a07ec77cc2e0ebc0b619c90c4ebaf824e9531a..68a45cab6d736cc1963c245bb0c5cf1e0e140e08 100644
--- a/doc/html/_sources/scoring/backbone_scorers.txt
+++ b/doc/html/_sources/scoring/backbone_scorers.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Backbone Scorers
 ================================================================================
 
@@ -249,10 +265,10 @@ CBetaScorer class
   The scorer needs to be initialized either by loading a predefined scorer (e.g.
   :func:`LoadCBetaScorer`) or by setting all energies (see :meth:`SetEnergy`).
 
-  :param cutoff: Radius in which other cbeta atoms are counted.
+  :param cutoff: Radius in which other cbeta atoms are considered.
   :type cutoff:  :class:`float`
   :param bins: Number of equally sized bins to discretize distances (range
-               of [0,*cutoff*]).
+               of [0, *cutoff*]).
   :type bins:  :class:`int`
   :param seq_sep: Minimal separation in sequence two cbeta atoms must have to
                   be considered.
diff --git a/doc/html/_sources/scoring/index.txt b/doc/html/_sources/scoring/index.txt
index 983d6b5587c5f70fc9088e6bdac386567fef16c3..d21154f06951fcdb6bbbe1c11f329f69f24bd57c 100644
--- a/doc/html/_sources/scoring/index.txt
+++ b/doc/html/_sources/scoring/index.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :mod:`~promod3.scoring` - Loop Scoring
 ================================================================================
 
@@ -7,7 +23,11 @@
 .. currentmodule:: promod3.scoring
 
 Tools and algorithms to score loops. The scoring system is split between an
-environment which contains model-specific data and scorers which evaluate loops.
+environment and scorers.
+Several scorers can be attached to the same environment containing the
+actual structural data of the current modelling problem.
+The environment is updated as the modelling proceeds and manages efficient
+spatial lookups to be used by the attached scorers.
 
 In this example, we load a structure, setup a score environment, link a few
 scorers to it and finally score some loops:
diff --git a/doc/html/_sources/scoring/other_scoring_functions.txt b/doc/html/_sources/scoring/other_scoring_functions.txt
index f505232e026655cdebf83d068269e805eb99fedd..80487531f986d6004e6764b8a8575be11b8bf6de 100644
--- a/doc/html/_sources/scoring/other_scoring_functions.txt
+++ b/doc/html/_sources/scoring/other_scoring_functions.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Other Scoring Functions
 ================================================================================
 
@@ -53,4 +69,3 @@ Scoring Functions from SCWRL3
 
 
 
-.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/doc/html/_sources/sidechain/disulfid.txt b/doc/html/_sources/sidechain/disulfid.txt
index 1cee3075640728b8c205c8bf9d9ff0128d6eeb9d..d078a6c5a65e20f2b4fc682f26a1e5b7853d6a92 100644
--- a/doc/html/_sources/sidechain/disulfid.txt
+++ b/doc/html/_sources/sidechain/disulfid.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Disulfid Bond Evaluation
 ================================================================================
 
diff --git a/doc/html/_sources/sidechain/frame.txt b/doc/html/_sources/sidechain/frame.txt
index d5e355915971ca7a0cd140036d366d9812f777e3..d8365f4a5316d2efebaaaafb50a87238b1b3ac2d 100644
--- a/doc/html/_sources/sidechain/frame.txt
+++ b/doc/html/_sources/sidechain/frame.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Frame
 ================================================================================
 
diff --git a/doc/html/_sources/sidechain/graph.txt b/doc/html/_sources/sidechain/graph.txt
index 118c72eabb98ed98acdc13eafcb6f3af4bbbb867..44606b2766a57c90bfa7f74d86cfc720ddf4ed71 100644
--- a/doc/html/_sources/sidechain/graph.txt
+++ b/doc/html/_sources/sidechain/graph.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Rotamer Graph
 ================================================================================
 
@@ -6,7 +22,7 @@ Rotamer Graph
 Once having a frame representing the rigid parts, the internal energies in
 rotamer groups can be calculated. To come to a final solution of the sidechain
 modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements a
+overall solution has to be found. ProMod3 implements a
 :class:`promod3.core.GraphMinimizer` that allows to find solutions using
 tree decomposition, A* and Monte Carlo algorithms.
 
diff --git a/doc/html/_sources/sidechain/index.txt b/doc/html/_sources/sidechain/index.txt
index c0a24dce4ca854bcd16c85d29094dcd1ff799f71..aeac7212ce7a9232b81c95d2178cb32d07ff6595 100644
--- a/doc/html/_sources/sidechain/index.txt
+++ b/doc/html/_sources/sidechain/index.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 :mod:`~promod3.sidechain` - Sidechain Modelling
 ================================================================================
 
@@ -9,7 +25,7 @@
 Tools and algorithms to model sidechains given backbone coordinates. The full
 module is heavily based on SCWRL4 [krivov2009]_ . The according paper describes
 the modelling of sidechains using two different rotamer models. A rigid model,
-as well as a flexible model. Both models are implemented in PROMOD3 and can be
+as well as a flexible model. Both models are implemented in ProMod3 and can be
 applied in flexible ways.
 
 The following code fragment shows an example of a basic sidechain reconstruction
@@ -37,4 +53,3 @@ Contents:
    subrotamer_optimizer
 
 
-.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.
diff --git a/doc/html/_sources/sidechain/loading.txt b/doc/html/_sources/sidechain/loading.txt
index b795abc601ad9c617895d86a63316a14623727bf..83e9390b16d8b8726c23a58f79dfdbf0eff22790 100644
--- a/doc/html/_sources/sidechain/loading.txt
+++ b/doc/html/_sources/sidechain/loading.txt
@@ -1,32 +1,50 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Loading Rotamer Libraries
 ================================================================================
 
 .. currentmodule:: promod3.sidechain
 
-Since the PROMOD3 sidechain modelling algorithms are mainly designed after the 
-work of the Dunbrack lab [krivov2009]_ , their backbone dependent rotamer 
-library is probably the way to go. There exists a binary version of their 
-2010 libary [shapovalov2011]_ , that can
-directly be loaded. As an alternative, there is also a binary file containing
-the backbone independent Penultimate library [lovell2000]_ .
+There are several rotamer libraries that can be used in ProMod3. ProMod3
+is optimized for the use with backbone dependent rotamer libraries such
+as the 2010 library provided by the Dunbrack lab [shapovalov2011]_. 
+You can request a licence `here <http://dunbrack.fccc.edu/bbdep2010/>`_
+and generate such a library as described in 
+extras/data_generation/rotamer_library/README. Alternatively, ProMod3
+provides its own backbone dependent or backbone independent libraries 
+that can be loaded with :meth:`LoadBBDepLib` / :meth:`LoadLib`.
 
-.. method:: LoadDunbrackLib()
+.. method:: LoadBBDepLib()
 
-  Loads the 2010 backbone dependent rotamer library from the dunbrack lab.
-  The library has been generated using the ReadDunbrackFile function
-  using the file with smoothing factor 5 and nonrotameric dihedrals
-  sampled in 20 degree steps.
+  A backbone dependent rotamer library shipped with ProMod3. You can find
+  details on how it is created in extras/data_generation/rotamer_library/README.
+  All scripts to build it are in the same directory as the README file and
+  build the basis for custom versions.
 
-  :returns:             The requested library
+  :returns:             The requested Library
   :rtype:               :class:`BBDepRotamerLib`
 
 
-.. method:: LoadPenultimateLib()
+.. method:: LoadLib()
 
-  Loads the backbone independent Penultimate library. The values for the dihedral
-  angles are directly extracted from the publication without considering the
-  probabilities specific for helices/sheets. Due to no assigned standard
-  deviations, the flexible rotamer model won't produce meaningful results.
+  A backbone independent rotamer library shipped with ProMod3. You can find
+  details on how it is created in extras/data_generation/rotamer_library/README.
+  All scripts to build it are in the same directory as the README file and
+  build the basis for custom versions.
 
   :returns:             The requested library
   :rtype:               :class:`RotamerLib`
@@ -36,8 +54,9 @@ the backbone independent Penultimate library [lovell2000]_ .
 
   Reads a file as it is provided when you get a licence for the 2010 library of
   the Dunbrack lab. It can only read the classic version, where all rotamers
-  are in a single file. Specific distributions of nonrotameric sidechains 
-  cannot be read.
+  are in a single file. Specific distributions of non-rotameric sidechains 
+  cannot be read. You can find an example described in 
+  extras/data_generation/rotamer_library/README
 
   :param filename:      Name of the file
   :type param:          :class:`str`
@@ -49,9 +68,3 @@ the backbone independent Penultimate library [lovell2000]_ .
 
   :returns: The read library
   :rtype:   :class:`BBDepRotamerLib`
-
-
-.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure.
-
-.. [lovell2000] Lovell SC, Word JM, Richardson JS, Richardson DC (2000). The penultimate rotamer library. Proteins.
-
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.txt
index 40f882320bb51f59b604a6ea7de7106d8582ca2a..30b3c7ca3b06602a1fbade371a3abdbc5a4e9029 100644
--- a/doc/html/_sources/sidechain/rotamer.txt
+++ b/doc/html/_sources/sidechain/rotamer.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Rotamers
 ================================================================================
 
@@ -7,7 +23,7 @@ A rotamer represents an amino acid sidechain and is basically a set of
 :class:`Particle` objects. There exist two types. The :class:`RRMRotamer` and 
 :class:`FRMRotamer`. 
 To gather all possible rotamers for one particular sidechain position,
-PROMOD3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
+ProMod3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
 Pairwise interactions between particles give raise to pairwise energies between 
 rotamers. Nevertheless, the energy calculation itself happens on the level
 of RotamerGroups and is mostly hidden away in the construction of the
@@ -264,7 +280,7 @@ Rotamers
 
   The FRMRotamer represents a rotamer of the so called flexible rotamer model,
   where one rotamer gets represented by several subrotamers.
-  The idea is, that all particles of all subrotamers are given at
+  The idea is that all particles of all subrotamers are given at
   initialization. Subrotamers are then defined by providing lists of indices.
   One particle can be part of several subrotamers.
 
diff --git a/doc/html/_sources/sidechain/rotamer_constructor.txt b/doc/html/_sources/sidechain/rotamer_constructor.txt
index 36c76a2c0857dc5bdbd5b3257e24e8b2bde5eaac..82f9626c2afedb57149fc5c55042ee13dcd8fcb8 100644
--- a/doc/html/_sources/sidechain/rotamer_constructor.txt
+++ b/doc/html/_sources/sidechain/rotamer_constructor.txt
@@ -1,10 +1,26 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Rotamer Constructor
 ================================================================================
 
 .. currentmodule:: promod3.sidechain
 
 Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by PROMOD3
+functionality provided by ProMod3
 
 
 Constructing Rotamers and Frame Residues
diff --git a/doc/html/_sources/sidechain/rotamer_id.txt b/doc/html/_sources/sidechain/rotamer_id.txt
index 7eac7b85ca8de53c2ee27619089aa93a1907da66..746a51641352c7295152567a742eda8befedc803 100644
--- a/doc/html/_sources/sidechain/rotamer_id.txt
+++ b/doc/html/_sources/sidechain/rotamer_id.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 RotamerID
 ================================================================================
 
diff --git a/doc/html/_sources/sidechain/rotamer_lib.txt b/doc/html/_sources/sidechain/rotamer_lib.txt
index 21ca7e4e93a69de5fe2a556da1e1b66a128d4ab1..0069c3888b70f7ad37acbf984cd3c95470af9840 100644
--- a/doc/html/_sources/sidechain/rotamer_lib.txt
+++ b/doc/html/_sources/sidechain/rotamer_lib.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Rotamer Library
 ================================================================================
 
@@ -9,7 +25,7 @@ sidechain can completely be described in terms of dihedral angles. Preferred
 combinations of such dihedral angles are a result of steric properties and
 can be gathered in rotamer libraries. Different libraries exist in the field
 and their main difference is, whether the provided sidechain conformations 
-are dependent on their backbone or not. PROMOD3 provides you with a 
+are dependent on their backbone or not. ProMod3 provides you with a 
 :class:`BBDepRotamerLib` organizing rotamers for the different aminoacids 
 in equidistant phi/psi bins, as well as a simple :class:`RotamerLib`.
 Both libraries are containers for :class:`RotamerLibEntry` and are optimized
@@ -168,10 +184,12 @@ The Backbone Dependent Rotamer Library
     added to the library or can be interpolated.
     In the first option, *phi* and *psi* simply get transformed to the 
     according bin using following formalism: bin = round((angle + pi)/bin_size).
-    In case of interpolation, the chi angles and the according standard 
-    deviations of the rotamers get bilinearly interpolated using the 
-    corresponding rotamers with same configuration from the neighbouring bins. 
-    This behaviour can be controlled with the SetInterpolate function.
+    In case of interpolation, the chi angles of rotameric dihedral angles and the 
+    according standard deviations of the rotamers get bilinearly interpolated 
+    using the corresponding rotamers with same configuration from the 
+    neighbouring bins. No interplation is applied to non-rotameric dihedral
+    angles (chi2 in ASP, ASN, HIS, PHE, TRP, TYR; chi3 in GLU, GLN).
+    This behaviour can be controlled with :meth:`SetInterpolate`.
     The query function follows following strategies in case of 
     special *id* requests.
 
@@ -220,7 +238,8 @@ The Backbone Dependent Rotamer Library
 
   .. method:: SetInterpolate(interpolate)
 
-    :param interpolate: Controls behaviour when QueryLib function gets called
+    :param interpolate: Controls behaviour when :meth:`QueryLib` 
+                        gets called
 
     :type interpolate:  :class:`bool`    
 
@@ -302,9 +321,9 @@ functionalities.
 
     Creates a :class:`RotamerLibEntry` from the given *res*.
     The function tries to automatically identify the :class:`RotamerID` based
-    on the residue name. The probability gets set to zero and the standard 
-    deviations to 0. All not required chi angles with their corresponding 
-    standard deviations are NaN.
+    on the residue name. The probability and standard deviations are set to 0.0, 
+    all not required chi angles with their corresponding  standard deviations to 
+    NaN.
 
     :param res:         Source of dihedral angles
 
@@ -418,4 +437,55 @@ functionalities.
     :returns:           :class:`bool` Whether both dihedrals are defined 
                         (not NaN) and within the specified threshold
 
+Rotamer Configurations  
+--------------------------------------------------------------------------------
+
+In rotamers, one distinguishes between rotameric and non-rotameric sidechain
+dihedral angles. The rotameric ones are around SP3-SP3 hybridized bonds and
+typically have three distinct configurations (trans, gauche-, gauche+).
+The non-rotameric ones behave differently. ProMod3 offers some functionality
+to estimate those configurations.
+
+.. class:: DihedralConfiguration
+
+  Enumerates the possible sidechain dihedral configurations
+
+  .. hlist::
+    :columns: 1
+
+    * TRANS - Trans configuration (120 < angle < -120)
+    * GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)
+    * GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)
+    * NON_ROTAMERIC - Dihedral without SP3-SP3 bond
+    * INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist...)
+
+.. method:: GetRotamericConfiguration(angle)
+
+  Evaluates the *angle* according to the ranges specified for 
+  :class:`DihedralConfiguration`. 
+
+  :param angle:         Angle to be evaluated
+  :type angle:          :class:`float`
+
+  :returns:             TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
+                        INVALID if *angle* is NaN.
+
+.. method:: GetDihedralConfiguration(entry, id, dihedral_idx) 
+
+  Estimates configuration of a sidechain dihedral angle in a specific 
+  :class:`RotamerLibEntry` with the knowledge of its identity. This allows
+  to also return NON_ROTAMERIC (e.g. chi2 for ASN).
+
+  :param entry:         Sidechain dihedral angle comes from here
+  :param id:            Identity of rotamer
+  :param dihedral_idx:  Specifies angle (0 => chi1, ..., 3 => chi4)
+
+  :type entry:          :class:`RotamerLibEntry`
+  :type id:             :class:`RotamerID`
+  :type dihedral_idx:   :class:`int`
+
+  :returns:             Result of :meth:`GetRotamericConfiguration` if specified
+                        angle is Rotameric, NON_ROTAMERIC if specified angle is 
+                        valid and non rotameric, INVALID otherwise.
+                        
 
diff --git a/doc/html/_sources/sidechain/subrotamer_optimizer.txt b/doc/html/_sources/sidechain/subrotamer_optimizer.txt
index e4124466394f2bdc0248aa40056a590f5b556dcb..27315888d85598b7f8830e1241b5139c65af0db5 100644
--- a/doc/html/_sources/sidechain/subrotamer_optimizer.txt
+++ b/doc/html/_sources/sidechain/subrotamer_optimizer.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Subrotamer Optimization
 ================================================================================
 
diff --git a/doc/html/_sources/users.txt b/doc/html/_sources/users.txt
index 7764b3750cebd2a03cc65dffecb0f9170092cae9..3b11ff195d4009fcf10bea662e5f54367150d90c 100644
--- a/doc/html/_sources/users.txt
+++ b/doc/html/_sources/users.txt
@@ -1,3 +1,19 @@
+..  Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+..                           Biozentrum - University of Basel
+..  
+..  Licensed under the Apache License, Version 2.0 (the "License");
+..  you may not use this file except in compliance with the License.
+..  You may obtain a copy of the License at
+..  
+..    http://www.apache.org/licenses/LICENSE-2.0
+..  
+..  Unless required by applicable law or agreed to in writing, software
+..  distributed under the License is distributed on an "AS IS" BASIS,
+..  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+..  See the License for the specific language governing permissions and
+..  limitations under the License.
+
+
 Documentation For Users
 =======================
 
@@ -12,6 +28,7 @@ Contents:
    gettingstarted
    actions/index
    buildsystem
+   container/index
    modelling/index
    sidechain/index
    scoring/index
diff --git a/doc/html/_static/alabaster.css b/doc/html/_static/alabaster.css
index 517cb43e58b2e57a766cbed1ca59eddbe7f4515c..bc420a48f3c057e08517ab5758a32d3b14428a4a 100644
--- a/doc/html/_static/alabaster.css
+++ b/doc/html/_static/alabaster.css
@@ -28,7 +28,6 @@ body {
     padding: 0;
 }
 
-
 div.document {
     width: 940px;
     margin: 30px auto 0 auto;
@@ -45,8 +44,6 @@ div.bodywrapper {
 
 div.sphinxsidebar {
     width: 220px;
-    font-size: 14px;
-    line-height: 1.5;
 }
 
 hr {
@@ -75,11 +72,6 @@ div.footer a {
     color: #888;
 }
 
-p.caption {
-    font-family: ;
-    font-size: inherit;
-}
-
 
 div.relations {
     display: none;
@@ -96,6 +88,11 @@ div.sphinxsidebar a:hover {
     border-bottom: 1px solid #999;
 }
 
+div.sphinxsidebar {
+    font-size: 14px;
+    line-height: 1.5;
+}
+
 div.sphinxsidebarwrapper {
     padding: 18px 10px;
 }
@@ -362,7 +359,7 @@ table.field-list p {
 }
 
 table.footnote td.label {
-    width: .1px;
+    width: 0px;
     padding: 0.3em 0 0.3em 0.5em;
 }
 
@@ -385,7 +382,6 @@ blockquote {
 }
 
 ul, ol {
-    /* Matches the 30px from the narrow-screen "li > ul" selector below */
     margin: 10px 0 10px 30px;
     padding: 0;
 }
@@ -423,11 +419,6 @@ a.reference {
     border-bottom: 1px dotted #004B6B;
 }
 
-/* Don't put an underline on images */
-a.image-reference, a.image-reference:hover {
-    border-bottom: none;
-}
-
 a.reference:hover {
     border-bottom: 1px solid #6D4100;
 }
@@ -477,11 +468,6 @@ a:hover tt, a:hover code {
     	margin-left: 0;
     }
 
-	li > ul {
-        /* Matches the 30px from the "ul, ol" selector above */
-		margin-left: 30px;
-	}
-
     .document {
     	width: auto;
     }
diff --git a/doc/html/_static/basic.css b/doc/html/_static/basic.css
index 65dfd7dfda92b36a93ea2b50d82d3917aec69c66..c89fc7e920b41365e5fb89c104b35fbd18179b89 100644
--- a/doc/html/_static/basic.css
+++ b/doc/html/_static/basic.css
@@ -52,8 +52,6 @@ div.sphinxsidebar {
     width: 230px;
     margin-left: -100%;
     font-size: 90%;
-    word-wrap: break-word;
-    overflow-wrap : break-word;
 }
 
 div.sphinxsidebar ul {
@@ -189,13 +187,6 @@ div.genindex-jumpbox {
 
 /* -- general body styles --------------------------------------------------- */
 
-div.body p, div.body dd, div.body li, div.body blockquote {
-    -moz-hyphens: auto;
-    -ms-hyphens: auto;
-    -webkit-hyphens: auto;
-    hyphens: auto;
-}
-
 a.headerlink {
     visibility: hidden;
 }
diff --git a/doc/html/_static/custom.css b/doc/html/_static/custom.css
deleted file mode 100644
index 2a924f1d6a8bc930c5296bdb2d5c2d3e39b04a1c..0000000000000000000000000000000000000000
--- a/doc/html/_static/custom.css
+++ /dev/null
@@ -1 +0,0 @@
-/* This file intentionally left blank. */
diff --git a/doc/html/_static/doctools.js b/doc/html/_static/doctools.js
index 816349563588e87ca99c7cf2d6e54268e52e761d..e2e70cc287e06e4af0b8ce70f28a65b44079cdae 100644
--- a/doc/html/_static/doctools.js
+++ b/doc/html/_static/doctools.js
@@ -124,7 +124,6 @@ var Documentation = {
     this.fixFirefoxAnchorBug();
     this.highlightSearchWords();
     this.initIndexTable();
-    
   },
 
   /**
@@ -253,29 +252,6 @@ var Documentation = {
     });
     var url = parts.join('/');
     return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
-  },
-
-  initOnKeyListeners: function() {
-    $(document).keyup(function(event) {
-      var activeElementType = document.activeElement.tagName;
-      // don't navigate when in search box or textarea
-      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
-        switch (event.keyCode) {
-          case 37: // left
-            var prevHref = $('link[rel="prev"]').prop('href');
-            if (prevHref) {
-              window.location.href = prevHref;
-              return false;
-            }
-          case 39: // right
-            var nextHref = $('link[rel="next"]').prop('href');
-            if (nextHref) {
-              window.location.href = nextHref;
-              return false;
-            }
-        }
-      }
-    });
   }
 };
 
@@ -284,4 +260,4 @@ _ = Documentation.gettext;
 
 $(document).ready(function() {
   Documentation.init();
-});
\ No newline at end of file
+});
diff --git a/doc/html/_static/jquery-1.11.1.js b/doc/html/_static/jquery-1.11.1.js
deleted file mode 100644
index d4b67f7e6c1a94df167f31657769717a71581066..0000000000000000000000000000000000000000
--- a/doc/html/_static/jquery-1.11.1.js
+++ /dev/null
@@ -1,10308 +0,0 @@
-/*!
- * jQuery JavaScript Library v1.11.1
- * http://jquery.com/
- *
- * Includes Sizzle.js
- * http://sizzlejs.com/
- *
- * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors
- * Released under the MIT license
- * http://jquery.org/license
- *
- * Date: 2014-05-01T17:42Z
- */
-
-(function( global, factory ) {
-
-	if ( typeof module === "object" && typeof module.exports === "object" ) {
-		// For CommonJS and CommonJS-like environments where a proper window is present,
-		// execute the factory and get jQuery
-		// For environments that do not inherently posses a window with a document
-		// (such as Node.js), expose a jQuery-making factory as module.exports
-		// This accentuates the need for the creation of a real window
-		// e.g. var jQuery = require("jquery")(window);
-		// See ticket #14549 for more info
-		module.exports = global.document ?
-			factory( global, true ) :
-			function( w ) {
-				if ( !w.document ) {
-					throw new Error( "jQuery requires a window with a document" );
-				}
-				return factory( w );
-			};
-	} else {
-		factory( global );
-	}
-
-// Pass this if window is not defined yet
-}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
-
-// Can't do this because several apps including ASP.NET trace
-// the stack via arguments.caller.callee and Firefox dies if
-// you try to trace through "use strict" call chains. (#13335)
-// Support: Firefox 18+
-//
-
-var deletedIds = [];
-
-var slice = deletedIds.slice;
-
-var concat = deletedIds.concat;
-
-var push = deletedIds.push;
-
-var indexOf = deletedIds.indexOf;
-
-var class2type = {};
-
-var toString = class2type.toString;
-
-var hasOwn = class2type.hasOwnProperty;
-
-var support = {};
-
-
-
-var
-	version = "1.11.1",
-
-	// Define a local copy of jQuery
-	jQuery = function( selector, context ) {
-		// The jQuery object is actually just the init constructor 'enhanced'
-		// Need init if jQuery is called (just allow error to be thrown if not included)
-		return new jQuery.fn.init( selector, context );
-	},
-
-	// Support: Android<4.1, IE<9
-	// Make sure we trim BOM and NBSP
-	rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
-
-	// Matches dashed string for camelizing
-	rmsPrefix = /^-ms-/,
-	rdashAlpha = /-([\da-z])/gi,
-
-	// Used by jQuery.camelCase as callback to replace()
-	fcamelCase = function( all, letter ) {
-		return letter.toUpperCase();
-	};
-
-jQuery.fn = jQuery.prototype = {
-	// The current version of jQuery being used
-	jquery: version,
-
-	constructor: jQuery,
-
-	// Start with an empty selector
-	selector: "",
-
-	// The default length of a jQuery object is 0
-	length: 0,
-
-	toArray: function() {
-		return slice.call( this );
-	},
-
-	// Get the Nth element in the matched element set OR
-	// Get the whole matched element set as a clean array
-	get: function( num ) {
-		return num != null ?
-
-			// Return just the one element from the set
-			( num < 0 ? this[ num + this.length ] : this[ num ] ) :
-
-			// Return all the elements in a clean array
-			slice.call( this );
-	},
-
-	// Take an array of elements and push it onto the stack
-	// (returning the new matched element set)
-	pushStack: function( elems ) {
-
-		// Build a new jQuery matched element set
-		var ret = jQuery.merge( this.constructor(), elems );
-
-		// Add the old object onto the stack (as a reference)
-		ret.prevObject = this;
-		ret.context = this.context;
-
-		// Return the newly-formed element set
-		return ret;
-	},
-
-	// Execute a callback for every element in the matched set.
-	// (You can seed the arguments with an array of args, but this is
-	// only used internally.)
-	each: function( callback, args ) {
-		return jQuery.each( this, callback, args );
-	},
-
-	map: function( callback ) {
-		return this.pushStack( jQuery.map(this, function( elem, i ) {
-			return callback.call( elem, i, elem );
-		}));
-	},
-
-	slice: function() {
-		return this.pushStack( slice.apply( this, arguments ) );
-	},
-
-	first: function() {
-		return this.eq( 0 );
-	},
-
-	last: function() {
-		return this.eq( -1 );
-	},
-
-	eq: function( i ) {
-		var len = this.length,
-			j = +i + ( i < 0 ? len : 0 );
-		return this.pushStack( j >= 0 && j < len ? [ this[j] ] : [] );
-	},
-
-	end: function() {
-		return this.prevObject || this.constructor(null);
-	},
-
-	// For internal use only.
-	// Behaves like an Array's method, not like a jQuery method.
-	push: push,
-	sort: deletedIds.sort,
-	splice: deletedIds.splice
-};
-
-jQuery.extend = jQuery.fn.extend = function() {
-	var src, copyIsArray, copy, name, options, clone,
-		target = arguments[0] || {},
-		i = 1,
-		length = arguments.length,
-		deep = false;
-
-	// Handle a deep copy situation
-	if ( typeof target === "boolean" ) {
-		deep = target;
-
-		// skip the boolean and the target
-		target = arguments[ i ] || {};
-		i++;
-	}
-
-	// Handle case when target is a string or something (possible in deep copy)
-	if ( typeof target !== "object" && !jQuery.isFunction(target) ) {
-		target = {};
-	}
-
-	// extend jQuery itself if only one argument is passed
-	if ( i === length ) {
-		target = this;
-		i--;
-	}
-
-	for ( ; i < length; i++ ) {
-		// Only deal with non-null/undefined values
-		if ( (options = arguments[ i ]) != null ) {
-			// Extend the base object
-			for ( name in options ) {
-				src = target[ name ];
-				copy = options[ name ];
-
-				// Prevent never-ending loop
-				if ( target === copy ) {
-					continue;
-				}
-
-				// Recurse if we're merging plain objects or arrays
-				if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) {
-					if ( copyIsArray ) {
-						copyIsArray = false;
-						clone = src && jQuery.isArray(src) ? src : [];
-
-					} else {
-						clone = src && jQuery.isPlainObject(src) ? src : {};
-					}
-
-					// Never move original objects, clone them
-					target[ name ] = jQuery.extend( deep, clone, copy );
-
-				// Don't bring in undefined values
-				} else if ( copy !== undefined ) {
-					target[ name ] = copy;
-				}
-			}
-		}
-	}
-
-	// Return the modified object
-	return target;
-};
-
-jQuery.extend({
-	// Unique for each copy of jQuery on the page
-	expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
-
-	// Assume jQuery is ready without the ready module
-	isReady: true,
-
-	error: function( msg ) {
-		throw new Error( msg );
-	},
-
-	noop: function() {},
-
-	// See test/unit/core.js for details concerning isFunction.
-	// Since version 1.3, DOM methods and functions like alert
-	// aren't supported. They return false on IE (#2968).
-	isFunction: function( obj ) {
-		return jQuery.type(obj) === "function";
-	},
-
-	isArray: Array.isArray || function( obj ) {
-		return jQuery.type(obj) === "array";
-	},
-
-	isWindow: function( obj ) {
-		/* jshint eqeqeq: false */
-		return obj != null && obj == obj.window;
-	},
-
-	isNumeric: function( obj ) {
-		// parseFloat NaNs numeric-cast false positives (null|true|false|"")
-		// ...but misinterprets leading-number strings, particularly hex literals ("0x...")
-		// subtraction forces infinities to NaN
-		return !jQuery.isArray( obj ) && obj - parseFloat( obj ) >= 0;
-	},
-
-	isEmptyObject: function( obj ) {
-		var name;
-		for ( name in obj ) {
-			return false;
-		}
-		return true;
-	},
-
-	isPlainObject: function( obj ) {
-		var key;
-
-		// Must be an Object.
-		// Because of IE, we also have to check the presence of the constructor property.
-		// Make sure that DOM nodes and window objects don't pass through, as well
-		if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) {
-			return false;
-		}
-
-		try {
-			// Not own constructor property must be Object
-			if ( obj.constructor &&
-				!hasOwn.call(obj, "constructor") &&
-				!hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
-				return false;
-			}
-		} catch ( e ) {
-			// IE8,9 Will throw exceptions on certain host objects #9897
-			return false;
-		}
-
-		// Support: IE<9
-		// Handle iteration over inherited properties before own properties.
-		if ( support.ownLast ) {
-			for ( key in obj ) {
-				return hasOwn.call( obj, key );
-			}
-		}
-
-		// Own properties are enumerated firstly, so to speed up,
-		// if last one is own, then all properties are own.
-		for ( key in obj ) {}
-
-		return key === undefined || hasOwn.call( obj, key );
-	},
-
-	type: function( obj ) {
-		if ( obj == null ) {
-			return obj + "";
-		}
-		return typeof obj === "object" || typeof obj === "function" ?
-			class2type[ toString.call(obj) ] || "object" :
-			typeof obj;
-	},
-
-	// Evaluates a script in a global context
-	// Workarounds based on findings by Jim Driscoll
-	// http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
-	globalEval: function( data ) {
-		if ( data && jQuery.trim( data ) ) {
-			// We use execScript on Internet Explorer
-			// We use an anonymous function so that context is window
-			// rather than jQuery in Firefox
-			( window.execScript || function( data ) {
-				window[ "eval" ].call( window, data );
-			} )( data );
-		}
-	},
-
-	// Convert dashed to camelCase; used by the css and data modules
-	// Microsoft forgot to hump their vendor prefix (#9572)
-	camelCase: function( string ) {
-		return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
-	},
-
-	nodeName: function( elem, name ) {
-		return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
-	},
-
-	// args is for internal usage only
-	each: function( obj, callback, args ) {
-		var value,
-			i = 0,
-			length = obj.length,
-			isArray = isArraylike( obj );
-
-		if ( args ) {
-			if ( isArray ) {
-				for ( ; i < length; i++ ) {
-					value = callback.apply( obj[ i ], args );
-
-					if ( value === false ) {
-						break;
-					}
-				}
-			} else {
-				for ( i in obj ) {
-					value = callback.apply( obj[ i ], args );
-
-					if ( value === false ) {
-						break;
-					}
-				}
-			}
-
-		// A special, fast, case for the most common use of each
-		} else {
-			if ( isArray ) {
-				for ( ; i < length; i++ ) {
-					value = callback.call( obj[ i ], i, obj[ i ] );
-
-					if ( value === false ) {
-						break;
-					}
-				}
-			} else {
-				for ( i in obj ) {
-					value = callback.call( obj[ i ], i, obj[ i ] );
-
-					if ( value === false ) {
-						break;
-					}
-				}
-			}
-		}
-
-		return obj;
-	},
-
-	// Support: Android<4.1, IE<9
-	trim: function( text ) {
-		return text == null ?
-			"" :
-			( text + "" ).replace( rtrim, "" );
-	},
-
-	// results is for internal usage only
-	makeArray: function( arr, results ) {
-		var ret = results || [];
-
-		if ( arr != null ) {
-			if ( isArraylike( Object(arr) ) ) {
-				jQuery.merge( ret,
-					typeof arr === "string" ?
-					[ arr ] : arr
-				);
-			} else {
-				push.call( ret, arr );
-			}
-		}
-
-		return ret;
-	},
-
-	inArray: function( elem, arr, i ) {
-		var len;
-
-		if ( arr ) {
-			if ( indexOf ) {
-				return indexOf.call( arr, elem, i );
-			}
-
-			len = arr.length;
-			i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0;
-
-			for ( ; i < len; i++ ) {
-				// Skip accessing in sparse arrays
-				if ( i in arr && arr[ i ] === elem ) {
-					return i;
-				}
-			}
-		}
-
-		return -1;
-	},
-
-	merge: function( first, second ) {
-		var len = +second.length,
-			j = 0,
-			i = first.length;
-
-		while ( j < len ) {
-			first[ i++ ] = second[ j++ ];
-		}
-
-		// Support: IE<9
-		// Workaround casting of .length to NaN on otherwise arraylike objects (e.g., NodeLists)
-		if ( len !== len ) {
-			while ( second[j] !== undefined ) {
-				first[ i++ ] = second[ j++ ];
-			}
-		}
-
-		first.length = i;
-
-		return first;
-	},
-
-	grep: function( elems, callback, invert ) {
-		var callbackInverse,
-			matches = [],
-			i = 0,
-			length = elems.length,
-			callbackExpect = !invert;
-
-		// Go through the array, only saving the items
-		// that pass the validator function
-		for ( ; i < length; i++ ) {
-			callbackInverse = !callback( elems[ i ], i );
-			if ( callbackInverse !== callbackExpect ) {
-				matches.push( elems[ i ] );
-			}
-		}
-
-		return matches;
-	},
-
-	// arg is for internal usage only
-	map: function( elems, callback, arg ) {
-		var value,
-			i = 0,
-			length = elems.length,
-			isArray = isArraylike( elems ),
-			ret = [];
-
-		// Go through the array, translating each of the items to their new values
-		if ( isArray ) {
-			for ( ; i < length; i++ ) {
-				value = callback( elems[ i ], i, arg );
-
-				if ( value != null ) {
-					ret.push( value );
-				}
-			}
-
-		// Go through every key on the object,
-		} else {
-			for ( i in elems ) {
-				value = callback( elems[ i ], i, arg );
-
-				if ( value != null ) {
-					ret.push( value );
-				}
-			}
-		}
-
-		// Flatten any nested arrays
-		return concat.apply( [], ret );
-	},
-
-	// A global GUID counter for objects
-	guid: 1,
-
-	// Bind a function to a context, optionally partially applying any
-	// arguments.
-	proxy: function( fn, context ) {
-		var args, proxy, tmp;
-
-		if ( typeof context === "string" ) {
-			tmp = fn[ context ];
-			context = fn;
-			fn = tmp;
-		}
-
-		// Quick check to determine if target is callable, in the spec
-		// this throws a TypeError, but we will just return undefined.
-		if ( !jQuery.isFunction( fn ) ) {
-			return undefined;
-		}
-
-		// Simulated bind
-		args = slice.call( arguments, 2 );
-		proxy = function() {
-			return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
-		};
-
-		// Set the guid of unique handler to the same of original handler, so it can be removed
-		proxy.guid = fn.guid = fn.guid || jQuery.guid++;
-
-		return proxy;
-	},
-
-	now: function() {
-		return +( new Date() );
-	},
-
-	// jQuery.support is not used in Core but other projects attach their
-	// properties to it so it needs to exist.
-	support: support
-});
-
-// Populate the class2type map
-jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) {
-	class2type[ "[object " + name + "]" ] = name.toLowerCase();
-});
-
-function isArraylike( obj ) {
-	var length = obj.length,
-		type = jQuery.type( obj );
-
-	if ( type === "function" || jQuery.isWindow( obj ) ) {
-		return false;
-	}
-
-	if ( obj.nodeType === 1 && length ) {
-		return true;
-	}
-
-	return type === "array" || length === 0 ||
-		typeof length === "number" && length > 0 && ( length - 1 ) in obj;
-}
-var Sizzle =
-/*!
- * Sizzle CSS Selector Engine v1.10.19
- * http://sizzlejs.com/
- *
- * Copyright 2013 jQuery Foundation, Inc. and other contributors
- * Released under the MIT license
- * http://jquery.org/license
- *
- * Date: 2014-04-18
- */
-(function( window ) {
-
-var i,
-	support,
-	Expr,
-	getText,
-	isXML,
-	tokenize,
-	compile,
-	select,
-	outermostContext,
-	sortInput,
-	hasDuplicate,
-
-	// Local document vars
-	setDocument,
-	document,
-	docElem,
-	documentIsHTML,
-	rbuggyQSA,
-	rbuggyMatches,
-	matches,
-	contains,
-
-	// Instance-specific data
-	expando = "sizzle" + -(new Date()),
-	preferredDoc = window.document,
-	dirruns = 0,
-	done = 0,
-	classCache = createCache(),
-	tokenCache = createCache(),
-	compilerCache = createCache(),
-	sortOrder = function( a, b ) {
-		if ( a === b ) {
-			hasDuplicate = true;
-		}
-		return 0;
-	},
-
-	// General-purpose constants
-	strundefined = typeof undefined,
-	MAX_NEGATIVE = 1 << 31,
-
-	// Instance methods
-	hasOwn = ({}).hasOwnProperty,
-	arr = [],
-	pop = arr.pop,
-	push_native = arr.push,
-	push = arr.push,
-	slice = arr.slice,
-	// Use a stripped-down indexOf if we can't use a native one
-	indexOf = arr.indexOf || function( elem ) {
-		var i = 0,
-			len = this.length;
-		for ( ; i < len; i++ ) {
-			if ( this[i] === elem ) {
-				return i;
-			}
-		}
-		return -1;
-	},
-
-	booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
-
-	// Regular expressions
-
-	// Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace
-	whitespace = "[\\x20\\t\\r\\n\\f]",
-	// http://www.w3.org/TR/css3-syntax/#characters
-	characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+",
-
-	// Loosely modeled on CSS identifier characters
-	// An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors
-	// Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
-	identifier = characterEncoding.replace( "w", "w#" ),
-
-	// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
-	attributes = "\\[" + whitespace + "*(" + characterEncoding + ")(?:" + whitespace +
-		// Operator (capture 2)
-		"*([*^$|!~]?=)" + whitespace +
-		// "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
-		"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
-		"*\\]",
-
-	pseudos = ":(" + characterEncoding + ")(?:\\((" +
-		// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
-		// 1. quoted (capture 3; capture 4 or capture 5)
-		"('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
-		// 2. simple (capture 6)
-		"((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
-		// 3. anything else (capture 2)
-		".*" +
-		")\\)|)",
-
-	// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
-	rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
-
-	rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
-	rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
-
-	rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ),
-
-	rpseudo = new RegExp( pseudos ),
-	ridentifier = new RegExp( "^" + identifier + "$" ),
-
-	matchExpr = {
-		"ID": new RegExp( "^#(" + characterEncoding + ")" ),
-		"CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ),
-		"TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ),
-		"ATTR": new RegExp( "^" + attributes ),
-		"PSEUDO": new RegExp( "^" + pseudos ),
-		"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
-			"*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
-			"*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
-		"bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
-		// For use in libraries implementing .is()
-		// We use this for POS matching in `select`
-		"needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
-			whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
-	},
-
-	rinputs = /^(?:input|select|textarea|button)$/i,
-	rheader = /^h\d$/i,
-
-	rnative = /^[^{]+\{\s*\[native \w/,
-
-	// Easily-parseable/retrievable ID or TAG or CLASS selectors
-	rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
-
-	rsibling = /[+~]/,
-	rescape = /'|\\/g,
-
-	// CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
-	runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
-	funescape = function( _, escaped, escapedWhitespace ) {
-		var high = "0x" + escaped - 0x10000;
-		// NaN means non-codepoint
-		// Support: Firefox<24
-		// Workaround erroneous numeric interpretation of +"0x"
-		return high !== high || escapedWhitespace ?
-			escaped :
-			high < 0 ?
-				// BMP codepoint
-				String.fromCharCode( high + 0x10000 ) :
-				// Supplemental Plane codepoint (surrogate pair)
-				String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
-	};
-
-// Optimize for push.apply( _, NodeList )
-try {
-	push.apply(
-		(arr = slice.call( preferredDoc.childNodes )),
-		preferredDoc.childNodes
-	);
-	// Support: Android<4.0
-	// Detect silently failing push.apply
-	arr[ preferredDoc.childNodes.length ].nodeType;
-} catch ( e ) {
-	push = { apply: arr.length ?
-
-		// Leverage slice if possible
-		function( target, els ) {
-			push_native.apply( target, slice.call(els) );
-		} :
-
-		// Support: IE<9
-		// Otherwise append directly
-		function( target, els ) {
-			var j = target.length,
-				i = 0;
-			// Can't trust NodeList.length
-			while ( (target[j++] = els[i++]) ) {}
-			target.length = j - 1;
-		}
-	};
-}
-
-function Sizzle( selector, context, results, seed ) {
-	var match, elem, m, nodeType,
-		// QSA vars
-		i, groups, old, nid, newContext, newSelector;
-
-	if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
-		setDocument( context );
-	}
-
-	context = context || document;
-	results = results || [];
-
-	if ( !selector || typeof selector !== "string" ) {
-		return results;
-	}
-
-	if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) {
-		return [];
-	}
-
-	if ( documentIsHTML && !seed ) {
-
-		// Shortcuts
-		if ( (match = rquickExpr.exec( selector )) ) {
-			// Speed-up: Sizzle("#ID")
-			if ( (m = match[1]) ) {
-				if ( nodeType === 9 ) {
-					elem = context.getElementById( m );
-					// Check parentNode to catch when Blackberry 4.6 returns
-					// nodes that are no longer in the document (jQuery #6963)
-					if ( elem && elem.parentNode ) {
-						// Handle the case where IE, Opera, and Webkit return items
-						// by name instead of ID
-						if ( elem.id === m ) {
-							results.push( elem );
-							return results;
-						}
-					} else {
-						return results;
-					}
-				} else {
-					// Context is not a document
-					if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) &&
-						contains( context, elem ) && elem.id === m ) {
-						results.push( elem );
-						return results;
-					}
-				}
-
-			// Speed-up: Sizzle("TAG")
-			} else if ( match[2] ) {
-				push.apply( results, context.getElementsByTagName( selector ) );
-				return results;
-
-			// Speed-up: Sizzle(".CLASS")
-			} else if ( (m = match[3]) && support.getElementsByClassName && context.getElementsByClassName ) {
-				push.apply( results, context.getElementsByClassName( m ) );
-				return results;
-			}
-		}
-
-		// QSA path
-		if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
-			nid = old = expando;
-			newContext = context;
-			newSelector = nodeType === 9 && selector;
-
-			// qSA works strangely on Element-rooted queries
-			// We can work around this by specifying an extra ID on the root
-			// and working up from there (Thanks to Andrew Dupont for the technique)
-			// IE 8 doesn't work on object elements
-			if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
-				groups = tokenize( selector );
-
-				if ( (old = context.getAttribute("id")) ) {
-					nid = old.replace( rescape, "\\$&" );
-				} else {
-					context.setAttribute( "id", nid );
-				}
-				nid = "[id='" + nid + "'] ";
-
-				i = groups.length;
-				while ( i-- ) {
-					groups[i] = nid + toSelector( groups[i] );
-				}
-				newContext = rsibling.test( selector ) && testContext( context.parentNode ) || context;
-				newSelector = groups.join(",");
-			}
-
-			if ( newSelector ) {
-				try {
-					push.apply( results,
-						newContext.querySelectorAll( newSelector )
-					);
-					return results;
-				} catch(qsaError) {
-				} finally {
-					if ( !old ) {
-						context.removeAttribute("id");
-					}
-				}
-			}
-		}
-	}
-
-	// All others
-	return select( selector.replace( rtrim, "$1" ), context, results, seed );
-}
-
-/**
- * Create key-value caches of limited size
- * @returns {Function(string, Object)} Returns the Object data after storing it on itself with
- *	property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
- *	deleting the oldest entry
- */
-function createCache() {
-	var keys = [];
-
-	function cache( key, value ) {
-		// Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
-		if ( keys.push( key + " " ) > Expr.cacheLength ) {
-			// Only keep the most recent entries
-			delete cache[ keys.shift() ];
-		}
-		return (cache[ key + " " ] = value);
-	}
-	return cache;
-}
-
-/**
- * Mark a function for special use by Sizzle
- * @param {Function} fn The function to mark
- */
-function markFunction( fn ) {
-	fn[ expando ] = true;
-	return fn;
-}
-
-/**
- * Support testing using an element
- * @param {Function} fn Passed the created div and expects a boolean result
- */
-function assert( fn ) {
-	var div = document.createElement("div");
-
-	try {
-		return !!fn( div );
-	} catch (e) {
-		return false;
-	} finally {
-		// Remove from its parent by default
-		if ( div.parentNode ) {
-			div.parentNode.removeChild( div );
-		}
-		// release memory in IE
-		div = null;
-	}
-}
-
-/**
- * Adds the same handler for all of the specified attrs
- * @param {String} attrs Pipe-separated list of attributes
- * @param {Function} handler The method that will be applied
- */
-function addHandle( attrs, handler ) {
-	var arr = attrs.split("|"),
-		i = attrs.length;
-
-	while ( i-- ) {
-		Expr.attrHandle[ arr[i] ] = handler;
-	}
-}
-
-/**
- * Checks document order of two siblings
- * @param {Element} a
- * @param {Element} b
- * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
- */
-function siblingCheck( a, b ) {
-	var cur = b && a,
-		diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
-			( ~b.sourceIndex || MAX_NEGATIVE ) -
-			( ~a.sourceIndex || MAX_NEGATIVE );
-
-	// Use IE sourceIndex if available on both nodes
-	if ( diff ) {
-		return diff;
-	}
-
-	// Check if b follows a
-	if ( cur ) {
-		while ( (cur = cur.nextSibling) ) {
-			if ( cur === b ) {
-				return -1;
-			}
-		}
-	}
-
-	return a ? 1 : -1;
-}
-
-/**
- * Returns a function to use in pseudos for input types
- * @param {String} type
- */
-function createInputPseudo( type ) {
-	return function( elem ) {
-		var name = elem.nodeName.toLowerCase();
-		return name === "input" && elem.type === type;
-	};
-}
-
-/**
- * Returns a function to use in pseudos for buttons
- * @param {String} type
- */
-function createButtonPseudo( type ) {
-	return function( elem ) {
-		var name = elem.nodeName.toLowerCase();
-		return (name === "input" || name === "button") && elem.type === type;
-	};
-}
-
-/**
- * Returns a function to use in pseudos for positionals
- * @param {Function} fn
- */
-function createPositionalPseudo( fn ) {
-	return markFunction(function( argument ) {
-		argument = +argument;
-		return markFunction(function( seed, matches ) {
-			var j,
-				matchIndexes = fn( [], seed.length, argument ),
-				i = matchIndexes.length;
-
-			// Match elements found at the specified indexes
-			while ( i-- ) {
-				if ( seed[ (j = matchIndexes[i]) ] ) {
-					seed[j] = !(matches[j] = seed[j]);
-				}
-			}
-		});
-	});
-}
-
-/**
- * Checks a node for validity as a Sizzle context
- * @param {Element|Object=} context
- * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
- */
-function testContext( context ) {
-	return context && typeof context.getElementsByTagName !== strundefined && context;
-}
-
-// Expose support vars for convenience
-support = Sizzle.support = {};
-
-/**
- * Detects XML nodes
- * @param {Element|Object} elem An element or a document
- * @returns {Boolean} True iff elem is a non-HTML XML node
- */
-isXML = Sizzle.isXML = function( elem ) {
-	// documentElement is verified for cases where it doesn't yet exist
-	// (such as loading iframes in IE - #4833)
-	var documentElement = elem && (elem.ownerDocument || elem).documentElement;
-	return documentElement ? documentElement.nodeName !== "HTML" : false;
-};
-
-/**
- * Sets document-related variables once based on the current document
- * @param {Element|Object} [doc] An element or document object to use to set the document
- * @returns {Object} Returns the current document
- */
-setDocument = Sizzle.setDocument = function( node ) {
-	var hasCompare,
-		doc = node ? node.ownerDocument || node : preferredDoc,
-		parent = doc.defaultView;
-
-	// If no document and documentElement is available, return
-	if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
-		return document;
-	}
-
-	// Set our document
-	document = doc;
-	docElem = doc.documentElement;
-
-	// Support tests
-	documentIsHTML = !isXML( doc );
-
-	// Support: IE>8
-	// If iframe document is assigned to "document" variable and if iframe has been reloaded,
-	// IE will throw "permission denied" error when accessing "document" variable, see jQuery #13936
-	// IE6-8 do not support the defaultView property so parent will be undefined
-	if ( parent && parent !== parent.top ) {
-		// IE11 does not have attachEvent, so all must suffer
-		if ( parent.addEventListener ) {
-			parent.addEventListener( "unload", function() {
-				setDocument();
-			}, false );
-		} else if ( parent.attachEvent ) {
-			parent.attachEvent( "onunload", function() {
-				setDocument();
-			});
-		}
-	}
-
-	/* Attributes
-	---------------------------------------------------------------------- */
-
-	// Support: IE<8
-	// Verify that getAttribute really returns attributes and not properties (excepting IE8 booleans)
-	support.attributes = assert(function( div ) {
-		div.className = "i";
-		return !div.getAttribute("className");
-	});
-
-	/* getElement(s)By*
-	---------------------------------------------------------------------- */
-
-	// Check if getElementsByTagName("*") returns only elements
-	support.getElementsByTagName = assert(function( div ) {
-		div.appendChild( doc.createComment("") );
-		return !div.getElementsByTagName("*").length;
-	});
-
-	// Check if getElementsByClassName can be trusted
-	support.getElementsByClassName = rnative.test( doc.getElementsByClassName ) && assert(function( div ) {
-		div.innerHTML = "<div class='a'></div><div class='a i'></div>";
-
-		// Support: Safari<4
-		// Catch class over-caching
-		div.firstChild.className = "i";
-		// Support: Opera<10
-		// Catch gEBCN failure to find non-leading classes
-		return div.getElementsByClassName("i").length === 2;
-	});
-
-	// Support: IE<10
-	// Check if getElementById returns elements by name
-	// The broken getElementById methods don't pick up programatically-set names,
-	// so use a roundabout getElementsByName test
-	support.getById = assert(function( div ) {
-		docElem.appendChild( div ).id = expando;
-		return !doc.getElementsByName || !doc.getElementsByName( expando ).length;
-	});
-
-	// ID find and filter
-	if ( support.getById ) {
-		Expr.find["ID"] = function( id, context ) {
-			if ( typeof context.getElementById !== strundefined && documentIsHTML ) {
-				var m = context.getElementById( id );
-				// Check parentNode to catch when Blackberry 4.6 returns
-				// nodes that are no longer in the document #6963
-				return m && m.parentNode ? [ m ] : [];
-			}
-		};
-		Expr.filter["ID"] = function( id ) {
-			var attrId = id.replace( runescape, funescape );
-			return function( elem ) {
-				return elem.getAttribute("id") === attrId;
-			};
-		};
-	} else {
-		// Support: IE6/7
-		// getElementById is not reliable as a find shortcut
-		delete Expr.find["ID"];
-
-		Expr.filter["ID"] =  function( id ) {
-			var attrId = id.replace( runescape, funescape );
-			return function( elem ) {
-				var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id");
-				return node && node.value === attrId;
-			};
-		};
-	}
-
-	// Tag
-	Expr.find["TAG"] = support.getElementsByTagName ?
-		function( tag, context ) {
-			if ( typeof context.getElementsByTagName !== strundefined ) {
-				return context.getElementsByTagName( tag );
-			}
-		} :
-		function( tag, context ) {
-			var elem,
-				tmp = [],
-				i = 0,
-				results = context.getElementsByTagName( tag );
-
-			// Filter out possible comments
-			if ( tag === "*" ) {
-				while ( (elem = results[i++]) ) {
-					if ( elem.nodeType === 1 ) {
-						tmp.push( elem );
-					}
-				}
-
-				return tmp;
-			}
-			return results;
-		};
-
-	// Class
-	Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
-		if ( typeof context.getElementsByClassName !== strundefined && documentIsHTML ) {
-			return context.getElementsByClassName( className );
-		}
-	};
-
-	/* QSA/matchesSelector
-	---------------------------------------------------------------------- */
-
-	// QSA and matchesSelector support
-
-	// matchesSelector(:active) reports false when true (IE9/Opera 11.5)
-	rbuggyMatches = [];
-
-	// qSa(:focus) reports false when true (Chrome 21)
-	// We allow this because of a bug in IE8/9 that throws an error
-	// whenever `document.activeElement` is accessed on an iframe
-	// So, we allow :focus to pass through QSA all the time to avoid the IE error
-	// See http://bugs.jquery.com/ticket/13378
-	rbuggyQSA = [];
-
-	if ( (support.qsa = rnative.test( doc.querySelectorAll )) ) {
-		// Build QSA regex
-		// Regex strategy adopted from Diego Perini
-		assert(function( div ) {
-			// Select is set to empty string on purpose
-			// This is to test IE's treatment of not explicitly
-			// setting a boolean content attribute,
-			// since its presence should be enough
-			// http://bugs.jquery.com/ticket/12359
-			div.innerHTML = "<select msallowclip=''><option selected=''></option></select>";
-
-			// Support: IE8, Opera 11-12.16
-			// Nothing should be selected when empty strings follow ^= or $= or *=
-			// The test attribute must be unknown in Opera but "safe" for WinRT
-			// http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
-			if ( div.querySelectorAll("[msallowclip^='']").length ) {
-				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
-			}
-
-			// Support: IE8
-			// Boolean attributes and "value" are not treated correctly
-			if ( !div.querySelectorAll("[selected]").length ) {
-				rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
-			}
-
-			// Webkit/Opera - :checked should return selected option elements
-			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
-			// IE8 throws error here and will not see later tests
-			if ( !div.querySelectorAll(":checked").length ) {
-				rbuggyQSA.push(":checked");
-			}
-		});
-
-		assert(function( div ) {
-			// Support: Windows 8 Native Apps
-			// The type and name attributes are restricted during .innerHTML assignment
-			var input = doc.createElement("input");
-			input.setAttribute( "type", "hidden" );
-			div.appendChild( input ).setAttribute( "name", "D" );
-
-			// Support: IE8
-			// Enforce case-sensitivity of name attribute
-			if ( div.querySelectorAll("[name=d]").length ) {
-				rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
-			}
-
-			// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
-			// IE8 throws error here and will not see later tests
-			if ( !div.querySelectorAll(":enabled").length ) {
-				rbuggyQSA.push( ":enabled", ":disabled" );
-			}
-
-			// Opera 10-11 does not throw on post-comma invalid pseudos
-			div.querySelectorAll("*,:x");
-			rbuggyQSA.push(",.*:");
-		});
-	}
-
-	if ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||
-		docElem.webkitMatchesSelector ||
-		docElem.mozMatchesSelector ||
-		docElem.oMatchesSelector ||
-		docElem.msMatchesSelector) )) ) {
-
-		assert(function( div ) {
-			// Check to see if it's possible to do matchesSelector
-			// on a disconnected node (IE 9)
-			support.disconnectedMatch = matches.call( div, "div" );
-
-			// This should fail with an exception
-			// Gecko does not error, returns false instead
-			matches.call( div, "[s!='']:x" );
-			rbuggyMatches.push( "!=", pseudos );
-		});
-	}
-
-	rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") );
-	rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") );
-
-	/* Contains
-	---------------------------------------------------------------------- */
-	hasCompare = rnative.test( docElem.compareDocumentPosition );
-
-	// Element contains another
-	// Purposefully does not implement inclusive descendent
-	// As in, an element does not contain itself
-	contains = hasCompare || rnative.test( docElem.contains ) ?
-		function( a, b ) {
-			var adown = a.nodeType === 9 ? a.documentElement : a,
-				bup = b && b.parentNode;
-			return a === bup || !!( bup && bup.nodeType === 1 && (
-				adown.contains ?
-					adown.contains( bup ) :
-					a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
-			));
-		} :
-		function( a, b ) {
-			if ( b ) {
-				while ( (b = b.parentNode) ) {
-					if ( b === a ) {
-						return true;
-					}
-				}
-			}
-			return false;
-		};
-
-	/* Sorting
-	---------------------------------------------------------------------- */
-
-	// Document order sorting
-	sortOrder = hasCompare ?
-	function( a, b ) {
-
-		// Flag for duplicate removal
-		if ( a === b ) {
-			hasDuplicate = true;
-			return 0;
-		}
-
-		// Sort on method existence if only one input has compareDocumentPosition
-		var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
-		if ( compare ) {
-			return compare;
-		}
-
-		// Calculate position if both inputs belong to the same document
-		compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?
-			a.compareDocumentPosition( b ) :
-
-			// Otherwise we know they are disconnected
-			1;
-
-		// Disconnected nodes
-		if ( compare & 1 ||
-			(!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
-
-			// Choose the first element that is related to our preferred document
-			if ( a === doc || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
-				return -1;
-			}
-			if ( b === doc || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
-				return 1;
-			}
-
-			// Maintain original order
-			return sortInput ?
-				( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) :
-				0;
-		}
-
-		return compare & 4 ? -1 : 1;
-	} :
-	function( a, b ) {
-		// Exit early if the nodes are identical
-		if ( a === b ) {
-			hasDuplicate = true;
-			return 0;
-		}
-
-		var cur,
-			i = 0,
-			aup = a.parentNode,
-			bup = b.parentNode,
-			ap = [ a ],
-			bp = [ b ];
-
-		// Parentless nodes are either documents or disconnected
-		if ( !aup || !bup ) {
-			return a === doc ? -1 :
-				b === doc ? 1 :
-				aup ? -1 :
-				bup ? 1 :
-				sortInput ?
-				( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) :
-				0;
-
-		// If the nodes are siblings, we can do a quick check
-		} else if ( aup === bup ) {
-			return siblingCheck( a, b );
-		}
-
-		// Otherwise we need full lists of their ancestors for comparison
-		cur = a;
-		while ( (cur = cur.parentNode) ) {
-			ap.unshift( cur );
-		}
-		cur = b;
-		while ( (cur = cur.parentNode) ) {
-			bp.unshift( cur );
-		}
-
-		// Walk down the tree looking for a discrepancy
-		while ( ap[i] === bp[i] ) {
-			i++;
-		}
-
-		return i ?
-			// Do a sibling check if the nodes have a common ancestor
-			siblingCheck( ap[i], bp[i] ) :
-
-			// Otherwise nodes in our document sort first
-			ap[i] === preferredDoc ? -1 :
-			bp[i] === preferredDoc ? 1 :
-			0;
-	};
-
-	return doc;
-};
-
-Sizzle.matches = function( expr, elements ) {
-	return Sizzle( expr, null, null, elements );
-};
-
-Sizzle.matchesSelector = function( elem, expr ) {
-	// Set document vars if needed
-	if ( ( elem.ownerDocument || elem ) !== document ) {
-		setDocument( elem );
-	}
-
-	// Make sure that attribute selectors are quoted
-	expr = expr.replace( rattributeQuotes, "='$1']" );
-
-	if ( support.matchesSelector && documentIsHTML &&
-		( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
-		( !rbuggyQSA     || !rbuggyQSA.test( expr ) ) ) {
-
-		try {
-			var ret = matches.call( elem, expr );
-
-			// IE 9's matchesSelector returns false on disconnected nodes
-			if ( ret || support.disconnectedMatch ||
-					// As well, disconnected nodes are said to be in a document
-					// fragment in IE 9
-					elem.document && elem.document.nodeType !== 11 ) {
-				return ret;
-			}
-		} catch(e) {}
-	}
-
-	return Sizzle( expr, document, null, [ elem ] ).length > 0;
-};
-
-Sizzle.contains = function( context, elem ) {
-	// Set document vars if needed
-	if ( ( context.ownerDocument || context ) !== document ) {
-		setDocument( context );
-	}
-	return contains( context, elem );
-};
-
-Sizzle.attr = function( elem, name ) {
-	// Set document vars if needed
-	if ( ( elem.ownerDocument || elem ) !== document ) {
-		setDocument( elem );
-	}
-
-	var fn = Expr.attrHandle[ name.toLowerCase() ],
-		// Don't get fooled by Object.prototype properties (jQuery #13807)
-		val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
-			fn( elem, name, !documentIsHTML ) :
-			undefined;
-
-	return val !== undefined ?
-		val :
-		support.attributes || !documentIsHTML ?
-			elem.getAttribute( name ) :
-			(val = elem.getAttributeNode(name)) && val.specified ?
-				val.value :
-				null;
-};
-
-Sizzle.error = function( msg ) {
-	throw new Error( "Syntax error, unrecognized expression: " + msg );
-};
-
-/**
- * Document sorting and removing duplicates
- * @param {ArrayLike} results
- */
-Sizzle.uniqueSort = function( results ) {
-	var elem,
-		duplicates = [],
-		j = 0,
-		i = 0;
-
-	// Unless we *know* we can detect duplicates, assume their presence
-	hasDuplicate = !support.detectDuplicates;
-	sortInput = !support.sortStable && results.slice( 0 );
-	results.sort( sortOrder );
-
-	if ( hasDuplicate ) {
-		while ( (elem = results[i++]) ) {
-			if ( elem === results[ i ] ) {
-				j = duplicates.push( i );
-			}
-		}
-		while ( j-- ) {
-			results.splice( duplicates[ j ], 1 );
-		}
-	}
-
-	// Clear input after sorting to release objects
-	// See https://github.com/jquery/sizzle/pull/225
-	sortInput = null;
-
-	return results;
-};
-
-/**
- * Utility function for retrieving the text value of an array of DOM nodes
- * @param {Array|Element} elem
- */
-getText = Sizzle.getText = function( elem ) {
-	var node,
-		ret = "",
-		i = 0,
-		nodeType = elem.nodeType;
-
-	if ( !nodeType ) {
-		// If no nodeType, this is expected to be an array
-		while ( (node = elem[i++]) ) {
-			// Do not traverse comment nodes
-			ret += getText( node );
-		}
-	} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
-		// Use textContent for elements
-		// innerText usage removed for consistency of new lines (jQuery #11153)
-		if ( typeof elem.textContent === "string" ) {
-			return elem.textContent;
-		} else {
-			// Traverse its children
-			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
-				ret += getText( elem );
-			}
-		}
-	} else if ( nodeType === 3 || nodeType === 4 ) {
-		return elem.nodeValue;
-	}
-	// Do not include comment or processing instruction nodes
-
-	return ret;
-};
-
-Expr = Sizzle.selectors = {
-
-	// Can be adjusted by the user
-	cacheLength: 50,
-
-	createPseudo: markFunction,
-
-	match: matchExpr,
-
-	attrHandle: {},
-
-	find: {},
-
-	relative: {
-		">": { dir: "parentNode", first: true },
-		" ": { dir: "parentNode" },
-		"+": { dir: "previousSibling", first: true },
-		"~": { dir: "previousSibling" }
-	},
-
-	preFilter: {
-		"ATTR": function( match ) {
-			match[1] = match[1].replace( runescape, funescape );
-
-			// Move the given value to match[3] whether quoted or unquoted
-			match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape );
-
-			if ( match[2] === "~=" ) {
-				match[3] = " " + match[3] + " ";
-			}
-
-			return match.slice( 0, 4 );
-		},
-
-		"CHILD": function( match ) {
-			/* matches from matchExpr["CHILD"]
-				1 type (only|nth|...)
-				2 what (child|of-type)
-				3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
-				4 xn-component of xn+y argument ([+-]?\d*n|)
-				5 sign of xn-component
-				6 x of xn-component
-				7 sign of y-component
-				8 y of y-component
-			*/
-			match[1] = match[1].toLowerCase();
-
-			if ( match[1].slice( 0, 3 ) === "nth" ) {
-				// nth-* requires argument
-				if ( !match[3] ) {
-					Sizzle.error( match[0] );
-				}
-
-				// numeric x and y parameters for Expr.filter.CHILD
-				// remember that false/true cast respectively to 0/1
-				match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
-				match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
-
-			// other types prohibit arguments
-			} else if ( match[3] ) {
-				Sizzle.error( match[0] );
-			}
-
-			return match;
-		},
-
-		"PSEUDO": function( match ) {
-			var excess,
-				unquoted = !match[6] && match[2];
-
-			if ( matchExpr["CHILD"].test( match[0] ) ) {
-				return null;
-			}
-
-			// Accept quoted arguments as-is
-			if ( match[3] ) {
-				match[2] = match[4] || match[5] || "";
-
-			// Strip excess characters from unquoted arguments
-			} else if ( unquoted && rpseudo.test( unquoted ) &&
-				// Get excess from tokenize (recursively)
-				(excess = tokenize( unquoted, true )) &&
-				// advance to the next closing parenthesis
-				(excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
-
-				// excess is a negative index
-				match[0] = match[0].slice( 0, excess );
-				match[2] = unquoted.slice( 0, excess );
-			}
-
-			// Return only captures needed by the pseudo filter method (type and argument)
-			return match.slice( 0, 3 );
-		}
-	},
-
-	filter: {
-
-		"TAG": function( nodeNameSelector ) {
-			var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
-			return nodeNameSelector === "*" ?
-				function() { return true; } :
-				function( elem ) {
-					return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
-				};
-		},
-
-		"CLASS": function( className ) {
-			var pattern = classCache[ className + " " ];
-
-			return pattern ||
-				(pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
-				classCache( className, function( elem ) {
-					return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== strundefined && elem.getAttribute("class") || "" );
-				});
-		},
-
-		"ATTR": function( name, operator, check ) {
-			return function( elem ) {
-				var result = Sizzle.attr( elem, name );
-
-				if ( result == null ) {
-					return operator === "!=";
-				}
-				if ( !operator ) {
-					return true;
-				}
-
-				result += "";
-
-				return operator === "=" ? result === check :
-					operator === "!=" ? result !== check :
-					operator === "^=" ? check && result.indexOf( check ) === 0 :
-					operator === "*=" ? check && result.indexOf( check ) > -1 :
-					operator === "$=" ? check && result.slice( -check.length ) === check :
-					operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 :
-					operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
-					false;
-			};
-		},
-
-		"CHILD": function( type, what, argument, first, last ) {
-			var simple = type.slice( 0, 3 ) !== "nth",
-				forward = type.slice( -4 ) !== "last",
-				ofType = what === "of-type";
-
-			return first === 1 && last === 0 ?
-
-				// Shortcut for :nth-*(n)
-				function( elem ) {
-					return !!elem.parentNode;
-				} :
-
-				function( elem, context, xml ) {
-					var cache, outerCache, node, diff, nodeIndex, start,
-						dir = simple !== forward ? "nextSibling" : "previousSibling",
-						parent = elem.parentNode,
-						name = ofType && elem.nodeName.toLowerCase(),
-						useCache = !xml && !ofType;
-
-					if ( parent ) {
-
-						// :(first|last|only)-(child|of-type)
-						if ( simple ) {
-							while ( dir ) {
-								node = elem;
-								while ( (node = node[ dir ]) ) {
-									if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) {
-										return false;
-									}
-								}
-								// Reverse direction for :only-* (if we haven't yet done so)
-								start = dir = type === "only" && !start && "nextSibling";
-							}
-							return true;
-						}
-
-						start = [ forward ? parent.firstChild : parent.lastChild ];
-
-						// non-xml :nth-child(...) stores cache data on `parent`
-						if ( forward && useCache ) {
-							// Seek `elem` from a previously-cached index
-							outerCache = parent[ expando ] || (parent[ expando ] = {});
-							cache = outerCache[ type ] || [];
-							nodeIndex = cache[0] === dirruns && cache[1];
-							diff = cache[0] === dirruns && cache[2];
-							node = nodeIndex && parent.childNodes[ nodeIndex ];
-
-							while ( (node = ++nodeIndex && node && node[ dir ] ||
-
-								// Fallback to seeking `elem` from the start
-								(diff = nodeIndex = 0) || start.pop()) ) {
-
-								// When found, cache indexes on `parent` and break
-								if ( node.nodeType === 1 && ++diff && node === elem ) {
-									outerCache[ type ] = [ dirruns, nodeIndex, diff ];
-									break;
-								}
-							}
-
-						// Use previously-cached element index if available
-						} else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) {
-							diff = cache[1];
-
-						// xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...)
-						} else {
-							// Use the same loop as above to seek `elem` from the start
-							while ( (node = ++nodeIndex && node && node[ dir ] ||
-								(diff = nodeIndex = 0) || start.pop()) ) {
-
-								if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) {
-									// Cache the index of each encountered element
-									if ( useCache ) {
-										(node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ];
-									}
-
-									if ( node === elem ) {
-										break;
-									}
-								}
-							}
-						}
-
-						// Incorporate the offset, then check against cycle size
-						diff -= last;
-						return diff === first || ( diff % first === 0 && diff / first >= 0 );
-					}
-				};
-		},
-
-		"PSEUDO": function( pseudo, argument ) {
-			// pseudo-class names are case-insensitive
-			// http://www.w3.org/TR/selectors/#pseudo-classes
-			// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
-			// Remember that setFilters inherits from pseudos
-			var args,
-				fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
-					Sizzle.error( "unsupported pseudo: " + pseudo );
-
-			// The user may use createPseudo to indicate that
-			// arguments are needed to create the filter function
-			// just as Sizzle does
-			if ( fn[ expando ] ) {
-				return fn( argument );
-			}
-
-			// But maintain support for old signatures
-			if ( fn.length > 1 ) {
-				args = [ pseudo, pseudo, "", argument ];
-				return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
-					markFunction(function( seed, matches ) {
-						var idx,
-							matched = fn( seed, argument ),
-							i = matched.length;
-						while ( i-- ) {
-							idx = indexOf.call( seed, matched[i] );
-							seed[ idx ] = !( matches[ idx ] = matched[i] );
-						}
-					}) :
-					function( elem ) {
-						return fn( elem, 0, args );
-					};
-			}
-
-			return fn;
-		}
-	},
-
-	pseudos: {
-		// Potentially complex pseudos
-		"not": markFunction(function( selector ) {
-			// Trim the selector passed to compile
-			// to avoid treating leading and trailing
-			// spaces as combinators
-			var input = [],
-				results = [],
-				matcher = compile( selector.replace( rtrim, "$1" ) );
-
-			return matcher[ expando ] ?
-				markFunction(function( seed, matches, context, xml ) {
-					var elem,
-						unmatched = matcher( seed, null, xml, [] ),
-						i = seed.length;
-
-					// Match elements unmatched by `matcher`
-					while ( i-- ) {
-						if ( (elem = unmatched[i]) ) {
-							seed[i] = !(matches[i] = elem);
-						}
-					}
-				}) :
-				function( elem, context, xml ) {
-					input[0] = elem;
-					matcher( input, null, xml, results );
-					return !results.pop();
-				};
-		}),
-
-		"has": markFunction(function( selector ) {
-			return function( elem ) {
-				return Sizzle( selector, elem ).length > 0;
-			};
-		}),
-
-		"contains": markFunction(function( text ) {
-			return function( elem ) {
-				return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
-			};
-		}),
-
-		// "Whether an element is represented by a :lang() selector
-		// is based solely on the element's language value
-		// being equal to the identifier C,
-		// or beginning with the identifier C immediately followed by "-".
-		// The matching of C against the element's language value is performed case-insensitively.
-		// The identifier C does not have to be a valid language name."
-		// http://www.w3.org/TR/selectors/#lang-pseudo
-		"lang": markFunction( function( lang ) {
-			// lang value must be a valid identifier
-			if ( !ridentifier.test(lang || "") ) {
-				Sizzle.error( "unsupported lang: " + lang );
-			}
-			lang = lang.replace( runescape, funescape ).toLowerCase();
-			return function( elem ) {
-				var elemLang;
-				do {
-					if ( (elemLang = documentIsHTML ?
-						elem.lang :
-						elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) {
-
-						elemLang = elemLang.toLowerCase();
-						return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
-					}
-				} while ( (elem = elem.parentNode) && elem.nodeType === 1 );
-				return false;
-			};
-		}),
-
-		// Miscellaneous
-		"target": function( elem ) {
-			var hash = window.location && window.location.hash;
-			return hash && hash.slice( 1 ) === elem.id;
-		},
-
-		"root": function( elem ) {
-			return elem === docElem;
-		},
-
-		"focus": function( elem ) {
-			return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
-		},
-
-		// Boolean properties
-		"enabled": function( elem ) {
-			return elem.disabled === false;
-		},
-
-		"disabled": function( elem ) {
-			return elem.disabled === true;
-		},
-
-		"checked": function( elem ) {
-			// In CSS3, :checked should return both checked and selected elements
-			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
-			var nodeName = elem.nodeName.toLowerCase();
-			return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
-		},
-
-		"selected": function( elem ) {
-			// Accessing this property makes selected-by-default
-			// options in Safari work properly
-			if ( elem.parentNode ) {
-				elem.parentNode.selectedIndex;
-			}
-
-			return elem.selected === true;
-		},
-
-		// Contents
-		"empty": function( elem ) {
-			// http://www.w3.org/TR/selectors/#empty-pseudo
-			// :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
-			//   but not by others (comment: 8; processing instruction: 7; etc.)
-			// nodeType < 6 works because attributes (2) do not appear as children
-			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
-				if ( elem.nodeType < 6 ) {
-					return false;
-				}
-			}
-			return true;
-		},
-
-		"parent": function( elem ) {
-			return !Expr.pseudos["empty"]( elem );
-		},
-
-		// Element/input types
-		"header": function( elem ) {
-			return rheader.test( elem.nodeName );
-		},
-
-		"input": function( elem ) {
-			return rinputs.test( elem.nodeName );
-		},
-
-		"button": function( elem ) {
-			var name = elem.nodeName.toLowerCase();
-			return name === "input" && elem.type === "button" || name === "button";
-		},
-
-		"text": function( elem ) {
-			var attr;
-			return elem.nodeName.toLowerCase() === "input" &&
-				elem.type === "text" &&
-
-				// Support: IE<8
-				// New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
-				( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" );
-		},
-
-		// Position-in-collection
-		"first": createPositionalPseudo(function() {
-			return [ 0 ];
-		}),
-
-		"last": createPositionalPseudo(function( matchIndexes, length ) {
-			return [ length - 1 ];
-		}),
-
-		"eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
-			return [ argument < 0 ? argument + length : argument ];
-		}),
-
-		"even": createPositionalPseudo(function( matchIndexes, length ) {
-			var i = 0;
-			for ( ; i < length; i += 2 ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		}),
-
-		"odd": createPositionalPseudo(function( matchIndexes, length ) {
-			var i = 1;
-			for ( ; i < length; i += 2 ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		}),
-
-		"lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
-			var i = argument < 0 ? argument + length : argument;
-			for ( ; --i >= 0; ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		}),
-
-		"gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
-			var i = argument < 0 ? argument + length : argument;
-			for ( ; ++i < length; ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		})
-	}
-};
-
-Expr.pseudos["nth"] = Expr.pseudos["eq"];
-
-// Add button/input type pseudos
-for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
-	Expr.pseudos[ i ] = createInputPseudo( i );
-}
-for ( i in { submit: true, reset: true } ) {
-	Expr.pseudos[ i ] = createButtonPseudo( i );
-}
-
-// Easy API for creating new setFilters
-function setFilters() {}
-setFilters.prototype = Expr.filters = Expr.pseudos;
-Expr.setFilters = new setFilters();
-
-tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
-	var matched, match, tokens, type,
-		soFar, groups, preFilters,
-		cached = tokenCache[ selector + " " ];
-
-	if ( cached ) {
-		return parseOnly ? 0 : cached.slice( 0 );
-	}
-
-	soFar = selector;
-	groups = [];
-	preFilters = Expr.preFilter;
-
-	while ( soFar ) {
-
-		// Comma and first run
-		if ( !matched || (match = rcomma.exec( soFar )) ) {
-			if ( match ) {
-				// Don't consume trailing commas as valid
-				soFar = soFar.slice( match[0].length ) || soFar;
-			}
-			groups.push( (tokens = []) );
-		}
-
-		matched = false;
-
-		// Combinators
-		if ( (match = rcombinators.exec( soFar )) ) {
-			matched = match.shift();
-			tokens.push({
-				value: matched,
-				// Cast descendant combinators to space
-				type: match[0].replace( rtrim, " " )
-			});
-			soFar = soFar.slice( matched.length );
-		}
-
-		// Filters
-		for ( type in Expr.filter ) {
-			if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
-				(match = preFilters[ type ]( match ))) ) {
-				matched = match.shift();
-				tokens.push({
-					value: matched,
-					type: type,
-					matches: match
-				});
-				soFar = soFar.slice( matched.length );
-			}
-		}
-
-		if ( !matched ) {
-			break;
-		}
-	}
-
-	// Return the length of the invalid excess
-	// if we're just parsing
-	// Otherwise, throw an error or return tokens
-	return parseOnly ?
-		soFar.length :
-		soFar ?
-			Sizzle.error( selector ) :
-			// Cache the tokens
-			tokenCache( selector, groups ).slice( 0 );
-};
-
-function toSelector( tokens ) {
-	var i = 0,
-		len = tokens.length,
-		selector = "";
-	for ( ; i < len; i++ ) {
-		selector += tokens[i].value;
-	}
-	return selector;
-}
-
-function addCombinator( matcher, combinator, base ) {
-	var dir = combinator.dir,
-		checkNonElements = base && dir === "parentNode",
-		doneName = done++;
-
-	return combinator.first ?
-		// Check against closest ancestor/preceding element
-		function( elem, context, xml ) {
-			while ( (elem = elem[ dir ]) ) {
-				if ( elem.nodeType === 1 || checkNonElements ) {
-					return matcher( elem, context, xml );
-				}
-			}
-		} :
-
-		// Check against all ancestor/preceding elements
-		function( elem, context, xml ) {
-			var oldCache, outerCache,
-				newCache = [ dirruns, doneName ];
-
-			// We can't set arbitrary data on XML nodes, so they don't benefit from dir caching
-			if ( xml ) {
-				while ( (elem = elem[ dir ]) ) {
-					if ( elem.nodeType === 1 || checkNonElements ) {
-						if ( matcher( elem, context, xml ) ) {
-							return true;
-						}
-					}
-				}
-			} else {
-				while ( (elem = elem[ dir ]) ) {
-					if ( elem.nodeType === 1 || checkNonElements ) {
-						outerCache = elem[ expando ] || (elem[ expando ] = {});
-						if ( (oldCache = outerCache[ dir ]) &&
-							oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
-
-							// Assign to newCache so results back-propagate to previous elements
-							return (newCache[ 2 ] = oldCache[ 2 ]);
-						} else {
-							// Reuse newcache so results back-propagate to previous elements
-							outerCache[ dir ] = newCache;
-
-							// A match means we're done; a fail means we have to keep checking
-							if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
-								return true;
-							}
-						}
-					}
-				}
-			}
-		};
-}
-
-function elementMatcher( matchers ) {
-	return matchers.length > 1 ?
-		function( elem, context, xml ) {
-			var i = matchers.length;
-			while ( i-- ) {
-				if ( !matchers[i]( elem, context, xml ) ) {
-					return false;
-				}
-			}
-			return true;
-		} :
-		matchers[0];
-}
-
-function multipleContexts( selector, contexts, results ) {
-	var i = 0,
-		len = contexts.length;
-	for ( ; i < len; i++ ) {
-		Sizzle( selector, contexts[i], results );
-	}
-	return results;
-}
-
-function condense( unmatched, map, filter, context, xml ) {
-	var elem,
-		newUnmatched = [],
-		i = 0,
-		len = unmatched.length,
-		mapped = map != null;
-
-	for ( ; i < len; i++ ) {
-		if ( (elem = unmatched[i]) ) {
-			if ( !filter || filter( elem, context, xml ) ) {
-				newUnmatched.push( elem );
-				if ( mapped ) {
-					map.push( i );
-				}
-			}
-		}
-	}
-
-	return newUnmatched;
-}
-
-function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
-	if ( postFilter && !postFilter[ expando ] ) {
-		postFilter = setMatcher( postFilter );
-	}
-	if ( postFinder && !postFinder[ expando ] ) {
-		postFinder = setMatcher( postFinder, postSelector );
-	}
-	return markFunction(function( seed, results, context, xml ) {
-		var temp, i, elem,
-			preMap = [],
-			postMap = [],
-			preexisting = results.length,
-
-			// Get initial elements from seed or context
-			elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
-
-			// Prefilter to get matcher input, preserving a map for seed-results synchronization
-			matcherIn = preFilter && ( seed || !selector ) ?
-				condense( elems, preMap, preFilter, context, xml ) :
-				elems,
-
-			matcherOut = matcher ?
-				// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
-				postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
-
-					// ...intermediate processing is necessary
-					[] :
-
-					// ...otherwise use results directly
-					results :
-				matcherIn;
-
-		// Find primary matches
-		if ( matcher ) {
-			matcher( matcherIn, matcherOut, context, xml );
-		}
-
-		// Apply postFilter
-		if ( postFilter ) {
-			temp = condense( matcherOut, postMap );
-			postFilter( temp, [], context, xml );
-
-			// Un-match failing elements by moving them back to matcherIn
-			i = temp.length;
-			while ( i-- ) {
-				if ( (elem = temp[i]) ) {
-					matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
-				}
-			}
-		}
-
-		if ( seed ) {
-			if ( postFinder || preFilter ) {
-				if ( postFinder ) {
-					// Get the final matcherOut by condensing this intermediate into postFinder contexts
-					temp = [];
-					i = matcherOut.length;
-					while ( i-- ) {
-						if ( (elem = matcherOut[i]) ) {
-							// Restore matcherIn since elem is not yet a final match
-							temp.push( (matcherIn[i] = elem) );
-						}
-					}
-					postFinder( null, (matcherOut = []), temp, xml );
-				}
-
-				// Move matched elements from seed to results to keep them synchronized
-				i = matcherOut.length;
-				while ( i-- ) {
-					if ( (elem = matcherOut[i]) &&
-						(temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) {
-
-						seed[temp] = !(results[temp] = elem);
-					}
-				}
-			}
-
-		// Add elements to results, through postFinder if defined
-		} else {
-			matcherOut = condense(
-				matcherOut === results ?
-					matcherOut.splice( preexisting, matcherOut.length ) :
-					matcherOut
-			);
-			if ( postFinder ) {
-				postFinder( null, results, matcherOut, xml );
-			} else {
-				push.apply( results, matcherOut );
-			}
-		}
-	});
-}
-
-function matcherFromTokens( tokens ) {
-	var checkContext, matcher, j,
-		len = tokens.length,
-		leadingRelative = Expr.relative[ tokens[0].type ],
-		implicitRelative = leadingRelative || Expr.relative[" "],
-		i = leadingRelative ? 1 : 0,
-
-		// The foundational matcher ensures that elements are reachable from top-level context(s)
-		matchContext = addCombinator( function( elem ) {
-			return elem === checkContext;
-		}, implicitRelative, true ),
-		matchAnyContext = addCombinator( function( elem ) {
-			return indexOf.call( checkContext, elem ) > -1;
-		}, implicitRelative, true ),
-		matchers = [ function( elem, context, xml ) {
-			return ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
-				(checkContext = context).nodeType ?
-					matchContext( elem, context, xml ) :
-					matchAnyContext( elem, context, xml ) );
-		} ];
-
-	for ( ; i < len; i++ ) {
-		if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
-			matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
-		} else {
-			matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
-
-			// Return special upon seeing a positional matcher
-			if ( matcher[ expando ] ) {
-				// Find the next relative operator (if any) for proper handling
-				j = ++i;
-				for ( ; j < len; j++ ) {
-					if ( Expr.relative[ tokens[j].type ] ) {
-						break;
-					}
-				}
-				return setMatcher(
-					i > 1 && elementMatcher( matchers ),
-					i > 1 && toSelector(
-						// If the preceding token was a descendant combinator, insert an implicit any-element `*`
-						tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" })
-					).replace( rtrim, "$1" ),
-					matcher,
-					i < j && matcherFromTokens( tokens.slice( i, j ) ),
-					j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
-					j < len && toSelector( tokens )
-				);
-			}
-			matchers.push( matcher );
-		}
-	}
-
-	return elementMatcher( matchers );
-}
-
-function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
-	var bySet = setMatchers.length > 0,
-		byElement = elementMatchers.length > 0,
-		superMatcher = function( seed, context, xml, results, outermost ) {
-			var elem, j, matcher,
-				matchedCount = 0,
-				i = "0",
-				unmatched = seed && [],
-				setMatched = [],
-				contextBackup = outermostContext,
-				// We must always have either seed elements or outermost context
-				elems = seed || byElement && Expr.find["TAG"]( "*", outermost ),
-				// Use integer dirruns iff this is the outermost matcher
-				dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),
-				len = elems.length;
-
-			if ( outermost ) {
-				outermostContext = context !== document && context;
-			}
-
-			// Add elements passing elementMatchers directly to results
-			// Keep `i` a string if there are no elements so `matchedCount` will be "00" below
-			// Support: IE<9, Safari
-			// Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
-			for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
-				if ( byElement && elem ) {
-					j = 0;
-					while ( (matcher = elementMatchers[j++]) ) {
-						if ( matcher( elem, context, xml ) ) {
-							results.push( elem );
-							break;
-						}
-					}
-					if ( outermost ) {
-						dirruns = dirrunsUnique;
-					}
-				}
-
-				// Track unmatched elements for set filters
-				if ( bySet ) {
-					// They will have gone through all possible matchers
-					if ( (elem = !matcher && elem) ) {
-						matchedCount--;
-					}
-
-					// Lengthen the array for every element, matched or not
-					if ( seed ) {
-						unmatched.push( elem );
-					}
-				}
-			}
-
-			// Apply set filters to unmatched elements
-			matchedCount += i;
-			if ( bySet && i !== matchedCount ) {
-				j = 0;
-				while ( (matcher = setMatchers[j++]) ) {
-					matcher( unmatched, setMatched, context, xml );
-				}
-
-				if ( seed ) {
-					// Reintegrate element matches to eliminate the need for sorting
-					if ( matchedCount > 0 ) {
-						while ( i-- ) {
-							if ( !(unmatched[i] || setMatched[i]) ) {
-								setMatched[i] = pop.call( results );
-							}
-						}
-					}
-
-					// Discard index placeholder values to get only actual matches
-					setMatched = condense( setMatched );
-				}
-
-				// Add matches to results
-				push.apply( results, setMatched );
-
-				// Seedless set matches succeeding multiple successful matchers stipulate sorting
-				if ( outermost && !seed && setMatched.length > 0 &&
-					( matchedCount + setMatchers.length ) > 1 ) {
-
-					Sizzle.uniqueSort( results );
-				}
-			}
-
-			// Override manipulation of globals by nested matchers
-			if ( outermost ) {
-				dirruns = dirrunsUnique;
-				outermostContext = contextBackup;
-			}
-
-			return unmatched;
-		};
-
-	return bySet ?
-		markFunction( superMatcher ) :
-		superMatcher;
-}
-
-compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
-	var i,
-		setMatchers = [],
-		elementMatchers = [],
-		cached = compilerCache[ selector + " " ];
-
-	if ( !cached ) {
-		// Generate a function of recursive functions that can be used to check each element
-		if ( !match ) {
-			match = tokenize( selector );
-		}
-		i = match.length;
-		while ( i-- ) {
-			cached = matcherFromTokens( match[i] );
-			if ( cached[ expando ] ) {
-				setMatchers.push( cached );
-			} else {
-				elementMatchers.push( cached );
-			}
-		}
-
-		// Cache the compiled function
-		cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
-
-		// Save selector and tokenization
-		cached.selector = selector;
-	}
-	return cached;
-};
-
-/**
- * A low-level selection function that works with Sizzle's compiled
- *  selector functions
- * @param {String|Function} selector A selector or a pre-compiled
- *  selector function built with Sizzle.compile
- * @param {Element} context
- * @param {Array} [results]
- * @param {Array} [seed] A set of elements to match against
- */
-select = Sizzle.select = function( selector, context, results, seed ) {
-	var i, tokens, token, type, find,
-		compiled = typeof selector === "function" && selector,
-		match = !seed && tokenize( (selector = compiled.selector || selector) );
-
-	results = results || [];
-
-	// Try to minimize operations if there is no seed and only one group
-	if ( match.length === 1 ) {
-
-		// Take a shortcut and set the context if the root selector is an ID
-		tokens = match[0] = match[0].slice( 0 );
-		if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
-				support.getById && context.nodeType === 9 && documentIsHTML &&
-				Expr.relative[ tokens[1].type ] ) {
-
-			context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
-			if ( !context ) {
-				return results;
-
-			// Precompiled matchers will still verify ancestry, so step up a level
-			} else if ( compiled ) {
-				context = context.parentNode;
-			}
-
-			selector = selector.slice( tokens.shift().value.length );
-		}
-
-		// Fetch a seed set for right-to-left matching
-		i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
-		while ( i-- ) {
-			token = tokens[i];
-
-			// Abort if we hit a combinator
-			if ( Expr.relative[ (type = token.type) ] ) {
-				break;
-			}
-			if ( (find = Expr.find[ type ]) ) {
-				// Search, expanding context for leading sibling combinators
-				if ( (seed = find(
-					token.matches[0].replace( runescape, funescape ),
-					rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
-				)) ) {
-
-					// If seed is empty or no tokens remain, we can return early
-					tokens.splice( i, 1 );
-					selector = seed.length && toSelector( tokens );
-					if ( !selector ) {
-						push.apply( results, seed );
-						return results;
-					}
-
-					break;
-				}
-			}
-		}
-	}
-
-	// Compile and execute a filtering function if one is not provided
-	// Provide `match` to avoid retokenization if we modified the selector above
-	( compiled || compile( selector, match ) )(
-		seed,
-		context,
-		!documentIsHTML,
-		results,
-		rsibling.test( selector ) && testContext( context.parentNode ) || context
-	);
-	return results;
-};
-
-// One-time assignments
-
-// Sort stability
-support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
-
-// Support: Chrome<14
-// Always assume duplicates if they aren't passed to the comparison function
-support.detectDuplicates = !!hasDuplicate;
-
-// Initialize against the default document
-setDocument();
-
-// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
-// Detached nodes confoundingly follow *each other*
-support.sortDetached = assert(function( div1 ) {
-	// Should return 1, but returns 4 (following)
-	return div1.compareDocumentPosition( document.createElement("div") ) & 1;
-});
-
-// Support: IE<8
-// Prevent attribute/property "interpolation"
-// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !assert(function( div ) {
-	div.innerHTML = "<a href='#'></a>";
-	return div.firstChild.getAttribute("href") === "#" ;
-}) ) {
-	addHandle( "type|href|height|width", function( elem, name, isXML ) {
-		if ( !isXML ) {
-			return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
-		}
-	});
-}
-
-// Support: IE<9
-// Use defaultValue in place of getAttribute("value")
-if ( !support.attributes || !assert(function( div ) {
-	div.innerHTML = "<input/>";
-	div.firstChild.setAttribute( "value", "" );
-	return div.firstChild.getAttribute( "value" ) === "";
-}) ) {
-	addHandle( "value", function( elem, name, isXML ) {
-		if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
-			return elem.defaultValue;
-		}
-	});
-}
-
-// Support: IE<9
-// Use getAttributeNode to fetch booleans when getAttribute lies
-if ( !assert(function( div ) {
-	return div.getAttribute("disabled") == null;
-}) ) {
-	addHandle( booleans, function( elem, name, isXML ) {
-		var val;
-		if ( !isXML ) {
-			return elem[ name ] === true ? name.toLowerCase() :
-					(val = elem.getAttributeNode( name )) && val.specified ?
-					val.value :
-				null;
-		}
-	});
-}
-
-return Sizzle;
-
-})( window );
-
-
-
-jQuery.find = Sizzle;
-jQuery.expr = Sizzle.selectors;
-jQuery.expr[":"] = jQuery.expr.pseudos;
-jQuery.unique = Sizzle.uniqueSort;
-jQuery.text = Sizzle.getText;
-jQuery.isXMLDoc = Sizzle.isXML;
-jQuery.contains = Sizzle.contains;
-
-
-
-var rneedsContext = jQuery.expr.match.needsContext;
-
-var rsingleTag = (/^<(\w+)\s*\/?>(?:<\/\1>|)$/);
-
-
-
-var risSimple = /^.[^:#\[\.,]*$/;
-
-// Implement the identical functionality for filter and not
-function winnow( elements, qualifier, not ) {
-	if ( jQuery.isFunction( qualifier ) ) {
-		return jQuery.grep( elements, function( elem, i ) {
-			/* jshint -W018 */
-			return !!qualifier.call( elem, i, elem ) !== not;
-		});
-
-	}
-
-	if ( qualifier.nodeType ) {
-		return jQuery.grep( elements, function( elem ) {
-			return ( elem === qualifier ) !== not;
-		});
-
-	}
-
-	if ( typeof qualifier === "string" ) {
-		if ( risSimple.test( qualifier ) ) {
-			return jQuery.filter( qualifier, elements, not );
-		}
-
-		qualifier = jQuery.filter( qualifier, elements );
-	}
-
-	return jQuery.grep( elements, function( elem ) {
-		return ( jQuery.inArray( elem, qualifier ) >= 0 ) !== not;
-	});
-}
-
-jQuery.filter = function( expr, elems, not ) {
-	var elem = elems[ 0 ];
-
-	if ( not ) {
-		expr = ":not(" + expr + ")";
-	}
-
-	return elems.length === 1 && elem.nodeType === 1 ?
-		jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] :
-		jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
-			return elem.nodeType === 1;
-		}));
-};
-
-jQuery.fn.extend({
-	find: function( selector ) {
-		var i,
-			ret = [],
-			self = this,
-			len = self.length;
-
-		if ( typeof selector !== "string" ) {
-			return this.pushStack( jQuery( selector ).filter(function() {
-				for ( i = 0; i < len; i++ ) {
-					if ( jQuery.contains( self[ i ], this ) ) {
-						return true;
-					}
-				}
-			}) );
-		}
-
-		for ( i = 0; i < len; i++ ) {
-			jQuery.find( selector, self[ i ], ret );
-		}
-
-		// Needed because $( selector, context ) becomes $( context ).find( selector )
-		ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret );
-		ret.selector = this.selector ? this.selector + " " + selector : selector;
-		return ret;
-	},
-	filter: function( selector ) {
-		return this.pushStack( winnow(this, selector || [], false) );
-	},
-	not: function( selector ) {
-		return this.pushStack( winnow(this, selector || [], true) );
-	},
-	is: function( selector ) {
-		return !!winnow(
-			this,
-
-			// If this is a positional/relative selector, check membership in the returned set
-			// so $("p:first").is("p:last") won't return true for a doc with two "p".
-			typeof selector === "string" && rneedsContext.test( selector ) ?
-				jQuery( selector ) :
-				selector || [],
-			false
-		).length;
-	}
-});
-
-
-// Initialize a jQuery object
-
-
-// A central reference to the root jQuery(document)
-var rootjQuery,
-
-	// Use the correct document accordingly with window argument (sandbox)
-	document = window.document,
-
-	// A simple way to check for HTML strings
-	// Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
-	// Strict HTML recognition (#11290: must start with <)
-	rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,
-
-	init = jQuery.fn.init = function( selector, context ) {
-		var match, elem;
-
-		// HANDLE: $(""), $(null), $(undefined), $(false)
-		if ( !selector ) {
-			return this;
-		}
-
-		// Handle HTML strings
-		if ( typeof selector === "string" ) {
-			if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
-				// Assume that strings that start and end with <> are HTML and skip the regex check
-				match = [ null, selector, null ];
-
-			} else {
-				match = rquickExpr.exec( selector );
-			}
-
-			// Match html or make sure no context is specified for #id
-			if ( match && (match[1] || !context) ) {
-
-				// HANDLE: $(html) -> $(array)
-				if ( match[1] ) {
-					context = context instanceof jQuery ? context[0] : context;
-
-					// scripts is true for back-compat
-					// Intentionally let the error be thrown if parseHTML is not present
-					jQuery.merge( this, jQuery.parseHTML(
-						match[1],
-						context && context.nodeType ? context.ownerDocument || context : document,
-						true
-					) );
-
-					// HANDLE: $(html, props)
-					if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) {
-						for ( match in context ) {
-							// Properties of context are called as methods if possible
-							if ( jQuery.isFunction( this[ match ] ) ) {
-								this[ match ]( context[ match ] );
-
-							// ...and otherwise set as attributes
-							} else {
-								this.attr( match, context[ match ] );
-							}
-						}
-					}
-
-					return this;
-
-				// HANDLE: $(#id)
-				} else {
-					elem = document.getElementById( match[2] );
-
-					// Check parentNode to catch when Blackberry 4.6 returns
-					// nodes that are no longer in the document #6963
-					if ( elem && elem.parentNode ) {
-						// Handle the case where IE and Opera return items
-						// by name instead of ID
-						if ( elem.id !== match[2] ) {
-							return rootjQuery.find( selector );
-						}
-
-						// Otherwise, we inject the element directly into the jQuery object
-						this.length = 1;
-						this[0] = elem;
-					}
-
-					this.context = document;
-					this.selector = selector;
-					return this;
-				}
-
-			// HANDLE: $(expr, $(...))
-			} else if ( !context || context.jquery ) {
-				return ( context || rootjQuery ).find( selector );
-
-			// HANDLE: $(expr, context)
-			// (which is just equivalent to: $(context).find(expr)
-			} else {
-				return this.constructor( context ).find( selector );
-			}
-
-		// HANDLE: $(DOMElement)
-		} else if ( selector.nodeType ) {
-			this.context = this[0] = selector;
-			this.length = 1;
-			return this;
-
-		// HANDLE: $(function)
-		// Shortcut for document ready
-		} else if ( jQuery.isFunction( selector ) ) {
-			return typeof rootjQuery.ready !== "undefined" ?
-				rootjQuery.ready( selector ) :
-				// Execute immediately if ready is not present
-				selector( jQuery );
-		}
-
-		if ( selector.selector !== undefined ) {
-			this.selector = selector.selector;
-			this.context = selector.context;
-		}
-
-		return jQuery.makeArray( selector, this );
-	};
-
-// Give the init function the jQuery prototype for later instantiation
-init.prototype = jQuery.fn;
-
-// Initialize central reference
-rootjQuery = jQuery( document );
-
-
-var rparentsprev = /^(?:parents|prev(?:Until|All))/,
-	// methods guaranteed to produce a unique set when starting from a unique set
-	guaranteedUnique = {
-		children: true,
-		contents: true,
-		next: true,
-		prev: true
-	};
-
-jQuery.extend({
-	dir: function( elem, dir, until ) {
-		var matched = [],
-			cur = elem[ dir ];
-
-		while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
-			if ( cur.nodeType === 1 ) {
-				matched.push( cur );
-			}
-			cur = cur[dir];
-		}
-		return matched;
-	},
-
-	sibling: function( n, elem ) {
-		var r = [];
-
-		for ( ; n; n = n.nextSibling ) {
-			if ( n.nodeType === 1 && n !== elem ) {
-				r.push( n );
-			}
-		}
-
-		return r;
-	}
-});
-
-jQuery.fn.extend({
-	has: function( target ) {
-		var i,
-			targets = jQuery( target, this ),
-			len = targets.length;
-
-		return this.filter(function() {
-			for ( i = 0; i < len; i++ ) {
-				if ( jQuery.contains( this, targets[i] ) ) {
-					return true;
-				}
-			}
-		});
-	},
-
-	closest: function( selectors, context ) {
-		var cur,
-			i = 0,
-			l = this.length,
-			matched = [],
-			pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ?
-				jQuery( selectors, context || this.context ) :
-				0;
-
-		for ( ; i < l; i++ ) {
-			for ( cur = this[i]; cur && cur !== context; cur = cur.parentNode ) {
-				// Always skip document fragments
-				if ( cur.nodeType < 11 && (pos ?
-					pos.index(cur) > -1 :
-
-					// Don't pass non-elements to Sizzle
-					cur.nodeType === 1 &&
-						jQuery.find.matchesSelector(cur, selectors)) ) {
-
-					matched.push( cur );
-					break;
-				}
-			}
-		}
-
-		return this.pushStack( matched.length > 1 ? jQuery.unique( matched ) : matched );
-	},
-
-	// Determine the position of an element within
-	// the matched set of elements
-	index: function( elem ) {
-
-		// No argument, return index in parent
-		if ( !elem ) {
-			return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1;
-		}
-
-		// index in selector
-		if ( typeof elem === "string" ) {
-			return jQuery.inArray( this[0], jQuery( elem ) );
-		}
-
-		// Locate the position of the desired element
-		return jQuery.inArray(
-			// If it receives a jQuery object, the first element is used
-			elem.jquery ? elem[0] : elem, this );
-	},
-
-	add: function( selector, context ) {
-		return this.pushStack(
-			jQuery.unique(
-				jQuery.merge( this.get(), jQuery( selector, context ) )
-			)
-		);
-	},
-
-	addBack: function( selector ) {
-		return this.add( selector == null ?
-			this.prevObject : this.prevObject.filter(selector)
-		);
-	}
-});
-
-function sibling( cur, dir ) {
-	do {
-		cur = cur[ dir ];
-	} while ( cur && cur.nodeType !== 1 );
-
-	return cur;
-}
-
-jQuery.each({
-	parent: function( elem ) {
-		var parent = elem.parentNode;
-		return parent && parent.nodeType !== 11 ? parent : null;
-	},
-	parents: function( elem ) {
-		return jQuery.dir( elem, "parentNode" );
-	},
-	parentsUntil: function( elem, i, until ) {
-		return jQuery.dir( elem, "parentNode", until );
-	},
-	next: function( elem ) {
-		return sibling( elem, "nextSibling" );
-	},
-	prev: function( elem ) {
-		return sibling( elem, "previousSibling" );
-	},
-	nextAll: function( elem ) {
-		return jQuery.dir( elem, "nextSibling" );
-	},
-	prevAll: function( elem ) {
-		return jQuery.dir( elem, "previousSibling" );
-	},
-	nextUntil: function( elem, i, until ) {
-		return jQuery.dir( elem, "nextSibling", until );
-	},
-	prevUntil: function( elem, i, until ) {
-		return jQuery.dir( elem, "previousSibling", until );
-	},
-	siblings: function( elem ) {
-		return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
-	},
-	children: function( elem ) {
-		return jQuery.sibling( elem.firstChild );
-	},
-	contents: function( elem ) {
-		return jQuery.nodeName( elem, "iframe" ) ?
-			elem.contentDocument || elem.contentWindow.document :
-			jQuery.merge( [], elem.childNodes );
-	}
-}, function( name, fn ) {
-	jQuery.fn[ name ] = function( until, selector ) {
-		var ret = jQuery.map( this, fn, until );
-
-		if ( name.slice( -5 ) !== "Until" ) {
-			selector = until;
-		}
-
-		if ( selector && typeof selector === "string" ) {
-			ret = jQuery.filter( selector, ret );
-		}
-
-		if ( this.length > 1 ) {
-			// Remove duplicates
-			if ( !guaranteedUnique[ name ] ) {
-				ret = jQuery.unique( ret );
-			}
-
-			// Reverse order for parents* and prev-derivatives
-			if ( rparentsprev.test( name ) ) {
-				ret = ret.reverse();
-			}
-		}
-
-		return this.pushStack( ret );
-	};
-});
-var rnotwhite = (/\S+/g);
-
-
-
-// String to Object options format cache
-var optionsCache = {};
-
-// Convert String-formatted options into Object-formatted ones and store in cache
-function createOptions( options ) {
-	var object = optionsCache[ options ] = {};
-	jQuery.each( options.match( rnotwhite ) || [], function( _, flag ) {
-		object[ flag ] = true;
-	});
-	return object;
-}
-
-/*
- * Create a callback list using the following parameters:
- *
- *	options: an optional list of space-separated options that will change how
- *			the callback list behaves or a more traditional option object
- *
- * By default a callback list will act like an event callback list and can be
- * "fired" multiple times.
- *
- * Possible options:
- *
- *	once:			will ensure the callback list can only be fired once (like a Deferred)
- *
- *	memory:			will keep track of previous values and will call any callback added
- *					after the list has been fired right away with the latest "memorized"
- *					values (like a Deferred)
- *
- *	unique:			will ensure a callback can only be added once (no duplicate in the list)
- *
- *	stopOnFalse:	interrupt callings when a callback returns false
- *
- */
-jQuery.Callbacks = function( options ) {
-
-	// Convert options from String-formatted to Object-formatted if needed
-	// (we check in cache first)
-	options = typeof options === "string" ?
-		( optionsCache[ options ] || createOptions( options ) ) :
-		jQuery.extend( {}, options );
-
-	var // Flag to know if list is currently firing
-		firing,
-		// Last fire value (for non-forgettable lists)
-		memory,
-		// Flag to know if list was already fired
-		fired,
-		// End of the loop when firing
-		firingLength,
-		// Index of currently firing callback (modified by remove if needed)
-		firingIndex,
-		// First callback to fire (used internally by add and fireWith)
-		firingStart,
-		// Actual callback list
-		list = [],
-		// Stack of fire calls for repeatable lists
-		stack = !options.once && [],
-		// Fire callbacks
-		fire = function( data ) {
-			memory = options.memory && data;
-			fired = true;
-			firingIndex = firingStart || 0;
-			firingStart = 0;
-			firingLength = list.length;
-			firing = true;
-			for ( ; list && firingIndex < firingLength; firingIndex++ ) {
-				if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) {
-					memory = false; // To prevent further calls using add
-					break;
-				}
-			}
-			firing = false;
-			if ( list ) {
-				if ( stack ) {
-					if ( stack.length ) {
-						fire( stack.shift() );
-					}
-				} else if ( memory ) {
-					list = [];
-				} else {
-					self.disable();
-				}
-			}
-		},
-		// Actual Callbacks object
-		self = {
-			// Add a callback or a collection of callbacks to the list
-			add: function() {
-				if ( list ) {
-					// First, we save the current length
-					var start = list.length;
-					(function add( args ) {
-						jQuery.each( args, function( _, arg ) {
-							var type = jQuery.type( arg );
-							if ( type === "function" ) {
-								if ( !options.unique || !self.has( arg ) ) {
-									list.push( arg );
-								}
-							} else if ( arg && arg.length && type !== "string" ) {
-								// Inspect recursively
-								add( arg );
-							}
-						});
-					})( arguments );
-					// Do we need to add the callbacks to the
-					// current firing batch?
-					if ( firing ) {
-						firingLength = list.length;
-					// With memory, if we're not firing then
-					// we should call right away
-					} else if ( memory ) {
-						firingStart = start;
-						fire( memory );
-					}
-				}
-				return this;
-			},
-			// Remove a callback from the list
-			remove: function() {
-				if ( list ) {
-					jQuery.each( arguments, function( _, arg ) {
-						var index;
-						while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
-							list.splice( index, 1 );
-							// Handle firing indexes
-							if ( firing ) {
-								if ( index <= firingLength ) {
-									firingLength--;
-								}
-								if ( index <= firingIndex ) {
-									firingIndex--;
-								}
-							}
-						}
-					});
-				}
-				return this;
-			},
-			// Check if a given callback is in the list.
-			// If no argument is given, return whether or not list has callbacks attached.
-			has: function( fn ) {
-				return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length );
-			},
-			// Remove all callbacks from the list
-			empty: function() {
-				list = [];
-				firingLength = 0;
-				return this;
-			},
-			// Have the list do nothing anymore
-			disable: function() {
-				list = stack = memory = undefined;
-				return this;
-			},
-			// Is it disabled?
-			disabled: function() {
-				return !list;
-			},
-			// Lock the list in its current state
-			lock: function() {
-				stack = undefined;
-				if ( !memory ) {
-					self.disable();
-				}
-				return this;
-			},
-			// Is it locked?
-			locked: function() {
-				return !stack;
-			},
-			// Call all callbacks with the given context and arguments
-			fireWith: function( context, args ) {
-				if ( list && ( !fired || stack ) ) {
-					args = args || [];
-					args = [ context, args.slice ? args.slice() : args ];
-					if ( firing ) {
-						stack.push( args );
-					} else {
-						fire( args );
-					}
-				}
-				return this;
-			},
-			// Call all the callbacks with the given arguments
-			fire: function() {
-				self.fireWith( this, arguments );
-				return this;
-			},
-			// To know if the callbacks have already been called at least once
-			fired: function() {
-				return !!fired;
-			}
-		};
-
-	return self;
-};
-
-
-jQuery.extend({
-
-	Deferred: function( func ) {
-		var tuples = [
-				// action, add listener, listener list, final state
-				[ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ],
-				[ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ],
-				[ "notify", "progress", jQuery.Callbacks("memory") ]
-			],
-			state = "pending",
-			promise = {
-				state: function() {
-					return state;
-				},
-				always: function() {
-					deferred.done( arguments ).fail( arguments );
-					return this;
-				},
-				then: function( /* fnDone, fnFail, fnProgress */ ) {
-					var fns = arguments;
-					return jQuery.Deferred(function( newDefer ) {
-						jQuery.each( tuples, function( i, tuple ) {
-							var fn = jQuery.isFunction( fns[ i ] ) && fns[ i ];
-							// deferred[ done | fail | progress ] for forwarding actions to newDefer
-							deferred[ tuple[1] ](function() {
-								var returned = fn && fn.apply( this, arguments );
-								if ( returned && jQuery.isFunction( returned.promise ) ) {
-									returned.promise()
-										.done( newDefer.resolve )
-										.fail( newDefer.reject )
-										.progress( newDefer.notify );
-								} else {
-									newDefer[ tuple[ 0 ] + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments );
-								}
-							});
-						});
-						fns = null;
-					}).promise();
-				},
-				// Get a promise for this deferred
-				// If obj is provided, the promise aspect is added to the object
-				promise: function( obj ) {
-					return obj != null ? jQuery.extend( obj, promise ) : promise;
-				}
-			},
-			deferred = {};
-
-		// Keep pipe for back-compat
-		promise.pipe = promise.then;
-
-		// Add list-specific methods
-		jQuery.each( tuples, function( i, tuple ) {
-			var list = tuple[ 2 ],
-				stateString = tuple[ 3 ];
-
-			// promise[ done | fail | progress ] = list.add
-			promise[ tuple[1] ] = list.add;
-
-			// Handle state
-			if ( stateString ) {
-				list.add(function() {
-					// state = [ resolved | rejected ]
-					state = stateString;
-
-				// [ reject_list | resolve_list ].disable; progress_list.lock
-				}, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );
-			}
-
-			// deferred[ resolve | reject | notify ]
-			deferred[ tuple[0] ] = function() {
-				deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments );
-				return this;
-			};
-			deferred[ tuple[0] + "With" ] = list.fireWith;
-		});
-
-		// Make the deferred a promise
-		promise.promise( deferred );
-
-		// Call given func if any
-		if ( func ) {
-			func.call( deferred, deferred );
-		}
-
-		// All done!
-		return deferred;
-	},
-
-	// Deferred helper
-	when: function( subordinate /* , ..., subordinateN */ ) {
-		var i = 0,
-			resolveValues = slice.call( arguments ),
-			length = resolveValues.length,
-
-			// the count of uncompleted subordinates
-			remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,
-
-			// the master Deferred. If resolveValues consist of only a single Deferred, just use that.
-			deferred = remaining === 1 ? subordinate : jQuery.Deferred(),
-
-			// Update function for both resolve and progress values
-			updateFunc = function( i, contexts, values ) {
-				return function( value ) {
-					contexts[ i ] = this;
-					values[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
-					if ( values === progressValues ) {
-						deferred.notifyWith( contexts, values );
-
-					} else if ( !(--remaining) ) {
-						deferred.resolveWith( contexts, values );
-					}
-				};
-			},
-
-			progressValues, progressContexts, resolveContexts;
-
-		// add listeners to Deferred subordinates; treat others as resolved
-		if ( length > 1 ) {
-			progressValues = new Array( length );
-			progressContexts = new Array( length );
-			resolveContexts = new Array( length );
-			for ( ; i < length; i++ ) {
-				if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {
-					resolveValues[ i ].promise()
-						.done( updateFunc( i, resolveContexts, resolveValues ) )
-						.fail( deferred.reject )
-						.progress( updateFunc( i, progressContexts, progressValues ) );
-				} else {
-					--remaining;
-				}
-			}
-		}
-
-		// if we're not waiting on anything, resolve the master
-		if ( !remaining ) {
-			deferred.resolveWith( resolveContexts, resolveValues );
-		}
-
-		return deferred.promise();
-	}
-});
-
-
-// The deferred used on DOM ready
-var readyList;
-
-jQuery.fn.ready = function( fn ) {
-	// Add the callback
-	jQuery.ready.promise().done( fn );
-
-	return this;
-};
-
-jQuery.extend({
-	// Is the DOM ready to be used? Set to true once it occurs.
-	isReady: false,
-
-	// A counter to track how many items to wait for before
-	// the ready event fires. See #6781
-	readyWait: 1,
-
-	// Hold (or release) the ready event
-	holdReady: function( hold ) {
-		if ( hold ) {
-			jQuery.readyWait++;
-		} else {
-			jQuery.ready( true );
-		}
-	},
-
-	// Handle when the DOM is ready
-	ready: function( wait ) {
-
-		// Abort if there are pending holds or we're already ready
-		if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
-			return;
-		}
-
-		// Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
-		if ( !document.body ) {
-			return setTimeout( jQuery.ready );
-		}
-
-		// Remember that the DOM is ready
-		jQuery.isReady = true;
-
-		// If a normal DOM Ready event fired, decrement, and wait if need be
-		if ( wait !== true && --jQuery.readyWait > 0 ) {
-			return;
-		}
-
-		// If there are functions bound, to execute
-		readyList.resolveWith( document, [ jQuery ] );
-
-		// Trigger any bound ready events
-		if ( jQuery.fn.triggerHandler ) {
-			jQuery( document ).triggerHandler( "ready" );
-			jQuery( document ).off( "ready" );
-		}
-	}
-});
-
-/**
- * Clean-up method for dom ready events
- */
-function detach() {
-	if ( document.addEventListener ) {
-		document.removeEventListener( "DOMContentLoaded", completed, false );
-		window.removeEventListener( "load", completed, false );
-
-	} else {
-		document.detachEvent( "onreadystatechange", completed );
-		window.detachEvent( "onload", completed );
-	}
-}
-
-/**
- * The ready event handler and self cleanup method
- */
-function completed() {
-	// readyState === "complete" is good enough for us to call the dom ready in oldIE
-	if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) {
-		detach();
-		jQuery.ready();
-	}
-}
-
-jQuery.ready.promise = function( obj ) {
-	if ( !readyList ) {
-
-		readyList = jQuery.Deferred();
-
-		// Catch cases where $(document).ready() is called after the browser event has already occurred.
-		// we once tried to use readyState "interactive" here, but it caused issues like the one
-		// discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15
-		if ( document.readyState === "complete" ) {
-			// Handle it asynchronously to allow scripts the opportunity to delay ready
-			setTimeout( jQuery.ready );
-
-		// Standards-based browsers support DOMContentLoaded
-		} else if ( document.addEventListener ) {
-			// Use the handy event callback
-			document.addEventListener( "DOMContentLoaded", completed, false );
-
-			// A fallback to window.onload, that will always work
-			window.addEventListener( "load", completed, false );
-
-		// If IE event model is used
-		} else {
-			// Ensure firing before onload, maybe late but safe also for iframes
-			document.attachEvent( "onreadystatechange", completed );
-
-			// A fallback to window.onload, that will always work
-			window.attachEvent( "onload", completed );
-
-			// If IE and not a frame
-			// continually check to see if the document is ready
-			var top = false;
-
-			try {
-				top = window.frameElement == null && document.documentElement;
-			} catch(e) {}
-
-			if ( top && top.doScroll ) {
-				(function doScrollCheck() {
-					if ( !jQuery.isReady ) {
-
-						try {
-							// Use the trick by Diego Perini
-							// http://javascript.nwbox.com/IEContentLoaded/
-							top.doScroll("left");
-						} catch(e) {
-							return setTimeout( doScrollCheck, 50 );
-						}
-
-						// detach all dom ready events
-						detach();
-
-						// and execute any waiting functions
-						jQuery.ready();
-					}
-				})();
-			}
-		}
-	}
-	return readyList.promise( obj );
-};
-
-
-var strundefined = typeof undefined;
-
-
-
-// Support: IE<9
-// Iteration over object's inherited properties before its own
-var i;
-for ( i in jQuery( support ) ) {
-	break;
-}
-support.ownLast = i !== "0";
-
-// Note: most support tests are defined in their respective modules.
-// false until the test is run
-support.inlineBlockNeedsLayout = false;
-
-// Execute ASAP in case we need to set body.style.zoom
-jQuery(function() {
-	// Minified: var a,b,c,d
-	var val, div, body, container;
-
-	body = document.getElementsByTagName( "body" )[ 0 ];
-	if ( !body || !body.style ) {
-		// Return for frameset docs that don't have a body
-		return;
-	}
-
-	// Setup
-	div = document.createElement( "div" );
-	container = document.createElement( "div" );
-	container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
-	body.appendChild( container ).appendChild( div );
-
-	if ( typeof div.style.zoom !== strundefined ) {
-		// Support: IE<8
-		// Check if natively block-level elements act like inline-block
-		// elements when setting their display to 'inline' and giving
-		// them layout
-		div.style.cssText = "display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1";
-
-		support.inlineBlockNeedsLayout = val = div.offsetWidth === 3;
-		if ( val ) {
-			// Prevent IE 6 from affecting layout for positioned elements #11048
-			// Prevent IE from shrinking the body in IE 7 mode #12869
-			// Support: IE<8
-			body.style.zoom = 1;
-		}
-	}
-
-	body.removeChild( container );
-});
-
-
-
-
-(function() {
-	var div = document.createElement( "div" );
-
-	// Execute the test only if not already executed in another module.
-	if (support.deleteExpando == null) {
-		// Support: IE<9
-		support.deleteExpando = true;
-		try {
-			delete div.test;
-		} catch( e ) {
-			support.deleteExpando = false;
-		}
-	}
-
-	// Null elements to avoid leaks in IE.
-	div = null;
-})();
-
-
-/**
- * Determines whether an object can have data
- */
-jQuery.acceptData = function( elem ) {
-	var noData = jQuery.noData[ (elem.nodeName + " ").toLowerCase() ],
-		nodeType = +elem.nodeType || 1;
-
-	// Do not set data on non-element DOM nodes because it will not be cleared (#8335).
-	return nodeType !== 1 && nodeType !== 9 ?
-		false :
-
-		// Nodes accept data unless otherwise specified; rejection can be conditional
-		!noData || noData !== true && elem.getAttribute("classid") === noData;
-};
-
-
-var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
-	rmultiDash = /([A-Z])/g;
-
-function dataAttr( elem, key, data ) {
-	// If nothing was found internally, try to fetch any
-	// data from the HTML5 data-* attribute
-	if ( data === undefined && elem.nodeType === 1 ) {
-
-		var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
-
-		data = elem.getAttribute( name );
-
-		if ( typeof data === "string" ) {
-			try {
-				data = data === "true" ? true :
-					data === "false" ? false :
-					data === "null" ? null :
-					// Only convert to a number if it doesn't change the string
-					+data + "" === data ? +data :
-					rbrace.test( data ) ? jQuery.parseJSON( data ) :
-					data;
-			} catch( e ) {}
-
-			// Make sure we set the data so it isn't changed later
-			jQuery.data( elem, key, data );
-
-		} else {
-			data = undefined;
-		}
-	}
-
-	return data;
-}
-
-// checks a cache object for emptiness
-function isEmptyDataObject( obj ) {
-	var name;
-	for ( name in obj ) {
-
-		// if the public data object is empty, the private is still empty
-		if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
-			continue;
-		}
-		if ( name !== "toJSON" ) {
-			return false;
-		}
-	}
-
-	return true;
-}
-
-function internalData( elem, name, data, pvt /* Internal Use Only */ ) {
-	if ( !jQuery.acceptData( elem ) ) {
-		return;
-	}
-
-	var ret, thisCache,
-		internalKey = jQuery.expando,
-
-		// We have to handle DOM nodes and JS objects differently because IE6-7
-		// can't GC object references properly across the DOM-JS boundary
-		isNode = elem.nodeType,
-
-		// Only DOM nodes need the global jQuery cache; JS object data is
-		// attached directly to the object so GC can occur automatically
-		cache = isNode ? jQuery.cache : elem,
-
-		// Only defining an ID for JS objects if its cache already exists allows
-		// the code to shortcut on the same path as a DOM node with no cache
-		id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey;
-
-	// Avoid doing any more work than we need to when trying to get data on an
-	// object that has no data at all
-	if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && data === undefined && typeof name === "string" ) {
-		return;
-	}
-
-	if ( !id ) {
-		// Only DOM nodes need a new unique ID for each element since their data
-		// ends up in the global cache
-		if ( isNode ) {
-			id = elem[ internalKey ] = deletedIds.pop() || jQuery.guid++;
-		} else {
-			id = internalKey;
-		}
-	}
-
-	if ( !cache[ id ] ) {
-		// Avoid exposing jQuery metadata on plain JS objects when the object
-		// is serialized using JSON.stringify
-		cache[ id ] = isNode ? {} : { toJSON: jQuery.noop };
-	}
-
-	// An object can be passed to jQuery.data instead of a key/value pair; this gets
-	// shallow copied over onto the existing cache
-	if ( typeof name === "object" || typeof name === "function" ) {
-		if ( pvt ) {
-			cache[ id ] = jQuery.extend( cache[ id ], name );
-		} else {
-			cache[ id ].data = jQuery.extend( cache[ id ].data, name );
-		}
-	}
-
-	thisCache = cache[ id ];
-
-	// jQuery data() is stored in a separate object inside the object's internal data
-	// cache in order to avoid key collisions between internal data and user-defined
-	// data.
-	if ( !pvt ) {
-		if ( !thisCache.data ) {
-			thisCache.data = {};
-		}
-
-		thisCache = thisCache.data;
-	}
-
-	if ( data !== undefined ) {
-		thisCache[ jQuery.camelCase( name ) ] = data;
-	}
-
-	// Check for both converted-to-camel and non-converted data property names
-	// If a data property was specified
-	if ( typeof name === "string" ) {
-
-		// First Try to find as-is property data
-		ret = thisCache[ name ];
-
-		// Test for null|undefined property data
-		if ( ret == null ) {
-
-			// Try to find the camelCased property
-			ret = thisCache[ jQuery.camelCase( name ) ];
-		}
-	} else {
-		ret = thisCache;
-	}
-
-	return ret;
-}
-
-function internalRemoveData( elem, name, pvt ) {
-	if ( !jQuery.acceptData( elem ) ) {
-		return;
-	}
-
-	var thisCache, i,
-		isNode = elem.nodeType,
-
-		// See jQuery.data for more information
-		cache = isNode ? jQuery.cache : elem,
-		id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
-
-	// If there is already no cache entry for this object, there is no
-	// purpose in continuing
-	if ( !cache[ id ] ) {
-		return;
-	}
-
-	if ( name ) {
-
-		thisCache = pvt ? cache[ id ] : cache[ id ].data;
-
-		if ( thisCache ) {
-
-			// Support array or space separated string names for data keys
-			if ( !jQuery.isArray( name ) ) {
-
-				// try the string as a key before any manipulation
-				if ( name in thisCache ) {
-					name = [ name ];
-				} else {
-
-					// split the camel cased version by spaces unless a key with the spaces exists
-					name = jQuery.camelCase( name );
-					if ( name in thisCache ) {
-						name = [ name ];
-					} else {
-						name = name.split(" ");
-					}
-				}
-			} else {
-				// If "name" is an array of keys...
-				// When data is initially created, via ("key", "val") signature,
-				// keys will be converted to camelCase.
-				// Since there is no way to tell _how_ a key was added, remove
-				// both plain key and camelCase key. #12786
-				// This will only penalize the array argument path.
-				name = name.concat( jQuery.map( name, jQuery.camelCase ) );
-			}
-
-			i = name.length;
-			while ( i-- ) {
-				delete thisCache[ name[i] ];
-			}
-
-			// If there is no data left in the cache, we want to continue
-			// and let the cache object itself get destroyed
-			if ( pvt ? !isEmptyDataObject(thisCache) : !jQuery.isEmptyObject(thisCache) ) {
-				return;
-			}
-		}
-	}
-
-	// See jQuery.data for more information
-	if ( !pvt ) {
-		delete cache[ id ].data;
-
-		// Don't destroy the parent cache unless the internal data object
-		// had been the only thing left in it
-		if ( !isEmptyDataObject( cache[ id ] ) ) {
-			return;
-		}
-	}
-
-	// Destroy the cache
-	if ( isNode ) {
-		jQuery.cleanData( [ elem ], true );
-
-	// Use delete when supported for expandos or `cache` is not a window per isWindow (#10080)
-	/* jshint eqeqeq: false */
-	} else if ( support.deleteExpando || cache != cache.window ) {
-		/* jshint eqeqeq: true */
-		delete cache[ id ];
-
-	// When all else fails, null
-	} else {
-		cache[ id ] = null;
-	}
-}
-
-jQuery.extend({
-	cache: {},
-
-	// The following elements (space-suffixed to avoid Object.prototype collisions)
-	// throw uncatchable exceptions if you attempt to set expando properties
-	noData: {
-		"applet ": true,
-		"embed ": true,
-		// ...but Flash objects (which have this classid) *can* handle expandos
-		"object ": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
-	},
-
-	hasData: function( elem ) {
-		elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
-		return !!elem && !isEmptyDataObject( elem );
-	},
-
-	data: function( elem, name, data ) {
-		return internalData( elem, name, data );
-	},
-
-	removeData: function( elem, name ) {
-		return internalRemoveData( elem, name );
-	},
-
-	// For internal use only.
-	_data: function( elem, name, data ) {
-		return internalData( elem, name, data, true );
-	},
-
-	_removeData: function( elem, name ) {
-		return internalRemoveData( elem, name, true );
-	}
-});
-
-jQuery.fn.extend({
-	data: function( key, value ) {
-		var i, name, data,
-			elem = this[0],
-			attrs = elem && elem.attributes;
-
-		// Special expections of .data basically thwart jQuery.access,
-		// so implement the relevant behavior ourselves
-
-		// Gets all values
-		if ( key === undefined ) {
-			if ( this.length ) {
-				data = jQuery.data( elem );
-
-				if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
-					i = attrs.length;
-					while ( i-- ) {
-
-						// Support: IE11+
-						// The attrs elements can be null (#14894)
-						if ( attrs[ i ] ) {
-							name = attrs[ i ].name;
-							if ( name.indexOf( "data-" ) === 0 ) {
-								name = jQuery.camelCase( name.slice(5) );
-								dataAttr( elem, name, data[ name ] );
-							}
-						}
-					}
-					jQuery._data( elem, "parsedAttrs", true );
-				}
-			}
-
-			return data;
-		}
-
-		// Sets multiple values
-		if ( typeof key === "object" ) {
-			return this.each(function() {
-				jQuery.data( this, key );
-			});
-		}
-
-		return arguments.length > 1 ?
-
-			// Sets one value
-			this.each(function() {
-				jQuery.data( this, key, value );
-			}) :
-
-			// Gets one value
-			// Try to fetch any internally stored data first
-			elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : undefined;
-	},
-
-	removeData: function( key ) {
-		return this.each(function() {
-			jQuery.removeData( this, key );
-		});
-	}
-});
-
-
-jQuery.extend({
-	queue: function( elem, type, data ) {
-		var queue;
-
-		if ( elem ) {
-			type = ( type || "fx" ) + "queue";
-			queue = jQuery._data( elem, type );
-
-			// Speed up dequeue by getting out quickly if this is just a lookup
-			if ( data ) {
-				if ( !queue || jQuery.isArray(data) ) {
-					queue = jQuery._data( elem, type, jQuery.makeArray(data) );
-				} else {
-					queue.push( data );
-				}
-			}
-			return queue || [];
-		}
-	},
-
-	dequeue: function( elem, type ) {
-		type = type || "fx";
-
-		var queue = jQuery.queue( elem, type ),
-			startLength = queue.length,
-			fn = queue.shift(),
-			hooks = jQuery._queueHooks( elem, type ),
-			next = function() {
-				jQuery.dequeue( elem, type );
-			};
-
-		// If the fx queue is dequeued, always remove the progress sentinel
-		if ( fn === "inprogress" ) {
-			fn = queue.shift();
-			startLength--;
-		}
-
-		if ( fn ) {
-
-			// Add a progress sentinel to prevent the fx queue from being
-			// automatically dequeued
-			if ( type === "fx" ) {
-				queue.unshift( "inprogress" );
-			}
-
-			// clear up the last queue stop function
-			delete hooks.stop;
-			fn.call( elem, next, hooks );
-		}
-
-		if ( !startLength && hooks ) {
-			hooks.empty.fire();
-		}
-	},
-
-	// not intended for public consumption - generates a queueHooks object, or returns the current one
-	_queueHooks: function( elem, type ) {
-		var key = type + "queueHooks";
-		return jQuery._data( elem, key ) || jQuery._data( elem, key, {
-			empty: jQuery.Callbacks("once memory").add(function() {
-				jQuery._removeData( elem, type + "queue" );
-				jQuery._removeData( elem, key );
-			})
-		});
-	}
-});
-
-jQuery.fn.extend({
-	queue: function( type, data ) {
-		var setter = 2;
-
-		if ( typeof type !== "string" ) {
-			data = type;
-			type = "fx";
-			setter--;
-		}
-
-		if ( arguments.length < setter ) {
-			return jQuery.queue( this[0], type );
-		}
-
-		return data === undefined ?
-			this :
-			this.each(function() {
-				var queue = jQuery.queue( this, type, data );
-
-				// ensure a hooks for this queue
-				jQuery._queueHooks( this, type );
-
-				if ( type === "fx" && queue[0] !== "inprogress" ) {
-					jQuery.dequeue( this, type );
-				}
-			});
-	},
-	dequeue: function( type ) {
-		return this.each(function() {
-			jQuery.dequeue( this, type );
-		});
-	},
-	clearQueue: function( type ) {
-		return this.queue( type || "fx", [] );
-	},
-	// Get a promise resolved when queues of a certain type
-	// are emptied (fx is the type by default)
-	promise: function( type, obj ) {
-		var tmp,
-			count = 1,
-			defer = jQuery.Deferred(),
-			elements = this,
-			i = this.length,
-			resolve = function() {
-				if ( !( --count ) ) {
-					defer.resolveWith( elements, [ elements ] );
-				}
-			};
-
-		if ( typeof type !== "string" ) {
-			obj = type;
-			type = undefined;
-		}
-		type = type || "fx";
-
-		while ( i-- ) {
-			tmp = jQuery._data( elements[ i ], type + "queueHooks" );
-			if ( tmp && tmp.empty ) {
-				count++;
-				tmp.empty.add( resolve );
-			}
-		}
-		resolve();
-		return defer.promise( obj );
-	}
-});
-var pnum = (/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/).source;
-
-var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
-
-var isHidden = function( elem, el ) {
-		// isHidden might be called from jQuery#filter function;
-		// in that case, element will be second argument
-		elem = el || elem;
-		return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem );
-	};
-
-
-
-// Multifunctional method to get and set values of a collection
-// The value/s can optionally be executed if it's a function
-var access = jQuery.access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
-	var i = 0,
-		length = elems.length,
-		bulk = key == null;
-
-	// Sets many values
-	if ( jQuery.type( key ) === "object" ) {
-		chainable = true;
-		for ( i in key ) {
-			jQuery.access( elems, fn, i, key[i], true, emptyGet, raw );
-		}
-
-	// Sets one value
-	} else if ( value !== undefined ) {
-		chainable = true;
-
-		if ( !jQuery.isFunction( value ) ) {
-			raw = true;
-		}
-
-		if ( bulk ) {
-			// Bulk operations run against the entire set
-			if ( raw ) {
-				fn.call( elems, value );
-				fn = null;
-
-			// ...except when executing function values
-			} else {
-				bulk = fn;
-				fn = function( elem, key, value ) {
-					return bulk.call( jQuery( elem ), value );
-				};
-			}
-		}
-
-		if ( fn ) {
-			for ( ; i < length; i++ ) {
-				fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) );
-			}
-		}
-	}
-
-	return chainable ?
-		elems :
-
-		// Gets
-		bulk ?
-			fn.call( elems ) :
-			length ? fn( elems[0], key ) : emptyGet;
-};
-var rcheckableType = (/^(?:checkbox|radio)$/i);
-
-
-
-(function() {
-	// Minified: var a,b,c
-	var input = document.createElement( "input" ),
-		div = document.createElement( "div" ),
-		fragment = document.createDocumentFragment();
-
-	// Setup
-	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
-
-	// IE strips leading whitespace when .innerHTML is used
-	support.leadingWhitespace = div.firstChild.nodeType === 3;
-
-	// Make sure that tbody elements aren't automatically inserted
-	// IE will insert them into empty tables
-	support.tbody = !div.getElementsByTagName( "tbody" ).length;
-
-	// Make sure that link elements get serialized correctly by innerHTML
-	// This requires a wrapper element in IE
-	support.htmlSerialize = !!div.getElementsByTagName( "link" ).length;
-
-	// Makes sure cloning an html5 element does not cause problems
-	// Where outerHTML is undefined, this still works
-	support.html5Clone =
-		document.createElement( "nav" ).cloneNode( true ).outerHTML !== "<:nav></:nav>";
-
-	// Check if a disconnected checkbox will retain its checked
-	// value of true after appended to the DOM (IE6/7)
-	input.type = "checkbox";
-	input.checked = true;
-	fragment.appendChild( input );
-	support.appendChecked = input.checked;
-
-	// Make sure textarea (and checkbox) defaultValue is properly cloned
-	// Support: IE6-IE11+
-	div.innerHTML = "<textarea>x</textarea>";
-	support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
-
-	// #11217 - WebKit loses check when the name is after the checked attribute
-	fragment.appendChild( div );
-	div.innerHTML = "<input type='radio' checked='checked' name='t'/>";
-
-	// Support: Safari 5.1, iOS 5.1, Android 4.x, Android 2.3
-	// old WebKit doesn't clone checked state correctly in fragments
-	support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
-
-	// Support: IE<9
-	// Opera does not clone events (and typeof div.attachEvent === undefined).
-	// IE9-10 clones events bound via attachEvent, but they don't trigger with .click()
-	support.noCloneEvent = true;
-	if ( div.attachEvent ) {
-		div.attachEvent( "onclick", function() {
-			support.noCloneEvent = false;
-		});
-
-		div.cloneNode( true ).click();
-	}
-
-	// Execute the test only if not already executed in another module.
-	if (support.deleteExpando == null) {
-		// Support: IE<9
-		support.deleteExpando = true;
-		try {
-			delete div.test;
-		} catch( e ) {
-			support.deleteExpando = false;
-		}
-	}
-})();
-
-
-(function() {
-	var i, eventName,
-		div = document.createElement( "div" );
-
-	// Support: IE<9 (lack submit/change bubble), Firefox 23+ (lack focusin event)
-	for ( i in { submit: true, change: true, focusin: true }) {
-		eventName = "on" + i;
-
-		if ( !(support[ i + "Bubbles" ] = eventName in window) ) {
-			// Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP)
-			div.setAttribute( eventName, "t" );
-			support[ i + "Bubbles" ] = div.attributes[ eventName ].expando === false;
-		}
-	}
-
-	// Null elements to avoid leaks in IE.
-	div = null;
-})();
-
-
-var rformElems = /^(?:input|select|textarea)$/i,
-	rkeyEvent = /^key/,
-	rmouseEvent = /^(?:mouse|pointer|contextmenu)|click/,
-	rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
-	rtypenamespace = /^([^.]*)(?:\.(.+)|)$/;
-
-function returnTrue() {
-	return true;
-}
-
-function returnFalse() {
-	return false;
-}
-
-function safeActiveElement() {
-	try {
-		return document.activeElement;
-	} catch ( err ) { }
-}
-
-/*
- * Helper functions for managing events -- not part of the public interface.
- * Props to Dean Edwards' addEvent library for many of the ideas.
- */
-jQuery.event = {
-
-	global: {},
-
-	add: function( elem, types, handler, data, selector ) {
-		var tmp, events, t, handleObjIn,
-			special, eventHandle, handleObj,
-			handlers, type, namespaces, origType,
-			elemData = jQuery._data( elem );
-
-		// Don't attach events to noData or text/comment nodes (but allow plain objects)
-		if ( !elemData ) {
-			return;
-		}
-
-		// Caller can pass in an object of custom data in lieu of the handler
-		if ( handler.handler ) {
-			handleObjIn = handler;
-			handler = handleObjIn.handler;
-			selector = handleObjIn.selector;
-		}
-
-		// Make sure that the handler has a unique ID, used to find/remove it later
-		if ( !handler.guid ) {
-			handler.guid = jQuery.guid++;
-		}
-
-		// Init the element's event structure and main handler, if this is the first
-		if ( !(events = elemData.events) ) {
-			events = elemData.events = {};
-		}
-		if ( !(eventHandle = elemData.handle) ) {
-			eventHandle = elemData.handle = function( e ) {
-				// Discard the second event of a jQuery.event.trigger() and
-				// when an event is called after a page has unloaded
-				return typeof jQuery !== strundefined && (!e || jQuery.event.triggered !== e.type) ?
-					jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
-					undefined;
-			};
-			// Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
-			eventHandle.elem = elem;
-		}
-
-		// Handle multiple events separated by a space
-		types = ( types || "" ).match( rnotwhite ) || [ "" ];
-		t = types.length;
-		while ( t-- ) {
-			tmp = rtypenamespace.exec( types[t] ) || [];
-			type = origType = tmp[1];
-			namespaces = ( tmp[2] || "" ).split( "." ).sort();
-
-			// There *must* be a type, no attaching namespace-only handlers
-			if ( !type ) {
-				continue;
-			}
-
-			// If event changes its type, use the special event handlers for the changed type
-			special = jQuery.event.special[ type ] || {};
-
-			// If selector defined, determine special event api type, otherwise given type
-			type = ( selector ? special.delegateType : special.bindType ) || type;
-
-			// Update special based on newly reset type
-			special = jQuery.event.special[ type ] || {};
-
-			// handleObj is passed to all event handlers
-			handleObj = jQuery.extend({
-				type: type,
-				origType: origType,
-				data: data,
-				handler: handler,
-				guid: handler.guid,
-				selector: selector,
-				needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
-				namespace: namespaces.join(".")
-			}, handleObjIn );
-
-			// Init the event handler queue if we're the first
-			if ( !(handlers = events[ type ]) ) {
-				handlers = events[ type ] = [];
-				handlers.delegateCount = 0;
-
-				// Only use addEventListener/attachEvent if the special events handler returns false
-				if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
-					// Bind the global event handler to the element
-					if ( elem.addEventListener ) {
-						elem.addEventListener( type, eventHandle, false );
-
-					} else if ( elem.attachEvent ) {
-						elem.attachEvent( "on" + type, eventHandle );
-					}
-				}
-			}
-
-			if ( special.add ) {
-				special.add.call( elem, handleObj );
-
-				if ( !handleObj.handler.guid ) {
-					handleObj.handler.guid = handler.guid;
-				}
-			}
-
-			// Add to the element's handler list, delegates in front
-			if ( selector ) {
-				handlers.splice( handlers.delegateCount++, 0, handleObj );
-			} else {
-				handlers.push( handleObj );
-			}
-
-			// Keep track of which events have ever been used, for event optimization
-			jQuery.event.global[ type ] = true;
-		}
-
-		// Nullify elem to prevent memory leaks in IE
-		elem = null;
-	},
-
-	// Detach an event or set of events from an element
-	remove: function( elem, types, handler, selector, mappedTypes ) {
-		var j, handleObj, tmp,
-			origCount, t, events,
-			special, handlers, type,
-			namespaces, origType,
-			elemData = jQuery.hasData( elem ) && jQuery._data( elem );
-
-		if ( !elemData || !(events = elemData.events) ) {
-			return;
-		}
-
-		// Once for each type.namespace in types; type may be omitted
-		types = ( types || "" ).match( rnotwhite ) || [ "" ];
-		t = types.length;
-		while ( t-- ) {
-			tmp = rtypenamespace.exec( types[t] ) || [];
-			type = origType = tmp[1];
-			namespaces = ( tmp[2] || "" ).split( "." ).sort();
-
-			// Unbind all events (on this namespace, if provided) for the element
-			if ( !type ) {
-				for ( type in events ) {
-					jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
-				}
-				continue;
-			}
-
-			special = jQuery.event.special[ type ] || {};
-			type = ( selector ? special.delegateType : special.bindType ) || type;
-			handlers = events[ type ] || [];
-			tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" );
-
-			// Remove matching events
-			origCount = j = handlers.length;
-			while ( j-- ) {
-				handleObj = handlers[ j ];
-
-				if ( ( mappedTypes || origType === handleObj.origType ) &&
-					( !handler || handler.guid === handleObj.guid ) &&
-					( !tmp || tmp.test( handleObj.namespace ) ) &&
-					( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
-					handlers.splice( j, 1 );
-
-					if ( handleObj.selector ) {
-						handlers.delegateCount--;
-					}
-					if ( special.remove ) {
-						special.remove.call( elem, handleObj );
-					}
-				}
-			}
-
-			// Remove generic event handler if we removed something and no more handlers exist
-			// (avoids potential for endless recursion during removal of special event handlers)
-			if ( origCount && !handlers.length ) {
-				if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
-					jQuery.removeEvent( elem, type, elemData.handle );
-				}
-
-				delete events[ type ];
-			}
-		}
-
-		// Remove the expando if it's no longer used
-		if ( jQuery.isEmptyObject( events ) ) {
-			delete elemData.handle;
-
-			// removeData also checks for emptiness and clears the expando if empty
-			// so use it instead of delete
-			jQuery._removeData( elem, "events" );
-		}
-	},
-
-	trigger: function( event, data, elem, onlyHandlers ) {
-		var handle, ontype, cur,
-			bubbleType, special, tmp, i,
-			eventPath = [ elem || document ],
-			type = hasOwn.call( event, "type" ) ? event.type : event,
-			namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : [];
-
-		cur = tmp = elem = elem || document;
-
-		// Don't do events on text and comment nodes
-		if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
-			return;
-		}
-
-		// focus/blur morphs to focusin/out; ensure we're not firing them right now
-		if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
-			return;
-		}
-
-		if ( type.indexOf(".") >= 0 ) {
-			// Namespaced trigger; create a regexp to match event type in handle()
-			namespaces = type.split(".");
-			type = namespaces.shift();
-			namespaces.sort();
-		}
-		ontype = type.indexOf(":") < 0 && "on" + type;
-
-		// Caller can pass in a jQuery.Event object, Object, or just an event type string
-		event = event[ jQuery.expando ] ?
-			event :
-			new jQuery.Event( type, typeof event === "object" && event );
-
-		// Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
-		event.isTrigger = onlyHandlers ? 2 : 3;
-		event.namespace = namespaces.join(".");
-		event.namespace_re = event.namespace ?
-			new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) :
-			null;
-
-		// Clean up the event in case it is being reused
-		event.result = undefined;
-		if ( !event.target ) {
-			event.target = elem;
-		}
-
-		// Clone any incoming data and prepend the event, creating the handler arg list
-		data = data == null ?
-			[ event ] :
-			jQuery.makeArray( data, [ event ] );
-
-		// Allow special events to draw outside the lines
-		special = jQuery.event.special[ type ] || {};
-		if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
-			return;
-		}
-
-		// Determine event propagation path in advance, per W3C events spec (#9951)
-		// Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
-		if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
-
-			bubbleType = special.delegateType || type;
-			if ( !rfocusMorph.test( bubbleType + type ) ) {
-				cur = cur.parentNode;
-			}
-			for ( ; cur; cur = cur.parentNode ) {
-				eventPath.push( cur );
-				tmp = cur;
-			}
-
-			// Only add window if we got to document (e.g., not plain obj or detached DOM)
-			if ( tmp === (elem.ownerDocument || document) ) {
-				eventPath.push( tmp.defaultView || tmp.parentWindow || window );
-			}
-		}
-
-		// Fire handlers on the event path
-		i = 0;
-		while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) {
-
-			event.type = i > 1 ?
-				bubbleType :
-				special.bindType || type;
-
-			// jQuery handler
-			handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
-			if ( handle ) {
-				handle.apply( cur, data );
-			}
-
-			// Native handler
-			handle = ontype && cur[ ontype ];
-			if ( handle && handle.apply && jQuery.acceptData( cur ) ) {
-				event.result = handle.apply( cur, data );
-				if ( event.result === false ) {
-					event.preventDefault();
-				}
-			}
-		}
-		event.type = type;
-
-		// If nobody prevented the default action, do it now
-		if ( !onlyHandlers && !event.isDefaultPrevented() ) {
-
-			if ( (!special._default || special._default.apply( eventPath.pop(), data ) === false) &&
-				jQuery.acceptData( elem ) ) {
-
-				// Call a native DOM method on the target with the same name name as the event.
-				// Can't use an .isFunction() check here because IE6/7 fails that test.
-				// Don't do default actions on window, that's where global variables be (#6170)
-				if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) {
-
-					// Don't re-trigger an onFOO event when we call its FOO() method
-					tmp = elem[ ontype ];
-
-					if ( tmp ) {
-						elem[ ontype ] = null;
-					}
-
-					// Prevent re-triggering of the same event, since we already bubbled it above
-					jQuery.event.triggered = type;
-					try {
-						elem[ type ]();
-					} catch ( e ) {
-						// IE<9 dies on focus/blur to hidden element (#1486,#12518)
-						// only reproducible on winXP IE8 native, not IE9 in IE8 mode
-					}
-					jQuery.event.triggered = undefined;
-
-					if ( tmp ) {
-						elem[ ontype ] = tmp;
-					}
-				}
-			}
-		}
-
-		return event.result;
-	},
-
-	dispatch: function( event ) {
-
-		// Make a writable jQuery.Event from the native event object
-		event = jQuery.event.fix( event );
-
-		var i, ret, handleObj, matched, j,
-			handlerQueue = [],
-			args = slice.call( arguments ),
-			handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [],
-			special = jQuery.event.special[ event.type ] || {};
-
-		// Use the fix-ed jQuery.Event rather than the (read-only) native event
-		args[0] = event;
-		event.delegateTarget = this;
-
-		// Call the preDispatch hook for the mapped type, and let it bail if desired
-		if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
-			return;
-		}
-
-		// Determine handlers
-		handlerQueue = jQuery.event.handlers.call( this, event, handlers );
-
-		// Run delegates first; they may want to stop propagation beneath us
-		i = 0;
-		while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) {
-			event.currentTarget = matched.elem;
-
-			j = 0;
-			while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) {
-
-				// Triggered event must either 1) have no namespace, or
-				// 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
-				if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) {
-
-					event.handleObj = handleObj;
-					event.data = handleObj.data;
-
-					ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
-							.apply( matched.elem, args );
-
-					if ( ret !== undefined ) {
-						if ( (event.result = ret) === false ) {
-							event.preventDefault();
-							event.stopPropagation();
-						}
-					}
-				}
-			}
-		}
-
-		// Call the postDispatch hook for the mapped type
-		if ( special.postDispatch ) {
-			special.postDispatch.call( this, event );
-		}
-
-		return event.result;
-	},
-
-	handlers: function( event, handlers ) {
-		var sel, handleObj, matches, i,
-			handlerQueue = [],
-			delegateCount = handlers.delegateCount,
-			cur = event.target;
-
-		// Find delegate handlers
-		// Black-hole SVG <use> instance trees (#13180)
-		// Avoid non-left-click bubbling in Firefox (#3861)
-		if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) {
-
-			/* jshint eqeqeq: false */
-			for ( ; cur != this; cur = cur.parentNode || this ) {
-				/* jshint eqeqeq: true */
-
-				// Don't check non-elements (#13208)
-				// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
-				if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) {
-					matches = [];
-					for ( i = 0; i < delegateCount; i++ ) {
-						handleObj = handlers[ i ];
-
-						// Don't conflict with Object.prototype properties (#13203)
-						sel = handleObj.selector + " ";
-
-						if ( matches[ sel ] === undefined ) {
-							matches[ sel ] = handleObj.needsContext ?
-								jQuery( sel, this ).index( cur ) >= 0 :
-								jQuery.find( sel, this, null, [ cur ] ).length;
-						}
-						if ( matches[ sel ] ) {
-							matches.push( handleObj );
-						}
-					}
-					if ( matches.length ) {
-						handlerQueue.push({ elem: cur, handlers: matches });
-					}
-				}
-			}
-		}
-
-		// Add the remaining (directly-bound) handlers
-		if ( delegateCount < handlers.length ) {
-			handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) });
-		}
-
-		return handlerQueue;
-	},
-
-	fix: function( event ) {
-		if ( event[ jQuery.expando ] ) {
-			return event;
-		}
-
-		// Create a writable copy of the event object and normalize some properties
-		var i, prop, copy,
-			type = event.type,
-			originalEvent = event,
-			fixHook = this.fixHooks[ type ];
-
-		if ( !fixHook ) {
-			this.fixHooks[ type ] = fixHook =
-				rmouseEvent.test( type ) ? this.mouseHooks :
-				rkeyEvent.test( type ) ? this.keyHooks :
-				{};
-		}
-		copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
-
-		event = new jQuery.Event( originalEvent );
-
-		i = copy.length;
-		while ( i-- ) {
-			prop = copy[ i ];
-			event[ prop ] = originalEvent[ prop ];
-		}
-
-		// Support: IE<9
-		// Fix target property (#1925)
-		if ( !event.target ) {
-			event.target = originalEvent.srcElement || document;
-		}
-
-		// Support: Chrome 23+, Safari?
-		// Target should not be a text node (#504, #13143)
-		if ( event.target.nodeType === 3 ) {
-			event.target = event.target.parentNode;
-		}
-
-		// Support: IE<9
-		// For mouse/key events, metaKey==false if it's undefined (#3368, #11328)
-		event.metaKey = !!event.metaKey;
-
-		return fixHook.filter ? fixHook.filter( event, originalEvent ) : event;
-	},
-
-	// Includes some event props shared by KeyEvent and MouseEvent
-	props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
-
-	fixHooks: {},
-
-	keyHooks: {
-		props: "char charCode key keyCode".split(" "),
-		filter: function( event, original ) {
-
-			// Add which for key events
-			if ( event.which == null ) {
-				event.which = original.charCode != null ? original.charCode : original.keyCode;
-			}
-
-			return event;
-		}
-	},
-
-	mouseHooks: {
-		props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
-		filter: function( event, original ) {
-			var body, eventDoc, doc,
-				button = original.button,
-				fromElement = original.fromElement;
-
-			// Calculate pageX/Y if missing and clientX/Y available
-			if ( event.pageX == null && original.clientX != null ) {
-				eventDoc = event.target.ownerDocument || document;
-				doc = eventDoc.documentElement;
-				body = eventDoc.body;
-
-				event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
-				event.pageY = original.clientY + ( doc && doc.scrollTop  || body && body.scrollTop  || 0 ) - ( doc && doc.clientTop  || body && body.clientTop  || 0 );
-			}
-
-			// Add relatedTarget, if necessary
-			if ( !event.relatedTarget && fromElement ) {
-				event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
-			}
-
-			// Add which for click: 1 === left; 2 === middle; 3 === right
-			// Note: button is not normalized, so don't use it
-			if ( !event.which && button !== undefined ) {
-				event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
-			}
-
-			return event;
-		}
-	},
-
-	special: {
-		load: {
-			// Prevent triggered image.load events from bubbling to window.load
-			noBubble: true
-		},
-		focus: {
-			// Fire native event if possible so blur/focus sequence is correct
-			trigger: function() {
-				if ( this !== safeActiveElement() && this.focus ) {
-					try {
-						this.focus();
-						return false;
-					} catch ( e ) {
-						// Support: IE<9
-						// If we error on focus to hidden element (#1486, #12518),
-						// let .trigger() run the handlers
-					}
-				}
-			},
-			delegateType: "focusin"
-		},
-		blur: {
-			trigger: function() {
-				if ( this === safeActiveElement() && this.blur ) {
-					this.blur();
-					return false;
-				}
-			},
-			delegateType: "focusout"
-		},
-		click: {
-			// For checkbox, fire native event so checked state will be right
-			trigger: function() {
-				if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) {
-					this.click();
-					return false;
-				}
-			},
-
-			// For cross-browser consistency, don't fire native .click() on links
-			_default: function( event ) {
-				return jQuery.nodeName( event.target, "a" );
-			}
-		},
-
-		beforeunload: {
-			postDispatch: function( event ) {
-
-				// Support: Firefox 20+
-				// Firefox doesn't alert if the returnValue field is not set.
-				if ( event.result !== undefined && event.originalEvent ) {
-					event.originalEvent.returnValue = event.result;
-				}
-			}
-		}
-	},
-
-	simulate: function( type, elem, event, bubble ) {
-		// Piggyback on a donor event to simulate a different one.
-		// Fake originalEvent to avoid donor's stopPropagation, but if the
-		// simulated event prevents default then we do the same on the donor.
-		var e = jQuery.extend(
-			new jQuery.Event(),
-			event,
-			{
-				type: type,
-				isSimulated: true,
-				originalEvent: {}
-			}
-		);
-		if ( bubble ) {
-			jQuery.event.trigger( e, null, elem );
-		} else {
-			jQuery.event.dispatch.call( elem, e );
-		}
-		if ( e.isDefaultPrevented() ) {
-			event.preventDefault();
-		}
-	}
-};
-
-jQuery.removeEvent = document.removeEventListener ?
-	function( elem, type, handle ) {
-		if ( elem.removeEventListener ) {
-			elem.removeEventListener( type, handle, false );
-		}
-	} :
-	function( elem, type, handle ) {
-		var name = "on" + type;
-
-		if ( elem.detachEvent ) {
-
-			// #8545, #7054, preventing memory leaks for custom events in IE6-8
-			// detachEvent needed property on element, by name of that event, to properly expose it to GC
-			if ( typeof elem[ name ] === strundefined ) {
-				elem[ name ] = null;
-			}
-
-			elem.detachEvent( name, handle );
-		}
-	};
-
-jQuery.Event = function( src, props ) {
-	// Allow instantiation without the 'new' keyword
-	if ( !(this instanceof jQuery.Event) ) {
-		return new jQuery.Event( src, props );
-	}
-
-	// Event object
-	if ( src && src.type ) {
-		this.originalEvent = src;
-		this.type = src.type;
-
-		// Events bubbling up the document may have been marked as prevented
-		// by a handler lower down the tree; reflect the correct value.
-		this.isDefaultPrevented = src.defaultPrevented ||
-				src.defaultPrevented === undefined &&
-				// Support: IE < 9, Android < 4.0
-				src.returnValue === false ?
-			returnTrue :
-			returnFalse;
-
-	// Event type
-	} else {
-		this.type = src;
-	}
-
-	// Put explicitly provided properties onto the event object
-	if ( props ) {
-		jQuery.extend( this, props );
-	}
-
-	// Create a timestamp if incoming event doesn't have one
-	this.timeStamp = src && src.timeStamp || jQuery.now();
-
-	// Mark it as fixed
-	this[ jQuery.expando ] = true;
-};
-
-// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
-// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
-jQuery.Event.prototype = {
-	isDefaultPrevented: returnFalse,
-	isPropagationStopped: returnFalse,
-	isImmediatePropagationStopped: returnFalse,
-
-	preventDefault: function() {
-		var e = this.originalEvent;
-
-		this.isDefaultPrevented = returnTrue;
-		if ( !e ) {
-			return;
-		}
-
-		// If preventDefault exists, run it on the original event
-		if ( e.preventDefault ) {
-			e.preventDefault();
-
-		// Support: IE
-		// Otherwise set the returnValue property of the original event to false
-		} else {
-			e.returnValue = false;
-		}
-	},
-	stopPropagation: function() {
-		var e = this.originalEvent;
-
-		this.isPropagationStopped = returnTrue;
-		if ( !e ) {
-			return;
-		}
-		// If stopPropagation exists, run it on the original event
-		if ( e.stopPropagation ) {
-			e.stopPropagation();
-		}
-
-		// Support: IE
-		// Set the cancelBubble property of the original event to true
-		e.cancelBubble = true;
-	},
-	stopImmediatePropagation: function() {
-		var e = this.originalEvent;
-
-		this.isImmediatePropagationStopped = returnTrue;
-
-		if ( e && e.stopImmediatePropagation ) {
-			e.stopImmediatePropagation();
-		}
-
-		this.stopPropagation();
-	}
-};
-
-// Create mouseenter/leave events using mouseover/out and event-time checks
-jQuery.each({
-	mouseenter: "mouseover",
-	mouseleave: "mouseout",
-	pointerenter: "pointerover",
-	pointerleave: "pointerout"
-}, function( orig, fix ) {
-	jQuery.event.special[ orig ] = {
-		delegateType: fix,
-		bindType: fix,
-
-		handle: function( event ) {
-			var ret,
-				target = this,
-				related = event.relatedTarget,
-				handleObj = event.handleObj;
-
-			// For mousenter/leave call the handler if related is outside the target.
-			// NB: No relatedTarget if the mouse left/entered the browser window
-			if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
-				event.type = handleObj.origType;
-				ret = handleObj.handler.apply( this, arguments );
-				event.type = fix;
-			}
-			return ret;
-		}
-	};
-});
-
-// IE submit delegation
-if ( !support.submitBubbles ) {
-
-	jQuery.event.special.submit = {
-		setup: function() {
-			// Only need this for delegated form submit events
-			if ( jQuery.nodeName( this, "form" ) ) {
-				return false;
-			}
-
-			// Lazy-add a submit handler when a descendant form may potentially be submitted
-			jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
-				// Node name check avoids a VML-related crash in IE (#9807)
-				var elem = e.target,
-					form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
-				if ( form && !jQuery._data( form, "submitBubbles" ) ) {
-					jQuery.event.add( form, "submit._submit", function( event ) {
-						event._submit_bubble = true;
-					});
-					jQuery._data( form, "submitBubbles", true );
-				}
-			});
-			// return undefined since we don't need an event listener
-		},
-
-		postDispatch: function( event ) {
-			// If form was submitted by the user, bubble the event up the tree
-			if ( event._submit_bubble ) {
-				delete event._submit_bubble;
-				if ( this.parentNode && !event.isTrigger ) {
-					jQuery.event.simulate( "submit", this.parentNode, event, true );
-				}
-			}
-		},
-
-		teardown: function() {
-			// Only need this for delegated form submit events
-			if ( jQuery.nodeName( this, "form" ) ) {
-				return false;
-			}
-
-			// Remove delegated handlers; cleanData eventually reaps submit handlers attached above
-			jQuery.event.remove( this, "._submit" );
-		}
-	};
-}
-
-// IE change delegation and checkbox/radio fix
-if ( !support.changeBubbles ) {
-
-	jQuery.event.special.change = {
-
-		setup: function() {
-
-			if ( rformElems.test( this.nodeName ) ) {
-				// IE doesn't fire change on a check/radio until blur; trigger it on click
-				// after a propertychange. Eat the blur-change in special.change.handle.
-				// This still fires onchange a second time for check/radio after blur.
-				if ( this.type === "checkbox" || this.type === "radio" ) {
-					jQuery.event.add( this, "propertychange._change", function( event ) {
-						if ( event.originalEvent.propertyName === "checked" ) {
-							this._just_changed = true;
-						}
-					});
-					jQuery.event.add( this, "click._change", function( event ) {
-						if ( this._just_changed && !event.isTrigger ) {
-							this._just_changed = false;
-						}
-						// Allow triggered, simulated change events (#11500)
-						jQuery.event.simulate( "change", this, event, true );
-					});
-				}
-				return false;
-			}
-			// Delegated event; lazy-add a change handler on descendant inputs
-			jQuery.event.add( this, "beforeactivate._change", function( e ) {
-				var elem = e.target;
-
-				if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) {
-					jQuery.event.add( elem, "change._change", function( event ) {
-						if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
-							jQuery.event.simulate( "change", this.parentNode, event, true );
-						}
-					});
-					jQuery._data( elem, "changeBubbles", true );
-				}
-			});
-		},
-
-		handle: function( event ) {
-			var elem = event.target;
-
-			// Swallow native change events from checkbox/radio, we already triggered them above
-			if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
-				return event.handleObj.handler.apply( this, arguments );
-			}
-		},
-
-		teardown: function() {
-			jQuery.event.remove( this, "._change" );
-
-			return !rformElems.test( this.nodeName );
-		}
-	};
-}
-
-// Create "bubbling" focus and blur events
-if ( !support.focusinBubbles ) {
-	jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
-
-		// Attach a single capturing handler on the document while someone wants focusin/focusout
-		var handler = function( event ) {
-				jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
-			};
-
-		jQuery.event.special[ fix ] = {
-			setup: function() {
-				var doc = this.ownerDocument || this,
-					attaches = jQuery._data( doc, fix );
-
-				if ( !attaches ) {
-					doc.addEventListener( orig, handler, true );
-				}
-				jQuery._data( doc, fix, ( attaches || 0 ) + 1 );
-			},
-			teardown: function() {
-				var doc = this.ownerDocument || this,
-					attaches = jQuery._data( doc, fix ) - 1;
-
-				if ( !attaches ) {
-					doc.removeEventListener( orig, handler, true );
-					jQuery._removeData( doc, fix );
-				} else {
-					jQuery._data( doc, fix, attaches );
-				}
-			}
-		};
-	});
-}
-
-jQuery.fn.extend({
-
-	on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
-		var type, origFn;
-
-		// Types can be a map of types/handlers
-		if ( typeof types === "object" ) {
-			// ( types-Object, selector, data )
-			if ( typeof selector !== "string" ) {
-				// ( types-Object, data )
-				data = data || selector;
-				selector = undefined;
-			}
-			for ( type in types ) {
-				this.on( type, selector, data, types[ type ], one );
-			}
-			return this;
-		}
-
-		if ( data == null && fn == null ) {
-			// ( types, fn )
-			fn = selector;
-			data = selector = undefined;
-		} else if ( fn == null ) {
-			if ( typeof selector === "string" ) {
-				// ( types, selector, fn )
-				fn = data;
-				data = undefined;
-			} else {
-				// ( types, data, fn )
-				fn = data;
-				data = selector;
-				selector = undefined;
-			}
-		}
-		if ( fn === false ) {
-			fn = returnFalse;
-		} else if ( !fn ) {
-			return this;
-		}
-
-		if ( one === 1 ) {
-			origFn = fn;
-			fn = function( event ) {
-				// Can use an empty set, since event contains the info
-				jQuery().off( event );
-				return origFn.apply( this, arguments );
-			};
-			// Use same guid so caller can remove using origFn
-			fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
-		}
-		return this.each( function() {
-			jQuery.event.add( this, types, fn, data, selector );
-		});
-	},
-	one: function( types, selector, data, fn ) {
-		return this.on( types, selector, data, fn, 1 );
-	},
-	off: function( types, selector, fn ) {
-		var handleObj, type;
-		if ( types && types.preventDefault && types.handleObj ) {
-			// ( event )  dispatched jQuery.Event
-			handleObj = types.handleObj;
-			jQuery( types.delegateTarget ).off(
-				handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
-				handleObj.selector,
-				handleObj.handler
-			);
-			return this;
-		}
-		if ( typeof types === "object" ) {
-			// ( types-object [, selector] )
-			for ( type in types ) {
-				this.off( type, selector, types[ type ] );
-			}
-			return this;
-		}
-		if ( selector === false || typeof selector === "function" ) {
-			// ( types [, fn] )
-			fn = selector;
-			selector = undefined;
-		}
-		if ( fn === false ) {
-			fn = returnFalse;
-		}
-		return this.each(function() {
-			jQuery.event.remove( this, types, fn, selector );
-		});
-	},
-
-	trigger: function( type, data ) {
-		return this.each(function() {
-			jQuery.event.trigger( type, data, this );
-		});
-	},
-	triggerHandler: function( type, data ) {
-		var elem = this[0];
-		if ( elem ) {
-			return jQuery.event.trigger( type, data, elem, true );
-		}
-	}
-});
-
-
-function createSafeFragment( document ) {
-	var list = nodeNames.split( "|" ),
-		safeFrag = document.createDocumentFragment();
-
-	if ( safeFrag.createElement ) {
-		while ( list.length ) {
-			safeFrag.createElement(
-				list.pop()
-			);
-		}
-	}
-	return safeFrag;
-}
-
-var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
-		"header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
-	rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g,
-	rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
-	rleadingWhitespace = /^\s+/,
-	rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,
-	rtagName = /<([\w:]+)/,
-	rtbody = /<tbody/i,
-	rhtml = /<|&#?\w+;/,
-	rnoInnerhtml = /<(?:script|style|link)/i,
-	// checked="checked" or checked
-	rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
-	rscriptType = /^$|\/(?:java|ecma)script/i,
-	rscriptTypeMasked = /^true\/(.*)/,
-	rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g,
-
-	// We have to close these tags to support XHTML (#13200)
-	wrapMap = {
-		option: [ 1, "<select multiple='multiple'>", "</select>" ],
-		legend: [ 1, "<fieldset>", "</fieldset>" ],
-		area: [ 1, "<map>", "</map>" ],
-		param: [ 1, "<object>", "</object>" ],
-		thead: [ 1, "<table>", "</table>" ],
-		tr: [ 2, "<table><tbody>", "</tbody></table>" ],
-		col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
-		td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
-
-		// IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags,
-		// unless wrapped in a div with non-breaking characters in front of it.
-		_default: support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X<div>", "</div>"  ]
-	},
-	safeFragment = createSafeFragment( document ),
-	fragmentDiv = safeFragment.appendChild( document.createElement("div") );
-
-wrapMap.optgroup = wrapMap.option;
-wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
-wrapMap.th = wrapMap.td;
-
-function getAll( context, tag ) {
-	var elems, elem,
-		i = 0,
-		found = typeof context.getElementsByTagName !== strundefined ? context.getElementsByTagName( tag || "*" ) :
-			typeof context.querySelectorAll !== strundefined ? context.querySelectorAll( tag || "*" ) :
-			undefined;
-
-	if ( !found ) {
-		for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) {
-			if ( !tag || jQuery.nodeName( elem, tag ) ) {
-				found.push( elem );
-			} else {
-				jQuery.merge( found, getAll( elem, tag ) );
-			}
-		}
-	}
-
-	return tag === undefined || tag && jQuery.nodeName( context, tag ) ?
-		jQuery.merge( [ context ], found ) :
-		found;
-}
-
-// Used in buildFragment, fixes the defaultChecked property
-function fixDefaultChecked( elem ) {
-	if ( rcheckableType.test( elem.type ) ) {
-		elem.defaultChecked = elem.checked;
-	}
-}
-
-// Support: IE<8
-// Manipulating tables requires a tbody
-function manipulationTarget( elem, content ) {
-	return jQuery.nodeName( elem, "table" ) &&
-		jQuery.nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ?
-
-		elem.getElementsByTagName("tbody")[0] ||
-			elem.appendChild( elem.ownerDocument.createElement("tbody") ) :
-		elem;
-}
-
-// Replace/restore the type attribute of script elements for safe DOM manipulation
-function disableScript( elem ) {
-	elem.type = (jQuery.find.attr( elem, "type" ) !== null) + "/" + elem.type;
-	return elem;
-}
-function restoreScript( elem ) {
-	var match = rscriptTypeMasked.exec( elem.type );
-	if ( match ) {
-		elem.type = match[1];
-	} else {
-		elem.removeAttribute("type");
-	}
-	return elem;
-}
-
-// Mark scripts as having already been evaluated
-function setGlobalEval( elems, refElements ) {
-	var elem,
-		i = 0;
-	for ( ; (elem = elems[i]) != null; i++ ) {
-		jQuery._data( elem, "globalEval", !refElements || jQuery._data( refElements[i], "globalEval" ) );
-	}
-}
-
-function cloneCopyEvent( src, dest ) {
-
-	if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) {
-		return;
-	}
-
-	var type, i, l,
-		oldData = jQuery._data( src ),
-		curData = jQuery._data( dest, oldData ),
-		events = oldData.events;
-
-	if ( events ) {
-		delete curData.handle;
-		curData.events = {};
-
-		for ( type in events ) {
-			for ( i = 0, l = events[ type ].length; i < l; i++ ) {
-				jQuery.event.add( dest, type, events[ type ][ i ] );
-			}
-		}
-	}
-
-	// make the cloned public data object a copy from the original
-	if ( curData.data ) {
-		curData.data = jQuery.extend( {}, curData.data );
-	}
-}
-
-function fixCloneNodeIssues( src, dest ) {
-	var nodeName, e, data;
-
-	// We do not need to do anything for non-Elements
-	if ( dest.nodeType !== 1 ) {
-		return;
-	}
-
-	nodeName = dest.nodeName.toLowerCase();
-
-	// IE6-8 copies events bound via attachEvent when using cloneNode.
-	if ( !support.noCloneEvent && dest[ jQuery.expando ] ) {
-		data = jQuery._data( dest );
-
-		for ( e in data.events ) {
-			jQuery.removeEvent( dest, e, data.handle );
-		}
-
-		// Event data gets referenced instead of copied if the expando gets copied too
-		dest.removeAttribute( jQuery.expando );
-	}
-
-	// IE blanks contents when cloning scripts, and tries to evaluate newly-set text
-	if ( nodeName === "script" && dest.text !== src.text ) {
-		disableScript( dest ).text = src.text;
-		restoreScript( dest );
-
-	// IE6-10 improperly clones children of object elements using classid.
-	// IE10 throws NoModificationAllowedError if parent is null, #12132.
-	} else if ( nodeName === "object" ) {
-		if ( dest.parentNode ) {
-			dest.outerHTML = src.outerHTML;
-		}
-
-		// This path appears unavoidable for IE9. When cloning an object
-		// element in IE9, the outerHTML strategy above is not sufficient.
-		// If the src has innerHTML and the destination does not,
-		// copy the src.innerHTML into the dest.innerHTML. #10324
-		if ( support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) {
-			dest.innerHTML = src.innerHTML;
-		}
-
-	} else if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
-		// IE6-8 fails to persist the checked state of a cloned checkbox
-		// or radio button. Worse, IE6-7 fail to give the cloned element
-		// a checked appearance if the defaultChecked value isn't also set
-
-		dest.defaultChecked = dest.checked = src.checked;
-
-		// IE6-7 get confused and end up setting the value of a cloned
-		// checkbox/radio button to an empty string instead of "on"
-		if ( dest.value !== src.value ) {
-			dest.value = src.value;
-		}
-
-	// IE6-8 fails to return the selected option to the default selected
-	// state when cloning options
-	} else if ( nodeName === "option" ) {
-		dest.defaultSelected = dest.selected = src.defaultSelected;
-
-	// IE6-8 fails to set the defaultValue to the correct value when
-	// cloning other types of input fields
-	} else if ( nodeName === "input" || nodeName === "textarea" ) {
-		dest.defaultValue = src.defaultValue;
-	}
-}
-
-jQuery.extend({
-	clone: function( elem, dataAndEvents, deepDataAndEvents ) {
-		var destElements, node, clone, i, srcElements,
-			inPage = jQuery.contains( elem.ownerDocument, elem );
-
-		if ( support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) {
-			clone = elem.cloneNode( true );
-
-		// IE<=8 does not properly clone detached, unknown element nodes
-		} else {
-			fragmentDiv.innerHTML = elem.outerHTML;
-			fragmentDiv.removeChild( clone = fragmentDiv.firstChild );
-		}
-
-		if ( (!support.noCloneEvent || !support.noCloneChecked) &&
-				(elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
-
-			// We eschew Sizzle here for performance reasons: http://jsperf.com/getall-vs-sizzle/2
-			destElements = getAll( clone );
-			srcElements = getAll( elem );
-
-			// Fix all IE cloning issues
-			for ( i = 0; (node = srcElements[i]) != null; ++i ) {
-				// Ensure that the destination node is not null; Fixes #9587
-				if ( destElements[i] ) {
-					fixCloneNodeIssues( node, destElements[i] );
-				}
-			}
-		}
-
-		// Copy the events from the original to the clone
-		if ( dataAndEvents ) {
-			if ( deepDataAndEvents ) {
-				srcElements = srcElements || getAll( elem );
-				destElements = destElements || getAll( clone );
-
-				for ( i = 0; (node = srcElements[i]) != null; i++ ) {
-					cloneCopyEvent( node, destElements[i] );
-				}
-			} else {
-				cloneCopyEvent( elem, clone );
-			}
-		}
-
-		// Preserve script evaluation history
-		destElements = getAll( clone, "script" );
-		if ( destElements.length > 0 ) {
-			setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
-		}
-
-		destElements = srcElements = node = null;
-
-		// Return the cloned set
-		return clone;
-	},
-
-	buildFragment: function( elems, context, scripts, selection ) {
-		var j, elem, contains,
-			tmp, tag, tbody, wrap,
-			l = elems.length,
-
-			// Ensure a safe fragment
-			safe = createSafeFragment( context ),
-
-			nodes = [],
-			i = 0;
-
-		for ( ; i < l; i++ ) {
-			elem = elems[ i ];
-
-			if ( elem || elem === 0 ) {
-
-				// Add nodes directly
-				if ( jQuery.type( elem ) === "object" ) {
-					jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
-
-				// Convert non-html into a text node
-				} else if ( !rhtml.test( elem ) ) {
-					nodes.push( context.createTextNode( elem ) );
-
-				// Convert html into DOM nodes
-				} else {
-					tmp = tmp || safe.appendChild( context.createElement("div") );
-
-					// Deserialize a standard representation
-					tag = (rtagName.exec( elem ) || [ "", "" ])[ 1 ].toLowerCase();
-					wrap = wrapMap[ tag ] || wrapMap._default;
-
-					tmp.innerHTML = wrap[1] + elem.replace( rxhtmlTag, "<$1></$2>" ) + wrap[2];
-
-					// Descend through wrappers to the right content
-					j = wrap[0];
-					while ( j-- ) {
-						tmp = tmp.lastChild;
-					}
-
-					// Manually add leading whitespace removed by IE
-					if ( !support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
-						nodes.push( context.createTextNode( rleadingWhitespace.exec( elem )[0] ) );
-					}
-
-					// Remove IE's autoinserted <tbody> from table fragments
-					if ( !support.tbody ) {
-
-						// String was a <table>, *may* have spurious <tbody>
-						elem = tag === "table" && !rtbody.test( elem ) ?
-							tmp.firstChild :
-
-							// String was a bare <thead> or <tfoot>
-							wrap[1] === "<table>" && !rtbody.test( elem ) ?
-								tmp :
-								0;
-
-						j = elem && elem.childNodes.length;
-						while ( j-- ) {
-							if ( jQuery.nodeName( (tbody = elem.childNodes[j]), "tbody" ) && !tbody.childNodes.length ) {
-								elem.removeChild( tbody );
-							}
-						}
-					}
-
-					jQuery.merge( nodes, tmp.childNodes );
-
-					// Fix #12392 for WebKit and IE > 9
-					tmp.textContent = "";
-
-					// Fix #12392 for oldIE
-					while ( tmp.firstChild ) {
-						tmp.removeChild( tmp.firstChild );
-					}
-
-					// Remember the top-level container for proper cleanup
-					tmp = safe.lastChild;
-				}
-			}
-		}
-
-		// Fix #11356: Clear elements from fragment
-		if ( tmp ) {
-			safe.removeChild( tmp );
-		}
-
-		// Reset defaultChecked for any radios and checkboxes
-		// about to be appended to the DOM in IE 6/7 (#8060)
-		if ( !support.appendChecked ) {
-			jQuery.grep( getAll( nodes, "input" ), fixDefaultChecked );
-		}
-
-		i = 0;
-		while ( (elem = nodes[ i++ ]) ) {
-
-			// #4087 - If origin and destination elements are the same, and this is
-			// that element, do not do anything
-			if ( selection && jQuery.inArray( elem, selection ) !== -1 ) {
-				continue;
-			}
-
-			contains = jQuery.contains( elem.ownerDocument, elem );
-
-			// Append to fragment
-			tmp = getAll( safe.appendChild( elem ), "script" );
-
-			// Preserve script evaluation history
-			if ( contains ) {
-				setGlobalEval( tmp );
-			}
-
-			// Capture executables
-			if ( scripts ) {
-				j = 0;
-				while ( (elem = tmp[ j++ ]) ) {
-					if ( rscriptType.test( elem.type || "" ) ) {
-						scripts.push( elem );
-					}
-				}
-			}
-		}
-
-		tmp = null;
-
-		return safe;
-	},
-
-	cleanData: function( elems, /* internal */ acceptData ) {
-		var elem, type, id, data,
-			i = 0,
-			internalKey = jQuery.expando,
-			cache = jQuery.cache,
-			deleteExpando = support.deleteExpando,
-			special = jQuery.event.special;
-
-		for ( ; (elem = elems[i]) != null; i++ ) {
-			if ( acceptData || jQuery.acceptData( elem ) ) {
-
-				id = elem[ internalKey ];
-				data = id && cache[ id ];
-
-				if ( data ) {
-					if ( data.events ) {
-						for ( type in data.events ) {
-							if ( special[ type ] ) {
-								jQuery.event.remove( elem, type );
-
-							// This is a shortcut to avoid jQuery.event.remove's overhead
-							} else {
-								jQuery.removeEvent( elem, type, data.handle );
-							}
-						}
-					}
-
-					// Remove cache only if it was not already removed by jQuery.event.remove
-					if ( cache[ id ] ) {
-
-						delete cache[ id ];
-
-						// IE does not allow us to delete expando properties from nodes,
-						// nor does it have a removeAttribute function on Document nodes;
-						// we must handle all of these cases
-						if ( deleteExpando ) {
-							delete elem[ internalKey ];
-
-						} else if ( typeof elem.removeAttribute !== strundefined ) {
-							elem.removeAttribute( internalKey );
-
-						} else {
-							elem[ internalKey ] = null;
-						}
-
-						deletedIds.push( id );
-					}
-				}
-			}
-		}
-	}
-});
-
-jQuery.fn.extend({
-	text: function( value ) {
-		return access( this, function( value ) {
-			return value === undefined ?
-				jQuery.text( this ) :
-				this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
-		}, null, value, arguments.length );
-	},
-
-	append: function() {
-		return this.domManip( arguments, function( elem ) {
-			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
-				var target = manipulationTarget( this, elem );
-				target.appendChild( elem );
-			}
-		});
-	},
-
-	prepend: function() {
-		return this.domManip( arguments, function( elem ) {
-			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
-				var target = manipulationTarget( this, elem );
-				target.insertBefore( elem, target.firstChild );
-			}
-		});
-	},
-
-	before: function() {
-		return this.domManip( arguments, function( elem ) {
-			if ( this.parentNode ) {
-				this.parentNode.insertBefore( elem, this );
-			}
-		});
-	},
-
-	after: function() {
-		return this.domManip( arguments, function( elem ) {
-			if ( this.parentNode ) {
-				this.parentNode.insertBefore( elem, this.nextSibling );
-			}
-		});
-	},
-
-	remove: function( selector, keepData /* Internal Use Only */ ) {
-		var elem,
-			elems = selector ? jQuery.filter( selector, this ) : this,
-			i = 0;
-
-		for ( ; (elem = elems[i]) != null; i++ ) {
-
-			if ( !keepData && elem.nodeType === 1 ) {
-				jQuery.cleanData( getAll( elem ) );
-			}
-
-			if ( elem.parentNode ) {
-				if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) {
-					setGlobalEval( getAll( elem, "script" ) );
-				}
-				elem.parentNode.removeChild( elem );
-			}
-		}
-
-		return this;
-	},
-
-	empty: function() {
-		var elem,
-			i = 0;
-
-		for ( ; (elem = this[i]) != null; i++ ) {
-			// Remove element nodes and prevent memory leaks
-			if ( elem.nodeType === 1 ) {
-				jQuery.cleanData( getAll( elem, false ) );
-			}
-
-			// Remove any remaining nodes
-			while ( elem.firstChild ) {
-				elem.removeChild( elem.firstChild );
-			}
-
-			// If this is a select, ensure that it displays empty (#12336)
-			// Support: IE<9
-			if ( elem.options && jQuery.nodeName( elem, "select" ) ) {
-				elem.options.length = 0;
-			}
-		}
-
-		return this;
-	},
-
-	clone: function( dataAndEvents, deepDataAndEvents ) {
-		dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
-		deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
-
-		return this.map(function() {
-			return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
-		});
-	},
-
-	html: function( value ) {
-		return access( this, function( value ) {
-			var elem = this[ 0 ] || {},
-				i = 0,
-				l = this.length;
-
-			if ( value === undefined ) {
-				return elem.nodeType === 1 ?
-					elem.innerHTML.replace( rinlinejQuery, "" ) :
-					undefined;
-			}
-
-			// See if we can take a shortcut and just use innerHTML
-			if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
-				( support.htmlSerialize || !rnoshimcache.test( value )  ) &&
-				( support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
-				!wrapMap[ (rtagName.exec( value ) || [ "", "" ])[ 1 ].toLowerCase() ] ) {
-
-				value = value.replace( rxhtmlTag, "<$1></$2>" );
-
-				try {
-					for (; i < l; i++ ) {
-						// Remove element nodes and prevent memory leaks
-						elem = this[i] || {};
-						if ( elem.nodeType === 1 ) {
-							jQuery.cleanData( getAll( elem, false ) );
-							elem.innerHTML = value;
-						}
-					}
-
-					elem = 0;
-
-				// If using innerHTML throws an exception, use the fallback method
-				} catch(e) {}
-			}
-
-			if ( elem ) {
-				this.empty().append( value );
-			}
-		}, null, value, arguments.length );
-	},
-
-	replaceWith: function() {
-		var arg = arguments[ 0 ];
-
-		// Make the changes, replacing each context element with the new content
-		this.domManip( arguments, function( elem ) {
-			arg = this.parentNode;
-
-			jQuery.cleanData( getAll( this ) );
-
-			if ( arg ) {
-				arg.replaceChild( elem, this );
-			}
-		});
-
-		// Force removal if there was no new content (e.g., from empty arguments)
-		return arg && (arg.length || arg.nodeType) ? this : this.remove();
-	},
-
-	detach: function( selector ) {
-		return this.remove( selector, true );
-	},
-
-	domManip: function( args, callback ) {
-
-		// Flatten any nested arrays
-		args = concat.apply( [], args );
-
-		var first, node, hasScripts,
-			scripts, doc, fragment,
-			i = 0,
-			l = this.length,
-			set = this,
-			iNoClone = l - 1,
-			value = args[0],
-			isFunction = jQuery.isFunction( value );
-
-		// We can't cloneNode fragments that contain checked, in WebKit
-		if ( isFunction ||
-				( l > 1 && typeof value === "string" &&
-					!support.checkClone && rchecked.test( value ) ) ) {
-			return this.each(function( index ) {
-				var self = set.eq( index );
-				if ( isFunction ) {
-					args[0] = value.call( this, index, self.html() );
-				}
-				self.domManip( args, callback );
-			});
-		}
-
-		if ( l ) {
-			fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this );
-			first = fragment.firstChild;
-
-			if ( fragment.childNodes.length === 1 ) {
-				fragment = first;
-			}
-
-			if ( first ) {
-				scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
-				hasScripts = scripts.length;
-
-				// Use the original fragment for the last item instead of the first because it can end up
-				// being emptied incorrectly in certain situations (#8070).
-				for ( ; i < l; i++ ) {
-					node = fragment;
-
-					if ( i !== iNoClone ) {
-						node = jQuery.clone( node, true, true );
-
-						// Keep references to cloned scripts for later restoration
-						if ( hasScripts ) {
-							jQuery.merge( scripts, getAll( node, "script" ) );
-						}
-					}
-
-					callback.call( this[i], node, i );
-				}
-
-				if ( hasScripts ) {
-					doc = scripts[ scripts.length - 1 ].ownerDocument;
-
-					// Reenable scripts
-					jQuery.map( scripts, restoreScript );
-
-					// Evaluate executable scripts on first document insertion
-					for ( i = 0; i < hasScripts; i++ ) {
-						node = scripts[ i ];
-						if ( rscriptType.test( node.type || "" ) &&
-							!jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) {
-
-							if ( node.src ) {
-								// Optional AJAX dependency, but won't run scripts if not present
-								if ( jQuery._evalUrl ) {
-									jQuery._evalUrl( node.src );
-								}
-							} else {
-								jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) );
-							}
-						}
-					}
-				}
-
-				// Fix #11809: Avoid leaking memory
-				fragment = first = null;
-			}
-		}
-
-		return this;
-	}
-});
-
-jQuery.each({
-	appendTo: "append",
-	prependTo: "prepend",
-	insertBefore: "before",
-	insertAfter: "after",
-	replaceAll: "replaceWith"
-}, function( name, original ) {
-	jQuery.fn[ name ] = function( selector ) {
-		var elems,
-			i = 0,
-			ret = [],
-			insert = jQuery( selector ),
-			last = insert.length - 1;
-
-		for ( ; i <= last; i++ ) {
-			elems = i === last ? this : this.clone(true);
-			jQuery( insert[i] )[ original ]( elems );
-
-			// Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get()
-			push.apply( ret, elems.get() );
-		}
-
-		return this.pushStack( ret );
-	};
-});
-
-
-var iframe,
-	elemdisplay = {};
-
-/**
- * Retrieve the actual display of a element
- * @param {String} name nodeName of the element
- * @param {Object} doc Document object
- */
-// Called only from within defaultDisplay
-function actualDisplay( name, doc ) {
-	var style,
-		elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ),
-
-		// getDefaultComputedStyle might be reliably used only on attached element
-		display = window.getDefaultComputedStyle && ( style = window.getDefaultComputedStyle( elem[ 0 ] ) ) ?
-
-			// Use of this method is a temporary fix (more like optmization) until something better comes along,
-			// since it was removed from specification and supported only in FF
-			style.display : jQuery.css( elem[ 0 ], "display" );
-
-	// We don't have any data stored on the element,
-	// so use "detach" method as fast way to get rid of the element
-	elem.detach();
-
-	return display;
-}
-
-/**
- * Try to determine the default display value of an element
- * @param {String} nodeName
- */
-function defaultDisplay( nodeName ) {
-	var doc = document,
-		display = elemdisplay[ nodeName ];
-
-	if ( !display ) {
-		display = actualDisplay( nodeName, doc );
-
-		// If the simple way fails, read from inside an iframe
-		if ( display === "none" || !display ) {
-
-			// Use the already-created iframe if possible
-			iframe = (iframe || jQuery( "<iframe frameborder='0' width='0' height='0'/>" )).appendTo( doc.documentElement );
-
-			// Always write a new HTML skeleton so Webkit and Firefox don't choke on reuse
-			doc = ( iframe[ 0 ].contentWindow || iframe[ 0 ].contentDocument ).document;
-
-			// Support: IE
-			doc.write();
-			doc.close();
-
-			display = actualDisplay( nodeName, doc );
-			iframe.detach();
-		}
-
-		// Store the correct default display
-		elemdisplay[ nodeName ] = display;
-	}
-
-	return display;
-}
-
-
-(function() {
-	var shrinkWrapBlocksVal;
-
-	support.shrinkWrapBlocks = function() {
-		if ( shrinkWrapBlocksVal != null ) {
-			return shrinkWrapBlocksVal;
-		}
-
-		// Will be changed later if needed.
-		shrinkWrapBlocksVal = false;
-
-		// Minified: var b,c,d
-		var div, body, container;
-
-		body = document.getElementsByTagName( "body" )[ 0 ];
-		if ( !body || !body.style ) {
-			// Test fired too early or in an unsupported environment, exit.
-			return;
-		}
-
-		// Setup
-		div = document.createElement( "div" );
-		container = document.createElement( "div" );
-		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
-		body.appendChild( container ).appendChild( div );
-
-		// Support: IE6
-		// Check if elements with layout shrink-wrap their children
-		if ( typeof div.style.zoom !== strundefined ) {
-			// Reset CSS: box-sizing; display; margin; border
-			div.style.cssText =
-				// Support: Firefox<29, Android 2.3
-				// Vendor-prefix box-sizing
-				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
-				"box-sizing:content-box;display:block;margin:0;border:0;" +
-				"padding:1px;width:1px;zoom:1";
-			div.appendChild( document.createElement( "div" ) ).style.width = "5px";
-			shrinkWrapBlocksVal = div.offsetWidth !== 3;
-		}
-
-		body.removeChild( container );
-
-		return shrinkWrapBlocksVal;
-	};
-
-})();
-var rmargin = (/^margin/);
-
-var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
-
-
-
-var getStyles, curCSS,
-	rposition = /^(top|right|bottom|left)$/;
-
-if ( window.getComputedStyle ) {
-	getStyles = function( elem ) {
-		return elem.ownerDocument.defaultView.getComputedStyle( elem, null );
-	};
-
-	curCSS = function( elem, name, computed ) {
-		var width, minWidth, maxWidth, ret,
-			style = elem.style;
-
-		computed = computed || getStyles( elem );
-
-		// getPropertyValue is only needed for .css('filter') in IE9, see #12537
-		ret = computed ? computed.getPropertyValue( name ) || computed[ name ] : undefined;
-
-		if ( computed ) {
-
-			if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
-				ret = jQuery.style( elem, name );
-			}
-
-			// A tribute to the "awesome hack by Dean Edwards"
-			// Chrome < 17 and Safari 5.0 uses "computed value" instead of "used value" for margin-right
-			// Safari 5.1.7 (at least) returns percentage for a larger set of values, but width seems to be reliably pixels
-			// this is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values
-			if ( rnumnonpx.test( ret ) && rmargin.test( name ) ) {
-
-				// Remember the original values
-				width = style.width;
-				minWidth = style.minWidth;
-				maxWidth = style.maxWidth;
-
-				// Put in the new values to get a computed value out
-				style.minWidth = style.maxWidth = style.width = ret;
-				ret = computed.width;
-
-				// Revert the changed values
-				style.width = width;
-				style.minWidth = minWidth;
-				style.maxWidth = maxWidth;
-			}
-		}
-
-		// Support: IE
-		// IE returns zIndex value as an integer.
-		return ret === undefined ?
-			ret :
-			ret + "";
-	};
-} else if ( document.documentElement.currentStyle ) {
-	getStyles = function( elem ) {
-		return elem.currentStyle;
-	};
-
-	curCSS = function( elem, name, computed ) {
-		var left, rs, rsLeft, ret,
-			style = elem.style;
-
-		computed = computed || getStyles( elem );
-		ret = computed ? computed[ name ] : undefined;
-
-		// Avoid setting ret to empty string here
-		// so we don't default to auto
-		if ( ret == null && style && style[ name ] ) {
-			ret = style[ name ];
-		}
-
-		// From the awesome hack by Dean Edwards
-		// http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
-
-		// If we're not dealing with a regular pixel number
-		// but a number that has a weird ending, we need to convert it to pixels
-		// but not position css attributes, as those are proportional to the parent element instead
-		// and we can't measure the parent instead because it might trigger a "stacking dolls" problem
-		if ( rnumnonpx.test( ret ) && !rposition.test( name ) ) {
-
-			// Remember the original values
-			left = style.left;
-			rs = elem.runtimeStyle;
-			rsLeft = rs && rs.left;
-
-			// Put in the new values to get a computed value out
-			if ( rsLeft ) {
-				rs.left = elem.currentStyle.left;
-			}
-			style.left = name === "fontSize" ? "1em" : ret;
-			ret = style.pixelLeft + "px";
-
-			// Revert the changed values
-			style.left = left;
-			if ( rsLeft ) {
-				rs.left = rsLeft;
-			}
-		}
-
-		// Support: IE
-		// IE returns zIndex value as an integer.
-		return ret === undefined ?
-			ret :
-			ret + "" || "auto";
-	};
-}
-
-
-
-
-function addGetHookIf( conditionFn, hookFn ) {
-	// Define the hook, we'll check on the first run if it's really needed.
-	return {
-		get: function() {
-			var condition = conditionFn();
-
-			if ( condition == null ) {
-				// The test was not ready at this point; screw the hook this time
-				// but check again when needed next time.
-				return;
-			}
-
-			if ( condition ) {
-				// Hook not needed (or it's not possible to use it due to missing dependency),
-				// remove it.
-				// Since there are no other hooks for marginRight, remove the whole object.
-				delete this.get;
-				return;
-			}
-
-			// Hook needed; redefine it so that the support test is not executed again.
-
-			return (this.get = hookFn).apply( this, arguments );
-		}
-	};
-}
-
-
-(function() {
-	// Minified: var b,c,d,e,f,g, h,i
-	var div, style, a, pixelPositionVal, boxSizingReliableVal,
-		reliableHiddenOffsetsVal, reliableMarginRightVal;
-
-	// Setup
-	div = document.createElement( "div" );
-	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
-	a = div.getElementsByTagName( "a" )[ 0 ];
-	style = a && a.style;
-
-	// Finish early in limited (non-browser) environments
-	if ( !style ) {
-		return;
-	}
-
-	style.cssText = "float:left;opacity:.5";
-
-	// Support: IE<9
-	// Make sure that element opacity exists (as opposed to filter)
-	support.opacity = style.opacity === "0.5";
-
-	// Verify style float existence
-	// (IE uses styleFloat instead of cssFloat)
-	support.cssFloat = !!style.cssFloat;
-
-	div.style.backgroundClip = "content-box";
-	div.cloneNode( true ).style.backgroundClip = "";
-	support.clearCloneStyle = div.style.backgroundClip === "content-box";
-
-	// Support: Firefox<29, Android 2.3
-	// Vendor-prefix box-sizing
-	support.boxSizing = style.boxSizing === "" || style.MozBoxSizing === "" ||
-		style.WebkitBoxSizing === "";
-
-	jQuery.extend(support, {
-		reliableHiddenOffsets: function() {
-			if ( reliableHiddenOffsetsVal == null ) {
-				computeStyleTests();
-			}
-			return reliableHiddenOffsetsVal;
-		},
-
-		boxSizingReliable: function() {
-			if ( boxSizingReliableVal == null ) {
-				computeStyleTests();
-			}
-			return boxSizingReliableVal;
-		},
-
-		pixelPosition: function() {
-			if ( pixelPositionVal == null ) {
-				computeStyleTests();
-			}
-			return pixelPositionVal;
-		},
-
-		// Support: Android 2.3
-		reliableMarginRight: function() {
-			if ( reliableMarginRightVal == null ) {
-				computeStyleTests();
-			}
-			return reliableMarginRightVal;
-		}
-	});
-
-	function computeStyleTests() {
-		// Minified: var b,c,d,j
-		var div, body, container, contents;
-
-		body = document.getElementsByTagName( "body" )[ 0 ];
-		if ( !body || !body.style ) {
-			// Test fired too early or in an unsupported environment, exit.
-			return;
-		}
-
-		// Setup
-		div = document.createElement( "div" );
-		container = document.createElement( "div" );
-		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
-		body.appendChild( container ).appendChild( div );
-
-		div.style.cssText =
-			// Support: Firefox<29, Android 2.3
-			// Vendor-prefix box-sizing
-			"-webkit-box-sizing:border-box;-moz-box-sizing:border-box;" +
-			"box-sizing:border-box;display:block;margin-top:1%;top:1%;" +
-			"border:1px;padding:1px;width:4px;position:absolute";
-
-		// Support: IE<9
-		// Assume reasonable values in the absence of getComputedStyle
-		pixelPositionVal = boxSizingReliableVal = false;
-		reliableMarginRightVal = true;
-
-		// Check for getComputedStyle so that this code is not run in IE<9.
-		if ( window.getComputedStyle ) {
-			pixelPositionVal = ( window.getComputedStyle( div, null ) || {} ).top !== "1%";
-			boxSizingReliableVal =
-				( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px";
-
-			// Support: Android 2.3
-			// Div with explicit width and no margin-right incorrectly
-			// gets computed margin-right based on width of container (#3333)
-			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
-			contents = div.appendChild( document.createElement( "div" ) );
-
-			// Reset CSS: box-sizing; display; margin; border; padding
-			contents.style.cssText = div.style.cssText =
-				// Support: Firefox<29, Android 2.3
-				// Vendor-prefix box-sizing
-				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
-				"box-sizing:content-box;display:block;margin:0;border:0;padding:0";
-			contents.style.marginRight = contents.style.width = "0";
-			div.style.width = "1px";
-
-			reliableMarginRightVal =
-				!parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight );
-		}
-
-		// Support: IE8
-		// Check if table cells still have offsetWidth/Height when they are set
-		// to display:none and there are still other visible table cells in a
-		// table row; if so, offsetWidth/Height are not reliable for use when
-		// determining if an element has been hidden directly using
-		// display:none (it is still safe to use offsets if a parent element is
-		// hidden; don safety goggles and see bug #4512 for more information).
-		div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
-		contents = div.getElementsByTagName( "td" );
-		contents[ 0 ].style.cssText = "margin:0;border:0;padding:0;display:none";
-		reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
-		if ( reliableHiddenOffsetsVal ) {
-			contents[ 0 ].style.display = "";
-			contents[ 1 ].style.display = "none";
-			reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
-		}
-
-		body.removeChild( container );
-	}
-
-})();
-
-
-// A method for quickly swapping in/out CSS properties to get correct calculations.
-jQuery.swap = function( elem, options, callback, args ) {
-	var ret, name,
-		old = {};
-
-	// Remember the old values, and insert the new ones
-	for ( name in options ) {
-		old[ name ] = elem.style[ name ];
-		elem.style[ name ] = options[ name ];
-	}
-
-	ret = callback.apply( elem, args || [] );
-
-	// Revert the old values
-	for ( name in options ) {
-		elem.style[ name ] = old[ name ];
-	}
-
-	return ret;
-};
-
-
-var
-		ralpha = /alpha\([^)]*\)/i,
-	ropacity = /opacity\s*=\s*([^)]*)/,
-
-	// swappable if display is none or starts with table except "table", "table-cell", or "table-caption"
-	// see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
-	rdisplayswap = /^(none|table(?!-c[ea]).+)/,
-	rnumsplit = new RegExp( "^(" + pnum + ")(.*)$", "i" ),
-	rrelNum = new RegExp( "^([+-])=(" + pnum + ")", "i" ),
-
-	cssShow = { position: "absolute", visibility: "hidden", display: "block" },
-	cssNormalTransform = {
-		letterSpacing: "0",
-		fontWeight: "400"
-	},
-
-	cssPrefixes = [ "Webkit", "O", "Moz", "ms" ];
-
-
-// return a css property mapped to a potentially vendor prefixed property
-function vendorPropName( style, name ) {
-
-	// shortcut for names that are not vendor prefixed
-	if ( name in style ) {
-		return name;
-	}
-
-	// check for vendor prefixed names
-	var capName = name.charAt(0).toUpperCase() + name.slice(1),
-		origName = name,
-		i = cssPrefixes.length;
-
-	while ( i-- ) {
-		name = cssPrefixes[ i ] + capName;
-		if ( name in style ) {
-			return name;
-		}
-	}
-
-	return origName;
-}
-
-function showHide( elements, show ) {
-	var display, elem, hidden,
-		values = [],
-		index = 0,
-		length = elements.length;
-
-	for ( ; index < length; index++ ) {
-		elem = elements[ index ];
-		if ( !elem.style ) {
-			continue;
-		}
-
-		values[ index ] = jQuery._data( elem, "olddisplay" );
-		display = elem.style.display;
-		if ( show ) {
-			// Reset the inline display of this element to learn if it is
-			// being hidden by cascaded rules or not
-			if ( !values[ index ] && display === "none" ) {
-				elem.style.display = "";
-			}
-
-			// Set elements which have been overridden with display: none
-			// in a stylesheet to whatever the default browser style is
-			// for such an element
-			if ( elem.style.display === "" && isHidden( elem ) ) {
-				values[ index ] = jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) );
-			}
-		} else {
-			hidden = isHidden( elem );
-
-			if ( display && display !== "none" || !hidden ) {
-				jQuery._data( elem, "olddisplay", hidden ? display : jQuery.css( elem, "display" ) );
-			}
-		}
-	}
-
-	// Set the display of most of the elements in a second loop
-	// to avoid the constant reflow
-	for ( index = 0; index < length; index++ ) {
-		elem = elements[ index ];
-		if ( !elem.style ) {
-			continue;
-		}
-		if ( !show || elem.style.display === "none" || elem.style.display === "" ) {
-			elem.style.display = show ? values[ index ] || "" : "none";
-		}
-	}
-
-	return elements;
-}
-
-function setPositiveNumber( elem, value, subtract ) {
-	var matches = rnumsplit.exec( value );
-	return matches ?
-		// Guard against undefined "subtract", e.g., when used as in cssHooks
-		Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) :
-		value;
-}
-
-function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
-	var i = extra === ( isBorderBox ? "border" : "content" ) ?
-		// If we already have the right measurement, avoid augmentation
-		4 :
-		// Otherwise initialize for horizontal or vertical properties
-		name === "width" ? 1 : 0,
-
-		val = 0;
-
-	for ( ; i < 4; i += 2 ) {
-		// both box models exclude margin, so add it if we want it
-		if ( extra === "margin" ) {
-			val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
-		}
-
-		if ( isBorderBox ) {
-			// border-box includes padding, so remove it if we want content
-			if ( extra === "content" ) {
-				val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
-			}
-
-			// at this point, extra isn't border nor margin, so remove border
-			if ( extra !== "margin" ) {
-				val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
-			}
-		} else {
-			// at this point, extra isn't content, so add padding
-			val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
-
-			// at this point, extra isn't content nor padding, so add border
-			if ( extra !== "padding" ) {
-				val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
-			}
-		}
-	}
-
-	return val;
-}
-
-function getWidthOrHeight( elem, name, extra ) {
-
-	// Start with offset property, which is equivalent to the border-box value
-	var valueIsBorderBox = true,
-		val = name === "width" ? elem.offsetWidth : elem.offsetHeight,
-		styles = getStyles( elem ),
-		isBorderBox = support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
-
-	// some non-html elements return undefined for offsetWidth, so check for null/undefined
-	// svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285
-	// MathML - https://bugzilla.mozilla.org/show_bug.cgi?id=491668
-	if ( val <= 0 || val == null ) {
-		// Fall back to computed then uncomputed css if necessary
-		val = curCSS( elem, name, styles );
-		if ( val < 0 || val == null ) {
-			val = elem.style[ name ];
-		}
-
-		// Computed unit is not pixels. Stop here and return.
-		if ( rnumnonpx.test(val) ) {
-			return val;
-		}
-
-		// we need the check for style in case a browser which returns unreliable values
-		// for getComputedStyle silently falls back to the reliable elem.style
-		valueIsBorderBox = isBorderBox && ( support.boxSizingReliable() || val === elem.style[ name ] );
-
-		// Normalize "", auto, and prepare for extra
-		val = parseFloat( val ) || 0;
-	}
-
-	// use the active box-sizing model to add/subtract irrelevant styles
-	return ( val +
-		augmentWidthOrHeight(
-			elem,
-			name,
-			extra || ( isBorderBox ? "border" : "content" ),
-			valueIsBorderBox,
-			styles
-		)
-	) + "px";
-}
-
-jQuery.extend({
-	// Add in style property hooks for overriding the default
-	// behavior of getting and setting a style property
-	cssHooks: {
-		opacity: {
-			get: function( elem, computed ) {
-				if ( computed ) {
-					// We should always get a number back from opacity
-					var ret = curCSS( elem, "opacity" );
-					return ret === "" ? "1" : ret;
-				}
-			}
-		}
-	},
-
-	// Don't automatically add "px" to these possibly-unitless properties
-	cssNumber: {
-		"columnCount": true,
-		"fillOpacity": true,
-		"flexGrow": true,
-		"flexShrink": true,
-		"fontWeight": true,
-		"lineHeight": true,
-		"opacity": true,
-		"order": true,
-		"orphans": true,
-		"widows": true,
-		"zIndex": true,
-		"zoom": true
-	},
-
-	// Add in properties whose names you wish to fix before
-	// setting or getting the value
-	cssProps: {
-		// normalize float css property
-		"float": support.cssFloat ? "cssFloat" : "styleFloat"
-	},
-
-	// Get and set the style property on a DOM Node
-	style: function( elem, name, value, extra ) {
-		// Don't set styles on text and comment nodes
-		if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
-			return;
-		}
-
-		// Make sure that we're working with the right name
-		var ret, type, hooks,
-			origName = jQuery.camelCase( name ),
-			style = elem.style;
-
-		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) );
-
-		// gets hook for the prefixed version
-		// followed by the unprefixed version
-		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
-		// Check if we're setting a value
-		if ( value !== undefined ) {
-			type = typeof value;
-
-			// convert relative number strings (+= or -=) to relative numbers. #7345
-			if ( type === "string" && (ret = rrelNum.exec( value )) ) {
-				value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) );
-				// Fixes bug #9237
-				type = "number";
-			}
-
-			// Make sure that null and NaN values aren't set. See: #7116
-			if ( value == null || value !== value ) {
-				return;
-			}
-
-			// If a number was passed in, add 'px' to the (except for certain CSS properties)
-			if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
-				value += "px";
-			}
-
-			// Fixes #8908, it can be done more correctly by specifing setters in cssHooks,
-			// but it would mean to define eight (for every problematic property) identical functions
-			if ( !support.clearCloneStyle && value === "" && name.indexOf("background") === 0 ) {
-				style[ name ] = "inherit";
-			}
-
-			// If a hook was provided, use that value, otherwise just set the specified value
-			if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) {
-
-				// Support: IE
-				// Swallow errors from 'invalid' CSS values (#5509)
-				try {
-					style[ name ] = value;
-				} catch(e) {}
-			}
-
-		} else {
-			// If a hook was provided get the non-computed value from there
-			if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
-				return ret;
-			}
-
-			// Otherwise just get the value from the style object
-			return style[ name ];
-		}
-	},
-
-	css: function( elem, name, extra, styles ) {
-		var num, val, hooks,
-			origName = jQuery.camelCase( name );
-
-		// Make sure that we're working with the right name
-		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) );
-
-		// gets hook for the prefixed version
-		// followed by the unprefixed version
-		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
-		// If a hook was provided get the computed value from there
-		if ( hooks && "get" in hooks ) {
-			val = hooks.get( elem, true, extra );
-		}
-
-		// Otherwise, if a way to get the computed value exists, use that
-		if ( val === undefined ) {
-			val = curCSS( elem, name, styles );
-		}
-
-		//convert "normal" to computed value
-		if ( val === "normal" && name in cssNormalTransform ) {
-			val = cssNormalTransform[ name ];
-		}
-
-		// Return, converting to number if forced or a qualifier was provided and val looks numeric
-		if ( extra === "" || extra ) {
-			num = parseFloat( val );
-			return extra === true || jQuery.isNumeric( num ) ? num || 0 : val;
-		}
-		return val;
-	}
-});
-
-jQuery.each([ "height", "width" ], function( i, name ) {
-	jQuery.cssHooks[ name ] = {
-		get: function( elem, computed, extra ) {
-			if ( computed ) {
-				// certain elements can have dimension info if we invisibly show them
-				// however, it must have a current display style that would benefit from this
-				return rdisplayswap.test( jQuery.css( elem, "display" ) ) && elem.offsetWidth === 0 ?
-					jQuery.swap( elem, cssShow, function() {
-						return getWidthOrHeight( elem, name, extra );
-					}) :
-					getWidthOrHeight( elem, name, extra );
-			}
-		},
-
-		set: function( elem, value, extra ) {
-			var styles = extra && getStyles( elem );
-			return setPositiveNumber( elem, value, extra ?
-				augmentWidthOrHeight(
-					elem,
-					name,
-					extra,
-					support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
-					styles
-				) : 0
-			);
-		}
-	};
-});
-
-if ( !support.opacity ) {
-	jQuery.cssHooks.opacity = {
-		get: function( elem, computed ) {
-			// IE uses filters for opacity
-			return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ?
-				( 0.01 * parseFloat( RegExp.$1 ) ) + "" :
-				computed ? "1" : "";
-		},
-
-		set: function( elem, value ) {
-			var style = elem.style,
-				currentStyle = elem.currentStyle,
-				opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "",
-				filter = currentStyle && currentStyle.filter || style.filter || "";
-
-			// IE has trouble with opacity if it does not have layout
-			// Force it by setting the zoom level
-			style.zoom = 1;
-
-			// if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652
-			// if value === "", then remove inline opacity #12685
-			if ( ( value >= 1 || value === "" ) &&
-					jQuery.trim( filter.replace( ralpha, "" ) ) === "" &&
-					style.removeAttribute ) {
-
-				// Setting style.filter to null, "" & " " still leave "filter:" in the cssText
-				// if "filter:" is present at all, clearType is disabled, we want to avoid this
-				// style.removeAttribute is IE Only, but so apparently is this code path...
-				style.removeAttribute( "filter" );
-
-				// if there is no filter style applied in a css rule or unset inline opacity, we are done
-				if ( value === "" || currentStyle && !currentStyle.filter ) {
-					return;
-				}
-			}
-
-			// otherwise, set new filter values
-			style.filter = ralpha.test( filter ) ?
-				filter.replace( ralpha, opacity ) :
-				filter + " " + opacity;
-		}
-	};
-}
-
-jQuery.cssHooks.marginRight = addGetHookIf( support.reliableMarginRight,
-	function( elem, computed ) {
-		if ( computed ) {
-			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
-			// Work around by temporarily setting element display to inline-block
-			return jQuery.swap( elem, { "display": "inline-block" },
-				curCSS, [ elem, "marginRight" ] );
-		}
-	}
-);
-
-// These hooks are used by animate to expand properties
-jQuery.each({
-	margin: "",
-	padding: "",
-	border: "Width"
-}, function( prefix, suffix ) {
-	jQuery.cssHooks[ prefix + suffix ] = {
-		expand: function( value ) {
-			var i = 0,
-				expanded = {},
-
-				// assumes a single number if not a string
-				parts = typeof value === "string" ? value.split(" ") : [ value ];
-
-			for ( ; i < 4; i++ ) {
-				expanded[ prefix + cssExpand[ i ] + suffix ] =
-					parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
-			}
-
-			return expanded;
-		}
-	};
-
-	if ( !rmargin.test( prefix ) ) {
-		jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
-	}
-});
-
-jQuery.fn.extend({
-	css: function( name, value ) {
-		return access( this, function( elem, name, value ) {
-			var styles, len,
-				map = {},
-				i = 0;
-
-			if ( jQuery.isArray( name ) ) {
-				styles = getStyles( elem );
-				len = name.length;
-
-				for ( ; i < len; i++ ) {
-					map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
-				}
-
-				return map;
-			}
-
-			return value !== undefined ?
-				jQuery.style( elem, name, value ) :
-				jQuery.css( elem, name );
-		}, name, value, arguments.length > 1 );
-	},
-	show: function() {
-		return showHide( this, true );
-	},
-	hide: function() {
-		return showHide( this );
-	},
-	toggle: function( state ) {
-		if ( typeof state === "boolean" ) {
-			return state ? this.show() : this.hide();
-		}
-
-		return this.each(function() {
-			if ( isHidden( this ) ) {
-				jQuery( this ).show();
-			} else {
-				jQuery( this ).hide();
-			}
-		});
-	}
-});
-
-
-function Tween( elem, options, prop, end, easing ) {
-	return new Tween.prototype.init( elem, options, prop, end, easing );
-}
-jQuery.Tween = Tween;
-
-Tween.prototype = {
-	constructor: Tween,
-	init: function( elem, options, prop, end, easing, unit ) {
-		this.elem = elem;
-		this.prop = prop;
-		this.easing = easing || "swing";
-		this.options = options;
-		this.start = this.now = this.cur();
-		this.end = end;
-		this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
-	},
-	cur: function() {
-		var hooks = Tween.propHooks[ this.prop ];
-
-		return hooks && hooks.get ?
-			hooks.get( this ) :
-			Tween.propHooks._default.get( this );
-	},
-	run: function( percent ) {
-		var eased,
-			hooks = Tween.propHooks[ this.prop ];
-
-		if ( this.options.duration ) {
-			this.pos = eased = jQuery.easing[ this.easing ](
-				percent, this.options.duration * percent, 0, 1, this.options.duration
-			);
-		} else {
-			this.pos = eased = percent;
-		}
-		this.now = ( this.end - this.start ) * eased + this.start;
-
-		if ( this.options.step ) {
-			this.options.step.call( this.elem, this.now, this );
-		}
-
-		if ( hooks && hooks.set ) {
-			hooks.set( this );
-		} else {
-			Tween.propHooks._default.set( this );
-		}
-		return this;
-	}
-};
-
-Tween.prototype.init.prototype = Tween.prototype;
-
-Tween.propHooks = {
-	_default: {
-		get: function( tween ) {
-			var result;
-
-			if ( tween.elem[ tween.prop ] != null &&
-				(!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) {
-				return tween.elem[ tween.prop ];
-			}
-
-			// passing an empty string as a 3rd parameter to .css will automatically
-			// attempt a parseFloat and fallback to a string if the parse fails
-			// so, simple values such as "10px" are parsed to Float.
-			// complex values such as "rotate(1rad)" are returned as is.
-			result = jQuery.css( tween.elem, tween.prop, "" );
-			// Empty strings, null, undefined and "auto" are converted to 0.
-			return !result || result === "auto" ? 0 : result;
-		},
-		set: function( tween ) {
-			// use step hook for back compat - use cssHook if its there - use .style if its
-			// available and use plain properties where available
-			if ( jQuery.fx.step[ tween.prop ] ) {
-				jQuery.fx.step[ tween.prop ]( tween );
-			} else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) {
-				jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
-			} else {
-				tween.elem[ tween.prop ] = tween.now;
-			}
-		}
-	}
-};
-
-// Support: IE <=9
-// Panic based approach to setting things on disconnected nodes
-
-Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
-	set: function( tween ) {
-		if ( tween.elem.nodeType && tween.elem.parentNode ) {
-			tween.elem[ tween.prop ] = tween.now;
-		}
-	}
-};
-
-jQuery.easing = {
-	linear: function( p ) {
-		return p;
-	},
-	swing: function( p ) {
-		return 0.5 - Math.cos( p * Math.PI ) / 2;
-	}
-};
-
-jQuery.fx = Tween.prototype.init;
-
-// Back Compat <1.8 extension point
-jQuery.fx.step = {};
-
-
-
-
-var
-	fxNow, timerId,
-	rfxtypes = /^(?:toggle|show|hide)$/,
-	rfxnum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ),
-	rrun = /queueHooks$/,
-	animationPrefilters = [ defaultPrefilter ],
-	tweeners = {
-		"*": [ function( prop, value ) {
-			var tween = this.createTween( prop, value ),
-				target = tween.cur(),
-				parts = rfxnum.exec( value ),
-				unit = parts && parts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
-
-				// Starting value computation is required for potential unit mismatches
-				start = ( jQuery.cssNumber[ prop ] || unit !== "px" && +target ) &&
-					rfxnum.exec( jQuery.css( tween.elem, prop ) ),
-				scale = 1,
-				maxIterations = 20;
-
-			if ( start && start[ 3 ] !== unit ) {
-				// Trust units reported by jQuery.css
-				unit = unit || start[ 3 ];
-
-				// Make sure we update the tween properties later on
-				parts = parts || [];
-
-				// Iteratively approximate from a nonzero starting point
-				start = +target || 1;
-
-				do {
-					// If previous iteration zeroed out, double until we get *something*
-					// Use a string for doubling factor so we don't accidentally see scale as unchanged below
-					scale = scale || ".5";
-
-					// Adjust and apply
-					start = start / scale;
-					jQuery.style( tween.elem, prop, start + unit );
-
-				// Update scale, tolerating zero or NaN from tween.cur()
-				// And breaking the loop if scale is unchanged or perfect, or if we've just had enough
-				} while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations );
-			}
-
-			// Update tween properties
-			if ( parts ) {
-				start = tween.start = +start || +target || 0;
-				tween.unit = unit;
-				// If a +=/-= token was provided, we're doing a relative animation
-				tween.end = parts[ 1 ] ?
-					start + ( parts[ 1 ] + 1 ) * parts[ 2 ] :
-					+parts[ 2 ];
-			}
-
-			return tween;
-		} ]
-	};
-
-// Animations created synchronously will run synchronously
-function createFxNow() {
-	setTimeout(function() {
-		fxNow = undefined;
-	});
-	return ( fxNow = jQuery.now() );
-}
-
-// Generate parameters to create a standard animation
-function genFx( type, includeWidth ) {
-	var which,
-		attrs = { height: type },
-		i = 0;
-
-	// if we include width, step value is 1 to do all cssExpand values,
-	// if we don't include width, step value is 2 to skip over Left and Right
-	includeWidth = includeWidth ? 1 : 0;
-	for ( ; i < 4 ; i += 2 - includeWidth ) {
-		which = cssExpand[ i ];
-		attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
-	}
-
-	if ( includeWidth ) {
-		attrs.opacity = attrs.width = type;
-	}
-
-	return attrs;
-}
-
-function createTween( value, prop, animation ) {
-	var tween,
-		collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ),
-		index = 0,
-		length = collection.length;
-	for ( ; index < length; index++ ) {
-		if ( (tween = collection[ index ].call( animation, prop, value )) ) {
-
-			// we're done with this property
-			return tween;
-		}
-	}
-}
-
-function defaultPrefilter( elem, props, opts ) {
-	/* jshint validthis: true */
-	var prop, value, toggle, tween, hooks, oldfire, display, checkDisplay,
-		anim = this,
-		orig = {},
-		style = elem.style,
-		hidden = elem.nodeType && isHidden( elem ),
-		dataShow = jQuery._data( elem, "fxshow" );
-
-	// handle queue: false promises
-	if ( !opts.queue ) {
-		hooks = jQuery._queueHooks( elem, "fx" );
-		if ( hooks.unqueued == null ) {
-			hooks.unqueued = 0;
-			oldfire = hooks.empty.fire;
-			hooks.empty.fire = function() {
-				if ( !hooks.unqueued ) {
-					oldfire();
-				}
-			};
-		}
-		hooks.unqueued++;
-
-		anim.always(function() {
-			// doing this makes sure that the complete handler will be called
-			// before this completes
-			anim.always(function() {
-				hooks.unqueued--;
-				if ( !jQuery.queue( elem, "fx" ).length ) {
-					hooks.empty.fire();
-				}
-			});
-		});
-	}
-
-	// height/width overflow pass
-	if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) {
-		// Make sure that nothing sneaks out
-		// Record all 3 overflow attributes because IE does not
-		// change the overflow attribute when overflowX and
-		// overflowY are set to the same value
-		opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
-
-		// Set display property to inline-block for height/width
-		// animations on inline elements that are having width/height animated
-		display = jQuery.css( elem, "display" );
-
-		// Test default display if display is currently "none"
-		checkDisplay = display === "none" ?
-			jQuery._data( elem, "olddisplay" ) || defaultDisplay( elem.nodeName ) : display;
-
-		if ( checkDisplay === "inline" && jQuery.css( elem, "float" ) === "none" ) {
-
-			// inline-level elements accept inline-block;
-			// block-level elements need to be inline with layout
-			if ( !support.inlineBlockNeedsLayout || defaultDisplay( elem.nodeName ) === "inline" ) {
-				style.display = "inline-block";
-			} else {
-				style.zoom = 1;
-			}
-		}
-	}
-
-	if ( opts.overflow ) {
-		style.overflow = "hidden";
-		if ( !support.shrinkWrapBlocks() ) {
-			anim.always(function() {
-				style.overflow = opts.overflow[ 0 ];
-				style.overflowX = opts.overflow[ 1 ];
-				style.overflowY = opts.overflow[ 2 ];
-			});
-		}
-	}
-
-	// show/hide pass
-	for ( prop in props ) {
-		value = props[ prop ];
-		if ( rfxtypes.exec( value ) ) {
-			delete props[ prop ];
-			toggle = toggle || value === "toggle";
-			if ( value === ( hidden ? "hide" : "show" ) ) {
-
-				// If there is dataShow left over from a stopped hide or show and we are going to proceed with show, we should pretend to be hidden
-				if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
-					hidden = true;
-				} else {
-					continue;
-				}
-			}
-			orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
-
-		// Any non-fx value stops us from restoring the original display value
-		} else {
-			display = undefined;
-		}
-	}
-
-	if ( !jQuery.isEmptyObject( orig ) ) {
-		if ( dataShow ) {
-			if ( "hidden" in dataShow ) {
-				hidden = dataShow.hidden;
-			}
-		} else {
-			dataShow = jQuery._data( elem, "fxshow", {} );
-		}
-
-		// store state if its toggle - enables .stop().toggle() to "reverse"
-		if ( toggle ) {
-			dataShow.hidden = !hidden;
-		}
-		if ( hidden ) {
-			jQuery( elem ).show();
-		} else {
-			anim.done(function() {
-				jQuery( elem ).hide();
-			});
-		}
-		anim.done(function() {
-			var prop;
-			jQuery._removeData( elem, "fxshow" );
-			for ( prop in orig ) {
-				jQuery.style( elem, prop, orig[ prop ] );
-			}
-		});
-		for ( prop in orig ) {
-			tween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
-
-			if ( !( prop in dataShow ) ) {
-				dataShow[ prop ] = tween.start;
-				if ( hidden ) {
-					tween.end = tween.start;
-					tween.start = prop === "width" || prop === "height" ? 1 : 0;
-				}
-			}
-		}
-
-	// If this is a noop like .hide().hide(), restore an overwritten display value
-	} else if ( (display === "none" ? defaultDisplay( elem.nodeName ) : display) === "inline" ) {
-		style.display = display;
-	}
-}
-
-function propFilter( props, specialEasing ) {
-	var index, name, easing, value, hooks;
-
-	// camelCase, specialEasing and expand cssHook pass
-	for ( index in props ) {
-		name = jQuery.camelCase( index );
-		easing = specialEasing[ name ];
-		value = props[ index ];
-		if ( jQuery.isArray( value ) ) {
-			easing = value[ 1 ];
-			value = props[ index ] = value[ 0 ];
-		}
-
-		if ( index !== name ) {
-			props[ name ] = value;
-			delete props[ index ];
-		}
-
-		hooks = jQuery.cssHooks[ name ];
-		if ( hooks && "expand" in hooks ) {
-			value = hooks.expand( value );
-			delete props[ name ];
-
-			// not quite $.extend, this wont overwrite keys already present.
-			// also - reusing 'index' from above because we have the correct "name"
-			for ( index in value ) {
-				if ( !( index in props ) ) {
-					props[ index ] = value[ index ];
-					specialEasing[ index ] = easing;
-				}
-			}
-		} else {
-			specialEasing[ name ] = easing;
-		}
-	}
-}
-
-function Animation( elem, properties, options ) {
-	var result,
-		stopped,
-		index = 0,
-		length = animationPrefilters.length,
-		deferred = jQuery.Deferred().always( function() {
-			// don't match elem in the :animated selector
-			delete tick.elem;
-		}),
-		tick = function() {
-			if ( stopped ) {
-				return false;
-			}
-			var currentTime = fxNow || createFxNow(),
-				remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
-				// archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497)
-				temp = remaining / animation.duration || 0,
-				percent = 1 - temp,
-				index = 0,
-				length = animation.tweens.length;
-
-			for ( ; index < length ; index++ ) {
-				animation.tweens[ index ].run( percent );
-			}
-
-			deferred.notifyWith( elem, [ animation, percent, remaining ]);
-
-			if ( percent < 1 && length ) {
-				return remaining;
-			} else {
-				deferred.resolveWith( elem, [ animation ] );
-				return false;
-			}
-		},
-		animation = deferred.promise({
-			elem: elem,
-			props: jQuery.extend( {}, properties ),
-			opts: jQuery.extend( true, { specialEasing: {} }, options ),
-			originalProperties: properties,
-			originalOptions: options,
-			startTime: fxNow || createFxNow(),
-			duration: options.duration,
-			tweens: [],
-			createTween: function( prop, end ) {
-				var tween = jQuery.Tween( elem, animation.opts, prop, end,
-						animation.opts.specialEasing[ prop ] || animation.opts.easing );
-				animation.tweens.push( tween );
-				return tween;
-			},
-			stop: function( gotoEnd ) {
-				var index = 0,
-					// if we are going to the end, we want to run all the tweens
-					// otherwise we skip this part
-					length = gotoEnd ? animation.tweens.length : 0;
-				if ( stopped ) {
-					return this;
-				}
-				stopped = true;
-				for ( ; index < length ; index++ ) {
-					animation.tweens[ index ].run( 1 );
-				}
-
-				// resolve when we played the last frame
-				// otherwise, reject
-				if ( gotoEnd ) {
-					deferred.resolveWith( elem, [ animation, gotoEnd ] );
-				} else {
-					deferred.rejectWith( elem, [ animation, gotoEnd ] );
-				}
-				return this;
-			}
-		}),
-		props = animation.props;
-
-	propFilter( props, animation.opts.specialEasing );
-
-	for ( ; index < length ; index++ ) {
-		result = animationPrefilters[ index ].call( animation, elem, props, animation.opts );
-		if ( result ) {
-			return result;
-		}
-	}
-
-	jQuery.map( props, createTween, animation );
-
-	if ( jQuery.isFunction( animation.opts.start ) ) {
-		animation.opts.start.call( elem, animation );
-	}
-
-	jQuery.fx.timer(
-		jQuery.extend( tick, {
-			elem: elem,
-			anim: animation,
-			queue: animation.opts.queue
-		})
-	);
-
-	// attach callbacks from options
-	return animation.progress( animation.opts.progress )
-		.done( animation.opts.done, animation.opts.complete )
-		.fail( animation.opts.fail )
-		.always( animation.opts.always );
-}
-
-jQuery.Animation = jQuery.extend( Animation, {
-	tweener: function( props, callback ) {
-		if ( jQuery.isFunction( props ) ) {
-			callback = props;
-			props = [ "*" ];
-		} else {
-			props = props.split(" ");
-		}
-
-		var prop,
-			index = 0,
-			length = props.length;
-
-		for ( ; index < length ; index++ ) {
-			prop = props[ index ];
-			tweeners[ prop ] = tweeners[ prop ] || [];
-			tweeners[ prop ].unshift( callback );
-		}
-	},
-
-	prefilter: function( callback, prepend ) {
-		if ( prepend ) {
-			animationPrefilters.unshift( callback );
-		} else {
-			animationPrefilters.push( callback );
-		}
-	}
-});
-
-jQuery.speed = function( speed, easing, fn ) {
-	var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
-		complete: fn || !fn && easing ||
-			jQuery.isFunction( speed ) && speed,
-		duration: speed,
-		easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
-	};
-
-	opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
-		opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
-
-	// normalize opt.queue - true/undefined/null -> "fx"
-	if ( opt.queue == null || opt.queue === true ) {
-		opt.queue = "fx";
-	}
-
-	// Queueing
-	opt.old = opt.complete;
-
-	opt.complete = function() {
-		if ( jQuery.isFunction( opt.old ) ) {
-			opt.old.call( this );
-		}
-
-		if ( opt.queue ) {
-			jQuery.dequeue( this, opt.queue );
-		}
-	};
-
-	return opt;
-};
-
-jQuery.fn.extend({
-	fadeTo: function( speed, to, easing, callback ) {
-
-		// show any hidden elements after setting opacity to 0
-		return this.filter( isHidden ).css( "opacity", 0 ).show()
-
-			// animate to the value specified
-			.end().animate({ opacity: to }, speed, easing, callback );
-	},
-	animate: function( prop, speed, easing, callback ) {
-		var empty = jQuery.isEmptyObject( prop ),
-			optall = jQuery.speed( speed, easing, callback ),
-			doAnimation = function() {
-				// Operate on a copy of prop so per-property easing won't be lost
-				var anim = Animation( this, jQuery.extend( {}, prop ), optall );
-
-				// Empty animations, or finishing resolves immediately
-				if ( empty || jQuery._data( this, "finish" ) ) {
-					anim.stop( true );
-				}
-			};
-			doAnimation.finish = doAnimation;
-
-		return empty || optall.queue === false ?
-			this.each( doAnimation ) :
-			this.queue( optall.queue, doAnimation );
-	},
-	stop: function( type, clearQueue, gotoEnd ) {
-		var stopQueue = function( hooks ) {
-			var stop = hooks.stop;
-			delete hooks.stop;
-			stop( gotoEnd );
-		};
-
-		if ( typeof type !== "string" ) {
-			gotoEnd = clearQueue;
-			clearQueue = type;
-			type = undefined;
-		}
-		if ( clearQueue && type !== false ) {
-			this.queue( type || "fx", [] );
-		}
-
-		return this.each(function() {
-			var dequeue = true,
-				index = type != null && type + "queueHooks",
-				timers = jQuery.timers,
-				data = jQuery._data( this );
-
-			if ( index ) {
-				if ( data[ index ] && data[ index ].stop ) {
-					stopQueue( data[ index ] );
-				}
-			} else {
-				for ( index in data ) {
-					if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
-						stopQueue( data[ index ] );
-					}
-				}
-			}
-
-			for ( index = timers.length; index--; ) {
-				if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
-					timers[ index ].anim.stop( gotoEnd );
-					dequeue = false;
-					timers.splice( index, 1 );
-				}
-			}
-
-			// start the next in the queue if the last step wasn't forced
-			// timers currently will call their complete callbacks, which will dequeue
-			// but only if they were gotoEnd
-			if ( dequeue || !gotoEnd ) {
-				jQuery.dequeue( this, type );
-			}
-		});
-	},
-	finish: function( type ) {
-		if ( type !== false ) {
-			type = type || "fx";
-		}
-		return this.each(function() {
-			var index,
-				data = jQuery._data( this ),
-				queue = data[ type + "queue" ],
-				hooks = data[ type + "queueHooks" ],
-				timers = jQuery.timers,
-				length = queue ? queue.length : 0;
-
-			// enable finishing flag on private data
-			data.finish = true;
-
-			// empty the queue first
-			jQuery.queue( this, type, [] );
-
-			if ( hooks && hooks.stop ) {
-				hooks.stop.call( this, true );
-			}
-
-			// look for any active animations, and finish them
-			for ( index = timers.length; index--; ) {
-				if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
-					timers[ index ].anim.stop( true );
-					timers.splice( index, 1 );
-				}
-			}
-
-			// look for any animations in the old queue and finish them
-			for ( index = 0; index < length; index++ ) {
-				if ( queue[ index ] && queue[ index ].finish ) {
-					queue[ index ].finish.call( this );
-				}
-			}
-
-			// turn off finishing flag
-			delete data.finish;
-		});
-	}
-});
-
-jQuery.each([ "toggle", "show", "hide" ], function( i, name ) {
-	var cssFn = jQuery.fn[ name ];
-	jQuery.fn[ name ] = function( speed, easing, callback ) {
-		return speed == null || typeof speed === "boolean" ?
-			cssFn.apply( this, arguments ) :
-			this.animate( genFx( name, true ), speed, easing, callback );
-	};
-});
-
-// Generate shortcuts for custom animations
-jQuery.each({
-	slideDown: genFx("show"),
-	slideUp: genFx("hide"),
-	slideToggle: genFx("toggle"),
-	fadeIn: { opacity: "show" },
-	fadeOut: { opacity: "hide" },
-	fadeToggle: { opacity: "toggle" }
-}, function( name, props ) {
-	jQuery.fn[ name ] = function( speed, easing, callback ) {
-		return this.animate( props, speed, easing, callback );
-	};
-});
-
-jQuery.timers = [];
-jQuery.fx.tick = function() {
-	var timer,
-		timers = jQuery.timers,
-		i = 0;
-
-	fxNow = jQuery.now();
-
-	for ( ; i < timers.length; i++ ) {
-		timer = timers[ i ];
-		// Checks the timer has not already been removed
-		if ( !timer() && timers[ i ] === timer ) {
-			timers.splice( i--, 1 );
-		}
-	}
-
-	if ( !timers.length ) {
-		jQuery.fx.stop();
-	}
-	fxNow = undefined;
-};
-
-jQuery.fx.timer = function( timer ) {
-	jQuery.timers.push( timer );
-	if ( timer() ) {
-		jQuery.fx.start();
-	} else {
-		jQuery.timers.pop();
-	}
-};
-
-jQuery.fx.interval = 13;
-
-jQuery.fx.start = function() {
-	if ( !timerId ) {
-		timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval );
-	}
-};
-
-jQuery.fx.stop = function() {
-	clearInterval( timerId );
-	timerId = null;
-};
-
-jQuery.fx.speeds = {
-	slow: 600,
-	fast: 200,
-	// Default speed
-	_default: 400
-};
-
-
-// Based off of the plugin by Clint Helfers, with permission.
-// http://blindsignals.com/index.php/2009/07/jquery-delay/
-jQuery.fn.delay = function( time, type ) {
-	time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
-	type = type || "fx";
-
-	return this.queue( type, function( next, hooks ) {
-		var timeout = setTimeout( next, time );
-		hooks.stop = function() {
-			clearTimeout( timeout );
-		};
-	});
-};
-
-
-(function() {
-	// Minified: var a,b,c,d,e
-	var input, div, select, a, opt;
-
-	// Setup
-	div = document.createElement( "div" );
-	div.setAttribute( "className", "t" );
-	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
-	a = div.getElementsByTagName("a")[ 0 ];
-
-	// First batch of tests.
-	select = document.createElement("select");
-	opt = select.appendChild( document.createElement("option") );
-	input = div.getElementsByTagName("input")[ 0 ];
-
-	a.style.cssText = "top:1px";
-
-	// Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
-	support.getSetAttribute = div.className !== "t";
-
-	// Get the style information from getAttribute
-	// (IE uses .cssText instead)
-	support.style = /top/.test( a.getAttribute("style") );
-
-	// Make sure that URLs aren't manipulated
-	// (IE normalizes it by default)
-	support.hrefNormalized = a.getAttribute("href") === "/a";
-
-	// Check the default checkbox/radio value ("" on WebKit; "on" elsewhere)
-	support.checkOn = !!input.value;
-
-	// Make sure that a selected-by-default option has a working selected property.
-	// (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
-	support.optSelected = opt.selected;
-
-	// Tests for enctype support on a form (#6743)
-	support.enctype = !!document.createElement("form").enctype;
-
-	// Make sure that the options inside disabled selects aren't marked as disabled
-	// (WebKit marks them as disabled)
-	select.disabled = true;
-	support.optDisabled = !opt.disabled;
-
-	// Support: IE8 only
-	// Check if we can trust getAttribute("value")
-	input = document.createElement( "input" );
-	input.setAttribute( "value", "" );
-	support.input = input.getAttribute( "value" ) === "";
-
-	// Check if an input maintains its value after becoming a radio
-	input.value = "t";
-	input.setAttribute( "type", "radio" );
-	support.radioValue = input.value === "t";
-})();
-
-
-var rreturn = /\r/g;
-
-jQuery.fn.extend({
-	val: function( value ) {
-		var hooks, ret, isFunction,
-			elem = this[0];
-
-		if ( !arguments.length ) {
-			if ( elem ) {
-				hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
-
-				if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
-					return ret;
-				}
-
-				ret = elem.value;
-
-				return typeof ret === "string" ?
-					// handle most common string cases
-					ret.replace(rreturn, "") :
-					// handle cases where value is null/undef or number
-					ret == null ? "" : ret;
-			}
-
-			return;
-		}
-
-		isFunction = jQuery.isFunction( value );
-
-		return this.each(function( i ) {
-			var val;
-
-			if ( this.nodeType !== 1 ) {
-				return;
-			}
-
-			if ( isFunction ) {
-				val = value.call( this, i, jQuery( this ).val() );
-			} else {
-				val = value;
-			}
-
-			// Treat null/undefined as ""; convert numbers to string
-			if ( val == null ) {
-				val = "";
-			} else if ( typeof val === "number" ) {
-				val += "";
-			} else if ( jQuery.isArray( val ) ) {
-				val = jQuery.map( val, function( value ) {
-					return value == null ? "" : value + "";
-				});
-			}
-
-			hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
-
-			// If set returns undefined, fall back to normal setting
-			if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
-				this.value = val;
-			}
-		});
-	}
-});
-
-jQuery.extend({
-	valHooks: {
-		option: {
-			get: function( elem ) {
-				var val = jQuery.find.attr( elem, "value" );
-				return val != null ?
-					val :
-					// Support: IE10-11+
-					// option.text throws exceptions (#14686, #14858)
-					jQuery.trim( jQuery.text( elem ) );
-			}
-		},
-		select: {
-			get: function( elem ) {
-				var value, option,
-					options = elem.options,
-					index = elem.selectedIndex,
-					one = elem.type === "select-one" || index < 0,
-					values = one ? null : [],
-					max = one ? index + 1 : options.length,
-					i = index < 0 ?
-						max :
-						one ? index : 0;
-
-				// Loop through all the selected options
-				for ( ; i < max; i++ ) {
-					option = options[ i ];
-
-					// oldIE doesn't update selected after form reset (#2551)
-					if ( ( option.selected || i === index ) &&
-							// Don't return options that are disabled or in a disabled optgroup
-							( support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) &&
-							( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) {
-
-						// Get the specific value for the option
-						value = jQuery( option ).val();
-
-						// We don't need an array for one selects
-						if ( one ) {
-							return value;
-						}
-
-						// Multi-Selects return an array
-						values.push( value );
-					}
-				}
-
-				return values;
-			},
-
-			set: function( elem, value ) {
-				var optionSet, option,
-					options = elem.options,
-					values = jQuery.makeArray( value ),
-					i = options.length;
-
-				while ( i-- ) {
-					option = options[ i ];
-
-					if ( jQuery.inArray( jQuery.valHooks.option.get( option ), values ) >= 0 ) {
-
-						// Support: IE6
-						// When new option element is added to select box we need to
-						// force reflow of newly added node in order to workaround delay
-						// of initialization properties
-						try {
-							option.selected = optionSet = true;
-
-						} catch ( _ ) {
-
-							// Will be executed only in IE6
-							option.scrollHeight;
-						}
-
-					} else {
-						option.selected = false;
-					}
-				}
-
-				// Force browsers to behave consistently when non-matching value is set
-				if ( !optionSet ) {
-					elem.selectedIndex = -1;
-				}
-
-				return options;
-			}
-		}
-	}
-});
-
-// Radios and checkboxes getter/setter
-jQuery.each([ "radio", "checkbox" ], function() {
-	jQuery.valHooks[ this ] = {
-		set: function( elem, value ) {
-			if ( jQuery.isArray( value ) ) {
-				return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
-			}
-		}
-	};
-	if ( !support.checkOn ) {
-		jQuery.valHooks[ this ].get = function( elem ) {
-			// Support: Webkit
-			// "" is returned instead of "on" if a value isn't specified
-			return elem.getAttribute("value") === null ? "on" : elem.value;
-		};
-	}
-});
-
-
-
-
-var nodeHook, boolHook,
-	attrHandle = jQuery.expr.attrHandle,
-	ruseDefault = /^(?:checked|selected)$/i,
-	getSetAttribute = support.getSetAttribute,
-	getSetInput = support.input;
-
-jQuery.fn.extend({
-	attr: function( name, value ) {
-		return access( this, jQuery.attr, name, value, arguments.length > 1 );
-	},
-
-	removeAttr: function( name ) {
-		return this.each(function() {
-			jQuery.removeAttr( this, name );
-		});
-	}
-});
-
-jQuery.extend({
-	attr: function( elem, name, value ) {
-		var hooks, ret,
-			nType = elem.nodeType;
-
-		// don't get/set attributes on text, comment and attribute nodes
-		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
-			return;
-		}
-
-		// Fallback to prop when attributes are not supported
-		if ( typeof elem.getAttribute === strundefined ) {
-			return jQuery.prop( elem, name, value );
-		}
-
-		// All attributes are lowercase
-		// Grab necessary hook if one is defined
-		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
-			name = name.toLowerCase();
-			hooks = jQuery.attrHooks[ name ] ||
-				( jQuery.expr.match.bool.test( name ) ? boolHook : nodeHook );
-		}
-
-		if ( value !== undefined ) {
-
-			if ( value === null ) {
-				jQuery.removeAttr( elem, name );
-
-			} else if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
-				return ret;
-
-			} else {
-				elem.setAttribute( name, value + "" );
-				return value;
-			}
-
-		} else if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
-			return ret;
-
-		} else {
-			ret = jQuery.find.attr( elem, name );
-
-			// Non-existent attributes return null, we normalize to undefined
-			return ret == null ?
-				undefined :
-				ret;
-		}
-	},
-
-	removeAttr: function( elem, value ) {
-		var name, propName,
-			i = 0,
-			attrNames = value && value.match( rnotwhite );
-
-		if ( attrNames && elem.nodeType === 1 ) {
-			while ( (name = attrNames[i++]) ) {
-				propName = jQuery.propFix[ name ] || name;
-
-				// Boolean attributes get special treatment (#10870)
-				if ( jQuery.expr.match.bool.test( name ) ) {
-					// Set corresponding property to false
-					if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
-						elem[ propName ] = false;
-					// Support: IE<9
-					// Also clear defaultChecked/defaultSelected (if appropriate)
-					} else {
-						elem[ jQuery.camelCase( "default-" + name ) ] =
-							elem[ propName ] = false;
-					}
-
-				// See #9699 for explanation of this approach (setting first, then removal)
-				} else {
-					jQuery.attr( elem, name, "" );
-				}
-
-				elem.removeAttribute( getSetAttribute ? name : propName );
-			}
-		}
-	},
-
-	attrHooks: {
-		type: {
-			set: function( elem, value ) {
-				if ( !support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
-					// Setting the type on a radio button after the value resets the value in IE6-9
-					// Reset value to default in case type is set after value during creation
-					var val = elem.value;
-					elem.setAttribute( "type", value );
-					if ( val ) {
-						elem.value = val;
-					}
-					return value;
-				}
-			}
-		}
-	}
-});
-
-// Hook for boolean attributes
-boolHook = {
-	set: function( elem, value, name ) {
-		if ( value === false ) {
-			// Remove boolean attributes when set to false
-			jQuery.removeAttr( elem, name );
-		} else if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
-			// IE<8 needs the *property* name
-			elem.setAttribute( !getSetAttribute && jQuery.propFix[ name ] || name, name );
-
-		// Use defaultChecked and defaultSelected for oldIE
-		} else {
-			elem[ jQuery.camelCase( "default-" + name ) ] = elem[ name ] = true;
-		}
-
-		return name;
-	}
-};
-
-// Retrieve booleans specially
-jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
-
-	var getter = attrHandle[ name ] || jQuery.find.attr;
-
-	attrHandle[ name ] = getSetInput && getSetAttribute || !ruseDefault.test( name ) ?
-		function( elem, name, isXML ) {
-			var ret, handle;
-			if ( !isXML ) {
-				// Avoid an infinite loop by temporarily removing this function from the getter
-				handle = attrHandle[ name ];
-				attrHandle[ name ] = ret;
-				ret = getter( elem, name, isXML ) != null ?
-					name.toLowerCase() :
-					null;
-				attrHandle[ name ] = handle;
-			}
-			return ret;
-		} :
-		function( elem, name, isXML ) {
-			if ( !isXML ) {
-				return elem[ jQuery.camelCase( "default-" + name ) ] ?
-					name.toLowerCase() :
-					null;
-			}
-		};
-});
-
-// fix oldIE attroperties
-if ( !getSetInput || !getSetAttribute ) {
-	jQuery.attrHooks.value = {
-		set: function( elem, value, name ) {
-			if ( jQuery.nodeName( elem, "input" ) ) {
-				// Does not return so that setAttribute is also used
-				elem.defaultValue = value;
-			} else {
-				// Use nodeHook if defined (#1954); otherwise setAttribute is fine
-				return nodeHook && nodeHook.set( elem, value, name );
-			}
-		}
-	};
-}
-
-// IE6/7 do not support getting/setting some attributes with get/setAttribute
-if ( !getSetAttribute ) {
-
-	// Use this for any attribute in IE6/7
-	// This fixes almost every IE6/7 issue
-	nodeHook = {
-		set: function( elem, value, name ) {
-			// Set the existing or create a new attribute node
-			var ret = elem.getAttributeNode( name );
-			if ( !ret ) {
-				elem.setAttributeNode(
-					(ret = elem.ownerDocument.createAttribute( name ))
-				);
-			}
-
-			ret.value = value += "";
-
-			// Break association with cloned elements by also using setAttribute (#9646)
-			if ( name === "value" || value === elem.getAttribute( name ) ) {
-				return value;
-			}
-		}
-	};
-
-	// Some attributes are constructed with empty-string values when not defined
-	attrHandle.id = attrHandle.name = attrHandle.coords =
-		function( elem, name, isXML ) {
-			var ret;
-			if ( !isXML ) {
-				return (ret = elem.getAttributeNode( name )) && ret.value !== "" ?
-					ret.value :
-					null;
-			}
-		};
-
-	// Fixing value retrieval on a button requires this module
-	jQuery.valHooks.button = {
-		get: function( elem, name ) {
-			var ret = elem.getAttributeNode( name );
-			if ( ret && ret.specified ) {
-				return ret.value;
-			}
-		},
-		set: nodeHook.set
-	};
-
-	// Set contenteditable to false on removals(#10429)
-	// Setting to empty string throws an error as an invalid value
-	jQuery.attrHooks.contenteditable = {
-		set: function( elem, value, name ) {
-			nodeHook.set( elem, value === "" ? false : value, name );
-		}
-	};
-
-	// Set width and height to auto instead of 0 on empty string( Bug #8150 )
-	// This is for removals
-	jQuery.each([ "width", "height" ], function( i, name ) {
-		jQuery.attrHooks[ name ] = {
-			set: function( elem, value ) {
-				if ( value === "" ) {
-					elem.setAttribute( name, "auto" );
-					return value;
-				}
-			}
-		};
-	});
-}
-
-if ( !support.style ) {
-	jQuery.attrHooks.style = {
-		get: function( elem ) {
-			// Return undefined in the case of empty string
-			// Note: IE uppercases css property names, but if we were to .toLowerCase()
-			// .cssText, that would destroy case senstitivity in URL's, like in "background"
-			return elem.style.cssText || undefined;
-		},
-		set: function( elem, value ) {
-			return ( elem.style.cssText = value + "" );
-		}
-	};
-}
-
-
-
-
-var rfocusable = /^(?:input|select|textarea|button|object)$/i,
-	rclickable = /^(?:a|area)$/i;
-
-jQuery.fn.extend({
-	prop: function( name, value ) {
-		return access( this, jQuery.prop, name, value, arguments.length > 1 );
-	},
-
-	removeProp: function( name ) {
-		name = jQuery.propFix[ name ] || name;
-		return this.each(function() {
-			// try/catch handles cases where IE balks (such as removing a property on window)
-			try {
-				this[ name ] = undefined;
-				delete this[ name ];
-			} catch( e ) {}
-		});
-	}
-});
-
-jQuery.extend({
-	propFix: {
-		"for": "htmlFor",
-		"class": "className"
-	},
-
-	prop: function( elem, name, value ) {
-		var ret, hooks, notxml,
-			nType = elem.nodeType;
-
-		// don't get/set properties on text, comment and attribute nodes
-		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
-			return;
-		}
-
-		notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
-
-		if ( notxml ) {
-			// Fix name and attach hooks
-			name = jQuery.propFix[ name ] || name;
-			hooks = jQuery.propHooks[ name ];
-		}
-
-		if ( value !== undefined ) {
-			return hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ?
-				ret :
-				( elem[ name ] = value );
-
-		} else {
-			return hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ?
-				ret :
-				elem[ name ];
-		}
-	},
-
-	propHooks: {
-		tabIndex: {
-			get: function( elem ) {
-				// elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
-				// http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
-				// Use proper attribute retrieval(#12072)
-				var tabindex = jQuery.find.attr( elem, "tabindex" );
-
-				return tabindex ?
-					parseInt( tabindex, 10 ) :
-					rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
-						0 :
-						-1;
-			}
-		}
-	}
-});
-
-// Some attributes require a special call on IE
-// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !support.hrefNormalized ) {
-	// href/src property should get the full normalized URL (#10299/#12915)
-	jQuery.each([ "href", "src" ], function( i, name ) {
-		jQuery.propHooks[ name ] = {
-			get: function( elem ) {
-				return elem.getAttribute( name, 4 );
-			}
-		};
-	});
-}
-
-// Support: Safari, IE9+
-// mis-reports the default selected property of an option
-// Accessing the parent's selectedIndex property fixes it
-if ( !support.optSelected ) {
-	jQuery.propHooks.selected = {
-		get: function( elem ) {
-			var parent = elem.parentNode;
-
-			if ( parent ) {
-				parent.selectedIndex;
-
-				// Make sure that it also works with optgroups, see #5701
-				if ( parent.parentNode ) {
-					parent.parentNode.selectedIndex;
-				}
-			}
-			return null;
-		}
-	};
-}
-
-jQuery.each([
-	"tabIndex",
-	"readOnly",
-	"maxLength",
-	"cellSpacing",
-	"cellPadding",
-	"rowSpan",
-	"colSpan",
-	"useMap",
-	"frameBorder",
-	"contentEditable"
-], function() {
-	jQuery.propFix[ this.toLowerCase() ] = this;
-});
-
-// IE6/7 call enctype encoding
-if ( !support.enctype ) {
-	jQuery.propFix.enctype = "encoding";
-}
-
-
-
-
-var rclass = /[\t\r\n\f]/g;
-
-jQuery.fn.extend({
-	addClass: function( value ) {
-		var classes, elem, cur, clazz, j, finalValue,
-			i = 0,
-			len = this.length,
-			proceed = typeof value === "string" && value;
-
-		if ( jQuery.isFunction( value ) ) {
-			return this.each(function( j ) {
-				jQuery( this ).addClass( value.call( this, j, this.className ) );
-			});
-		}
-
-		if ( proceed ) {
-			// The disjunction here is for better compressibility (see removeClass)
-			classes = ( value || "" ).match( rnotwhite ) || [];
-
-			for ( ; i < len; i++ ) {
-				elem = this[ i ];
-				cur = elem.nodeType === 1 && ( elem.className ?
-					( " " + elem.className + " " ).replace( rclass, " " ) :
-					" "
-				);
-
-				if ( cur ) {
-					j = 0;
-					while ( (clazz = classes[j++]) ) {
-						if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
-							cur += clazz + " ";
-						}
-					}
-
-					// only assign if different to avoid unneeded rendering.
-					finalValue = jQuery.trim( cur );
-					if ( elem.className !== finalValue ) {
-						elem.className = finalValue;
-					}
-				}
-			}
-		}
-
-		return this;
-	},
-
-	removeClass: function( value ) {
-		var classes, elem, cur, clazz, j, finalValue,
-			i = 0,
-			len = this.length,
-			proceed = arguments.length === 0 || typeof value === "string" && value;
-
-		if ( jQuery.isFunction( value ) ) {
-			return this.each(function( j ) {
-				jQuery( this ).removeClass( value.call( this, j, this.className ) );
-			});
-		}
-		if ( proceed ) {
-			classes = ( value || "" ).match( rnotwhite ) || [];
-
-			for ( ; i < len; i++ ) {
-				elem = this[ i ];
-				// This expression is here for better compressibility (see addClass)
-				cur = elem.nodeType === 1 && ( elem.className ?
-					( " " + elem.className + " " ).replace( rclass, " " ) :
-					""
-				);
-
-				if ( cur ) {
-					j = 0;
-					while ( (clazz = classes[j++]) ) {
-						// Remove *all* instances
-						while ( cur.indexOf( " " + clazz + " " ) >= 0 ) {
-							cur = cur.replace( " " + clazz + " ", " " );
-						}
-					}
-
-					// only assign if different to avoid unneeded rendering.
-					finalValue = value ? jQuery.trim( cur ) : "";
-					if ( elem.className !== finalValue ) {
-						elem.className = finalValue;
-					}
-				}
-			}
-		}
-
-		return this;
-	},
-
-	toggleClass: function( value, stateVal ) {
-		var type = typeof value;
-
-		if ( typeof stateVal === "boolean" && type === "string" ) {
-			return stateVal ? this.addClass( value ) : this.removeClass( value );
-		}
-
-		if ( jQuery.isFunction( value ) ) {
-			return this.each(function( i ) {
-				jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
-			});
-		}
-
-		return this.each(function() {
-			if ( type === "string" ) {
-				// toggle individual class names
-				var className,
-					i = 0,
-					self = jQuery( this ),
-					classNames = value.match( rnotwhite ) || [];
-
-				while ( (className = classNames[ i++ ]) ) {
-					// check each className given, space separated list
-					if ( self.hasClass( className ) ) {
-						self.removeClass( className );
-					} else {
-						self.addClass( className );
-					}
-				}
-
-			// Toggle whole class name
-			} else if ( type === strundefined || type === "boolean" ) {
-				if ( this.className ) {
-					// store className if set
-					jQuery._data( this, "__className__", this.className );
-				}
-
-				// If the element has a class name or if we're passed "false",
-				// then remove the whole classname (if there was one, the above saved it).
-				// Otherwise bring back whatever was previously saved (if anything),
-				// falling back to the empty string if nothing was stored.
-				this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
-			}
-		});
-	},
-
-	hasClass: function( selector ) {
-		var className = " " + selector + " ",
-			i = 0,
-			l = this.length;
-		for ( ; i < l; i++ ) {
-			if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) {
-				return true;
-			}
-		}
-
-		return false;
-	}
-});
-
-
-
-
-// Return jQuery for attributes-only inclusion
-
-
-jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
-	"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
-	"change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
-
-	// Handle event binding
-	jQuery.fn[ name ] = function( data, fn ) {
-		return arguments.length > 0 ?
-			this.on( name, null, data, fn ) :
-			this.trigger( name );
-	};
-});
-
-jQuery.fn.extend({
-	hover: function( fnOver, fnOut ) {
-		return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
-	},
-
-	bind: function( types, data, fn ) {
-		return this.on( types, null, data, fn );
-	},
-	unbind: function( types, fn ) {
-		return this.off( types, null, fn );
-	},
-
-	delegate: function( selector, types, data, fn ) {
-		return this.on( types, selector, data, fn );
-	},
-	undelegate: function( selector, types, fn ) {
-		// ( namespace ) or ( selector, types [, fn] )
-		return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn );
-	}
-});
-
-
-var nonce = jQuery.now();
-
-var rquery = (/\?/);
-
-
-
-var rvalidtokens = /(,)|(\[|{)|(}|])|"(?:[^"\\\r\n]|\\["\\\/bfnrt]|\\u[\da-fA-F]{4})*"\s*:?|true|false|null|-?(?!0\d)\d+(?:\.\d+|)(?:[eE][+-]?\d+|)/g;
-
-jQuery.parseJSON = function( data ) {
-	// Attempt to parse using the native JSON parser first
-	if ( window.JSON && window.JSON.parse ) {
-		// Support: Android 2.3
-		// Workaround failure to string-cast null input
-		return window.JSON.parse( data + "" );
-	}
-
-	var requireNonComma,
-		depth = null,
-		str = jQuery.trim( data + "" );
-
-	// Guard against invalid (and possibly dangerous) input by ensuring that nothing remains
-	// after removing valid tokens
-	return str && !jQuery.trim( str.replace( rvalidtokens, function( token, comma, open, close ) {
-
-		// Force termination if we see a misplaced comma
-		if ( requireNonComma && comma ) {
-			depth = 0;
-		}
-
-		// Perform no more replacements after returning to outermost depth
-		if ( depth === 0 ) {
-			return token;
-		}
-
-		// Commas must not follow "[", "{", or ","
-		requireNonComma = open || comma;
-
-		// Determine new depth
-		// array/object open ("[" or "{"): depth += true - false (increment)
-		// array/object close ("]" or "}"): depth += false - true (decrement)
-		// other cases ("," or primitive): depth += true - true (numeric cast)
-		depth += !close - !open;
-
-		// Remove this token
-		return "";
-	}) ) ?
-		( Function( "return " + str ) )() :
-		jQuery.error( "Invalid JSON: " + data );
-};
-
-
-// Cross-browser xml parsing
-jQuery.parseXML = function( data ) {
-	var xml, tmp;
-	if ( !data || typeof data !== "string" ) {
-		return null;
-	}
-	try {
-		if ( window.DOMParser ) { // Standard
-			tmp = new DOMParser();
-			xml = tmp.parseFromString( data, "text/xml" );
-		} else { // IE
-			xml = new ActiveXObject( "Microsoft.XMLDOM" );
-			xml.async = "false";
-			xml.loadXML( data );
-		}
-	} catch( e ) {
-		xml = undefined;
-	}
-	if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
-		jQuery.error( "Invalid XML: " + data );
-	}
-	return xml;
-};
-
-
-var
-	// Document location
-	ajaxLocParts,
-	ajaxLocation,
-
-	rhash = /#.*$/,
-	rts = /([?&])_=[^&]*/,
-	rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
-	// #7653, #8125, #8152: local protocol detection
-	rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
-	rnoContent = /^(?:GET|HEAD)$/,
-	rprotocol = /^\/\//,
-	rurl = /^([\w.+-]+:)(?:\/\/(?:[^\/?#]*@|)([^\/?#:]*)(?::(\d+)|)|)/,
-
-	/* Prefilters
-	 * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
-	 * 2) These are called:
-	 *    - BEFORE asking for a transport
-	 *    - AFTER param serialization (s.data is a string if s.processData is true)
-	 * 3) key is the dataType
-	 * 4) the catchall symbol "*" can be used
-	 * 5) execution will start with transport dataType and THEN continue down to "*" if needed
-	 */
-	prefilters = {},
-
-	/* Transports bindings
-	 * 1) key is the dataType
-	 * 2) the catchall symbol "*" can be used
-	 * 3) selection will start with transport dataType and THEN go to "*" if needed
-	 */
-	transports = {},
-
-	// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
-	allTypes = "*/".concat("*");
-
-// #8138, IE may throw an exception when accessing
-// a field from window.location if document.domain has been set
-try {
-	ajaxLocation = location.href;
-} catch( e ) {
-	// Use the href attribute of an A element
-	// since IE will modify it given document.location
-	ajaxLocation = document.createElement( "a" );
-	ajaxLocation.href = "";
-	ajaxLocation = ajaxLocation.href;
-}
-
-// Segment location into parts
-ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
-
-// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
-function addToPrefiltersOrTransports( structure ) {
-
-	// dataTypeExpression is optional and defaults to "*"
-	return function( dataTypeExpression, func ) {
-
-		if ( typeof dataTypeExpression !== "string" ) {
-			func = dataTypeExpression;
-			dataTypeExpression = "*";
-		}
-
-		var dataType,
-			i = 0,
-			dataTypes = dataTypeExpression.toLowerCase().match( rnotwhite ) || [];
-
-		if ( jQuery.isFunction( func ) ) {
-			// For each dataType in the dataTypeExpression
-			while ( (dataType = dataTypes[i++]) ) {
-				// Prepend if requested
-				if ( dataType.charAt( 0 ) === "+" ) {
-					dataType = dataType.slice( 1 ) || "*";
-					(structure[ dataType ] = structure[ dataType ] || []).unshift( func );
-
-				// Otherwise append
-				} else {
-					(structure[ dataType ] = structure[ dataType ] || []).push( func );
-				}
-			}
-		}
-	};
-}
-
-// Base inspection function for prefilters and transports
-function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
-
-	var inspected = {},
-		seekingTransport = ( structure === transports );
-
-	function inspect( dataType ) {
-		var selected;
-		inspected[ dataType ] = true;
-		jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
-			var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
-			if ( typeof dataTypeOrTransport === "string" && !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
-				options.dataTypes.unshift( dataTypeOrTransport );
-				inspect( dataTypeOrTransport );
-				return false;
-			} else if ( seekingTransport ) {
-				return !( selected = dataTypeOrTransport );
-			}
-		});
-		return selected;
-	}
-
-	return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
-}
-
-// A special extend for ajax options
-// that takes "flat" options (not to be deep extended)
-// Fixes #9887
-function ajaxExtend( target, src ) {
-	var deep, key,
-		flatOptions = jQuery.ajaxSettings.flatOptions || {};
-
-	for ( key in src ) {
-		if ( src[ key ] !== undefined ) {
-			( flatOptions[ key ] ? target : ( deep || (deep = {}) ) )[ key ] = src[ key ];
-		}
-	}
-	if ( deep ) {
-		jQuery.extend( true, target, deep );
-	}
-
-	return target;
-}
-
-/* Handles responses to an ajax request:
- * - finds the right dataType (mediates between content-type and expected dataType)
- * - returns the corresponding response
- */
-function ajaxHandleResponses( s, jqXHR, responses ) {
-	var firstDataType, ct, finalDataType, type,
-		contents = s.contents,
-		dataTypes = s.dataTypes;
-
-	// Remove auto dataType and get content-type in the process
-	while ( dataTypes[ 0 ] === "*" ) {
-		dataTypes.shift();
-		if ( ct === undefined ) {
-			ct = s.mimeType || jqXHR.getResponseHeader("Content-Type");
-		}
-	}
-
-	// Check if we're dealing with a known content-type
-	if ( ct ) {
-		for ( type in contents ) {
-			if ( contents[ type ] && contents[ type ].test( ct ) ) {
-				dataTypes.unshift( type );
-				break;
-			}
-		}
-	}
-
-	// Check to see if we have a response for the expected dataType
-	if ( dataTypes[ 0 ] in responses ) {
-		finalDataType = dataTypes[ 0 ];
-	} else {
-		// Try convertible dataTypes
-		for ( type in responses ) {
-			if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
-				finalDataType = type;
-				break;
-			}
-			if ( !firstDataType ) {
-				firstDataType = type;
-			}
-		}
-		// Or just use first one
-		finalDataType = finalDataType || firstDataType;
-	}
-
-	// If we found a dataType
-	// We add the dataType to the list if needed
-	// and return the corresponding response
-	if ( finalDataType ) {
-		if ( finalDataType !== dataTypes[ 0 ] ) {
-			dataTypes.unshift( finalDataType );
-		}
-		return responses[ finalDataType ];
-	}
-}
-
-/* Chain conversions given the request and the original response
- * Also sets the responseXXX fields on the jqXHR instance
- */
-function ajaxConvert( s, response, jqXHR, isSuccess ) {
-	var conv2, current, conv, tmp, prev,
-		converters = {},
-		// Work with a copy of dataTypes in case we need to modify it for conversion
-		dataTypes = s.dataTypes.slice();
-
-	// Create converters map with lowercased keys
-	if ( dataTypes[ 1 ] ) {
-		for ( conv in s.converters ) {
-			converters[ conv.toLowerCase() ] = s.converters[ conv ];
-		}
-	}
-
-	current = dataTypes.shift();
-
-	// Convert to each sequential dataType
-	while ( current ) {
-
-		if ( s.responseFields[ current ] ) {
-			jqXHR[ s.responseFields[ current ] ] = response;
-		}
-
-		// Apply the dataFilter if provided
-		if ( !prev && isSuccess && s.dataFilter ) {
-			response = s.dataFilter( response, s.dataType );
-		}
-
-		prev = current;
-		current = dataTypes.shift();
-
-		if ( current ) {
-
-			// There's only work to do if current dataType is non-auto
-			if ( current === "*" ) {
-
-				current = prev;
-
-			// Convert response if prev dataType is non-auto and differs from current
-			} else if ( prev !== "*" && prev !== current ) {
-
-				// Seek a direct converter
-				conv = converters[ prev + " " + current ] || converters[ "* " + current ];
-
-				// If none found, seek a pair
-				if ( !conv ) {
-					for ( conv2 in converters ) {
-
-						// If conv2 outputs current
-						tmp = conv2.split( " " );
-						if ( tmp[ 1 ] === current ) {
-
-							// If prev can be converted to accepted input
-							conv = converters[ prev + " " + tmp[ 0 ] ] ||
-								converters[ "* " + tmp[ 0 ] ];
-							if ( conv ) {
-								// Condense equivalence converters
-								if ( conv === true ) {
-									conv = converters[ conv2 ];
-
-								// Otherwise, insert the intermediate dataType
-								} else if ( converters[ conv2 ] !== true ) {
-									current = tmp[ 0 ];
-									dataTypes.unshift( tmp[ 1 ] );
-								}
-								break;
-							}
-						}
-					}
-				}
-
-				// Apply converter (if not an equivalence)
-				if ( conv !== true ) {
-
-					// Unless errors are allowed to bubble, catch and return them
-					if ( conv && s[ "throws" ] ) {
-						response = conv( response );
-					} else {
-						try {
-							response = conv( response );
-						} catch ( e ) {
-							return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current };
-						}
-					}
-				}
-			}
-		}
-	}
-
-	return { state: "success", data: response };
-}
-
-jQuery.extend({
-
-	// Counter for holding the number of active queries
-	active: 0,
-
-	// Last-Modified header cache for next request
-	lastModified: {},
-	etag: {},
-
-	ajaxSettings: {
-		url: ajaxLocation,
-		type: "GET",
-		isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
-		global: true,
-		processData: true,
-		async: true,
-		contentType: "application/x-www-form-urlencoded; charset=UTF-8",
-		/*
-		timeout: 0,
-		data: null,
-		dataType: null,
-		username: null,
-		password: null,
-		cache: null,
-		throws: false,
-		traditional: false,
-		headers: {},
-		*/
-
-		accepts: {
-			"*": allTypes,
-			text: "text/plain",
-			html: "text/html",
-			xml: "application/xml, text/xml",
-			json: "application/json, text/javascript"
-		},
-
-		contents: {
-			xml: /xml/,
-			html: /html/,
-			json: /json/
-		},
-
-		responseFields: {
-			xml: "responseXML",
-			text: "responseText",
-			json: "responseJSON"
-		},
-
-		// Data converters
-		// Keys separate source (or catchall "*") and destination types with a single space
-		converters: {
-
-			// Convert anything to text
-			"* text": String,
-
-			// Text to html (true = no transformation)
-			"text html": true,
-
-			// Evaluate text as a json expression
-			"text json": jQuery.parseJSON,
-
-			// Parse text as xml
-			"text xml": jQuery.parseXML
-		},
-
-		// For options that shouldn't be deep extended:
-		// you can add your own custom options here if
-		// and when you create one that shouldn't be
-		// deep extended (see ajaxExtend)
-		flatOptions: {
-			url: true,
-			context: true
-		}
-	},
-
-	// Creates a full fledged settings object into target
-	// with both ajaxSettings and settings fields.
-	// If target is omitted, writes into ajaxSettings.
-	ajaxSetup: function( target, settings ) {
-		return settings ?
-
-			// Building a settings object
-			ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
-
-			// Extending ajaxSettings
-			ajaxExtend( jQuery.ajaxSettings, target );
-	},
-
-	ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
-	ajaxTransport: addToPrefiltersOrTransports( transports ),
-
-	// Main method
-	ajax: function( url, options ) {
-
-		// If url is an object, simulate pre-1.5 signature
-		if ( typeof url === "object" ) {
-			options = url;
-			url = undefined;
-		}
-
-		// Force options to be an object
-		options = options || {};
-
-		var // Cross-domain detection vars
-			parts,
-			// Loop variable
-			i,
-			// URL without anti-cache param
-			cacheURL,
-			// Response headers as string
-			responseHeadersString,
-			// timeout handle
-			timeoutTimer,
-
-			// To know if global events are to be dispatched
-			fireGlobals,
-
-			transport,
-			// Response headers
-			responseHeaders,
-			// Create the final options object
-			s = jQuery.ajaxSetup( {}, options ),
-			// Callbacks context
-			callbackContext = s.context || s,
-			// Context for global events is callbackContext if it is a DOM node or jQuery collection
-			globalEventContext = s.context && ( callbackContext.nodeType || callbackContext.jquery ) ?
-				jQuery( callbackContext ) :
-				jQuery.event,
-			// Deferreds
-			deferred = jQuery.Deferred(),
-			completeDeferred = jQuery.Callbacks("once memory"),
-			// Status-dependent callbacks
-			statusCode = s.statusCode || {},
-			// Headers (they are sent all at once)
-			requestHeaders = {},
-			requestHeadersNames = {},
-			// The jqXHR state
-			state = 0,
-			// Default abort message
-			strAbort = "canceled",
-			// Fake xhr
-			jqXHR = {
-				readyState: 0,
-
-				// Builds headers hashtable if needed
-				getResponseHeader: function( key ) {
-					var match;
-					if ( state === 2 ) {
-						if ( !responseHeaders ) {
-							responseHeaders = {};
-							while ( (match = rheaders.exec( responseHeadersString )) ) {
-								responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
-							}
-						}
-						match = responseHeaders[ key.toLowerCase() ];
-					}
-					return match == null ? null : match;
-				},
-
-				// Raw string
-				getAllResponseHeaders: function() {
-					return state === 2 ? responseHeadersString : null;
-				},
-
-				// Caches the header
-				setRequestHeader: function( name, value ) {
-					var lname = name.toLowerCase();
-					if ( !state ) {
-						name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
-						requestHeaders[ name ] = value;
-					}
-					return this;
-				},
-
-				// Overrides response content-type header
-				overrideMimeType: function( type ) {
-					if ( !state ) {
-						s.mimeType = type;
-					}
-					return this;
-				},
-
-				// Status-dependent callbacks
-				statusCode: function( map ) {
-					var code;
-					if ( map ) {
-						if ( state < 2 ) {
-							for ( code in map ) {
-								// Lazy-add the new callback in a way that preserves old ones
-								statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
-							}
-						} else {
-							// Execute the appropriate callbacks
-							jqXHR.always( map[ jqXHR.status ] );
-						}
-					}
-					return this;
-				},
-
-				// Cancel the request
-				abort: function( statusText ) {
-					var finalText = statusText || strAbort;
-					if ( transport ) {
-						transport.abort( finalText );
-					}
-					done( 0, finalText );
-					return this;
-				}
-			};
-
-		// Attach deferreds
-		deferred.promise( jqXHR ).complete = completeDeferred.add;
-		jqXHR.success = jqXHR.done;
-		jqXHR.error = jqXHR.fail;
-
-		// Remove hash character (#7531: and string promotion)
-		// Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
-		// Handle falsy url in the settings object (#10093: consistency with old signature)
-		// We also use the url parameter if available
-		s.url = ( ( url || s.url || ajaxLocation ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
-
-		// Alias method option to type as per ticket #12004
-		s.type = options.method || options.type || s.method || s.type;
-
-		// Extract dataTypes list
-		s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().match( rnotwhite ) || [ "" ];
-
-		// A cross-domain request is in order when we have a protocol:host:port mismatch
-		if ( s.crossDomain == null ) {
-			parts = rurl.exec( s.url.toLowerCase() );
-			s.crossDomain = !!( parts &&
-				( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] ||
-					( parts[ 3 ] || ( parts[ 1 ] === "http:" ? "80" : "443" ) ) !==
-						( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? "80" : "443" ) ) )
-			);
-		}
-
-		// Convert data if not already a string
-		if ( s.data && s.processData && typeof s.data !== "string" ) {
-			s.data = jQuery.param( s.data, s.traditional );
-		}
-
-		// Apply prefilters
-		inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
-
-		// If request was aborted inside a prefilter, stop there
-		if ( state === 2 ) {
-			return jqXHR;
-		}
-
-		// We can fire global events as of now if asked to
-		fireGlobals = s.global;
-
-		// Watch for a new set of requests
-		if ( fireGlobals && jQuery.active++ === 0 ) {
-			jQuery.event.trigger("ajaxStart");
-		}
-
-		// Uppercase the type
-		s.type = s.type.toUpperCase();
-
-		// Determine if request has content
-		s.hasContent = !rnoContent.test( s.type );
-
-		// Save the URL in case we're toying with the If-Modified-Since
-		// and/or If-None-Match header later on
-		cacheURL = s.url;
-
-		// More options handling for requests with no content
-		if ( !s.hasContent ) {
-
-			// If data is available, append data to url
-			if ( s.data ) {
-				cacheURL = ( s.url += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data );
-				// #9682: remove data so that it's not used in an eventual retry
-				delete s.data;
-			}
-
-			// Add anti-cache in url if needed
-			if ( s.cache === false ) {
-				s.url = rts.test( cacheURL ) ?
-
-					// If there is already a '_' parameter, set its value
-					cacheURL.replace( rts, "$1_=" + nonce++ ) :
-
-					// Otherwise add one to the end
-					cacheURL + ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + nonce++;
-			}
-		}
-
-		// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
-		if ( s.ifModified ) {
-			if ( jQuery.lastModified[ cacheURL ] ) {
-				jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
-			}
-			if ( jQuery.etag[ cacheURL ] ) {
-				jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
-			}
-		}
-
-		// Set the correct header, if data is being sent
-		if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
-			jqXHR.setRequestHeader( "Content-Type", s.contentType );
-		}
-
-		// Set the Accepts header for the server, depending on the dataType
-		jqXHR.setRequestHeader(
-			"Accept",
-			s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
-				s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
-				s.accepts[ "*" ]
-		);
-
-		// Check for headers option
-		for ( i in s.headers ) {
-			jqXHR.setRequestHeader( i, s.headers[ i ] );
-		}
-
-		// Allow custom headers/mimetypes and early abort
-		if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
-			// Abort if not done already and return
-			return jqXHR.abort();
-		}
-
-		// aborting is no longer a cancellation
-		strAbort = "abort";
-
-		// Install callbacks on deferreds
-		for ( i in { success: 1, error: 1, complete: 1 } ) {
-			jqXHR[ i ]( s[ i ] );
-		}
-
-		// Get transport
-		transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
-
-		// If no transport, we auto-abort
-		if ( !transport ) {
-			done( -1, "No Transport" );
-		} else {
-			jqXHR.readyState = 1;
-
-			// Send global event
-			if ( fireGlobals ) {
-				globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
-			}
-			// Timeout
-			if ( s.async && s.timeout > 0 ) {
-				timeoutTimer = setTimeout(function() {
-					jqXHR.abort("timeout");
-				}, s.timeout );
-			}
-
-			try {
-				state = 1;
-				transport.send( requestHeaders, done );
-			} catch ( e ) {
-				// Propagate exception as error if not done
-				if ( state < 2 ) {
-					done( -1, e );
-				// Simply rethrow otherwise
-				} else {
-					throw e;
-				}
-			}
-		}
-
-		// Callback for when everything is done
-		function done( status, nativeStatusText, responses, headers ) {
-			var isSuccess, success, error, response, modified,
-				statusText = nativeStatusText;
-
-			// Called once
-			if ( state === 2 ) {
-				return;
-			}
-
-			// State is "done" now
-			state = 2;
-
-			// Clear timeout if it exists
-			if ( timeoutTimer ) {
-				clearTimeout( timeoutTimer );
-			}
-
-			// Dereference transport for early garbage collection
-			// (no matter how long the jqXHR object will be used)
-			transport = undefined;
-
-			// Cache response headers
-			responseHeadersString = headers || "";
-
-			// Set readyState
-			jqXHR.readyState = status > 0 ? 4 : 0;
-
-			// Determine if successful
-			isSuccess = status >= 200 && status < 300 || status === 304;
-
-			// Get response data
-			if ( responses ) {
-				response = ajaxHandleResponses( s, jqXHR, responses );
-			}
-
-			// Convert no matter what (that way responseXXX fields are always set)
-			response = ajaxConvert( s, response, jqXHR, isSuccess );
-
-			// If successful, handle type chaining
-			if ( isSuccess ) {
-
-				// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
-				if ( s.ifModified ) {
-					modified = jqXHR.getResponseHeader("Last-Modified");
-					if ( modified ) {
-						jQuery.lastModified[ cacheURL ] = modified;
-					}
-					modified = jqXHR.getResponseHeader("etag");
-					if ( modified ) {
-						jQuery.etag[ cacheURL ] = modified;
-					}
-				}
-
-				// if no content
-				if ( status === 204 || s.type === "HEAD" ) {
-					statusText = "nocontent";
-
-				// if not modified
-				} else if ( status === 304 ) {
-					statusText = "notmodified";
-
-				// If we have data, let's convert it
-				} else {
-					statusText = response.state;
-					success = response.data;
-					error = response.error;
-					isSuccess = !error;
-				}
-			} else {
-				// We extract error from statusText
-				// then normalize statusText and status for non-aborts
-				error = statusText;
-				if ( status || !statusText ) {
-					statusText = "error";
-					if ( status < 0 ) {
-						status = 0;
-					}
-				}
-			}
-
-			// Set data for the fake xhr object
-			jqXHR.status = status;
-			jqXHR.statusText = ( nativeStatusText || statusText ) + "";
-
-			// Success/Error
-			if ( isSuccess ) {
-				deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
-			} else {
-				deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
-			}
-
-			// Status-dependent callbacks
-			jqXHR.statusCode( statusCode );
-			statusCode = undefined;
-
-			if ( fireGlobals ) {
-				globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
-					[ jqXHR, s, isSuccess ? success : error ] );
-			}
-
-			// Complete
-			completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
-
-			if ( fireGlobals ) {
-				globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
-				// Handle the global AJAX counter
-				if ( !( --jQuery.active ) ) {
-					jQuery.event.trigger("ajaxStop");
-				}
-			}
-		}
-
-		return jqXHR;
-	},
-
-	getJSON: function( url, data, callback ) {
-		return jQuery.get( url, data, callback, "json" );
-	},
-
-	getScript: function( url, callback ) {
-		return jQuery.get( url, undefined, callback, "script" );
-	}
-});
-
-jQuery.each( [ "get", "post" ], function( i, method ) {
-	jQuery[ method ] = function( url, data, callback, type ) {
-		// shift arguments if data argument was omitted
-		if ( jQuery.isFunction( data ) ) {
-			type = type || callback;
-			callback = data;
-			data = undefined;
-		}
-
-		return jQuery.ajax({
-			url: url,
-			type: method,
-			dataType: type,
-			data: data,
-			success: callback
-		});
-	};
-});
-
-// Attach a bunch of functions for handling common AJAX events
-jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) {
-	jQuery.fn[ type ] = function( fn ) {
-		return this.on( type, fn );
-	};
-});
-
-
-jQuery._evalUrl = function( url ) {
-	return jQuery.ajax({
-		url: url,
-		type: "GET",
-		dataType: "script",
-		async: false,
-		global: false,
-		"throws": true
-	});
-};
-
-
-jQuery.fn.extend({
-	wrapAll: function( html ) {
-		if ( jQuery.isFunction( html ) ) {
-			return this.each(function(i) {
-				jQuery(this).wrapAll( html.call(this, i) );
-			});
-		}
-
-		if ( this[0] ) {
-			// The elements to wrap the target around
-			var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
-
-			if ( this[0].parentNode ) {
-				wrap.insertBefore( this[0] );
-			}
-
-			wrap.map(function() {
-				var elem = this;
-
-				while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
-					elem = elem.firstChild;
-				}
-
-				return elem;
-			}).append( this );
-		}
-
-		return this;
-	},
-
-	wrapInner: function( html ) {
-		if ( jQuery.isFunction( html ) ) {
-			return this.each(function(i) {
-				jQuery(this).wrapInner( html.call(this, i) );
-			});
-		}
-
-		return this.each(function() {
-			var self = jQuery( this ),
-				contents = self.contents();
-
-			if ( contents.length ) {
-				contents.wrapAll( html );
-
-			} else {
-				self.append( html );
-			}
-		});
-	},
-
-	wrap: function( html ) {
-		var isFunction = jQuery.isFunction( html );
-
-		return this.each(function(i) {
-			jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
-		});
-	},
-
-	unwrap: function() {
-		return this.parent().each(function() {
-			if ( !jQuery.nodeName( this, "body" ) ) {
-				jQuery( this ).replaceWith( this.childNodes );
-			}
-		}).end();
-	}
-});
-
-
-jQuery.expr.filters.hidden = function( elem ) {
-	// Support: Opera <= 12.12
-	// Opera reports offsetWidths and offsetHeights less than zero on some elements
-	return elem.offsetWidth <= 0 && elem.offsetHeight <= 0 ||
-		(!support.reliableHiddenOffsets() &&
-			((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none");
-};
-
-jQuery.expr.filters.visible = function( elem ) {
-	return !jQuery.expr.filters.hidden( elem );
-};
-
-
-
-
-var r20 = /%20/g,
-	rbracket = /\[\]$/,
-	rCRLF = /\r?\n/g,
-	rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
-	rsubmittable = /^(?:input|select|textarea|keygen)/i;
-
-function buildParams( prefix, obj, traditional, add ) {
-	var name;
-
-	if ( jQuery.isArray( obj ) ) {
-		// Serialize array item.
-		jQuery.each( obj, function( i, v ) {
-			if ( traditional || rbracket.test( prefix ) ) {
-				// Treat each array item as a scalar.
-				add( prefix, v );
-
-			} else {
-				// Item is non-scalar (array or object), encode its numeric index.
-				buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
-			}
-		});
-
-	} else if ( !traditional && jQuery.type( obj ) === "object" ) {
-		// Serialize object item.
-		for ( name in obj ) {
-			buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
-		}
-
-	} else {
-		// Serialize scalar item.
-		add( prefix, obj );
-	}
-}
-
-// Serialize an array of form elements or a set of
-// key/values into a query string
-jQuery.param = function( a, traditional ) {
-	var prefix,
-		s = [],
-		add = function( key, value ) {
-			// If value is a function, invoke it and return its value
-			value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value );
-			s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
-		};
-
-	// Set traditional to true for jQuery <= 1.3.2 behavior.
-	if ( traditional === undefined ) {
-		traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional;
-	}
-
-	// If an array was passed in, assume that it is an array of form elements.
-	if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
-		// Serialize the form elements
-		jQuery.each( a, function() {
-			add( this.name, this.value );
-		});
-
-	} else {
-		// If traditional, encode the "old" way (the way 1.3.2 or older
-		// did it), otherwise encode params recursively.
-		for ( prefix in a ) {
-			buildParams( prefix, a[ prefix ], traditional, add );
-		}
-	}
-
-	// Return the resulting serialization
-	return s.join( "&" ).replace( r20, "+" );
-};
-
-jQuery.fn.extend({
-	serialize: function() {
-		return jQuery.param( this.serializeArray() );
-	},
-	serializeArray: function() {
-		return this.map(function() {
-			// Can add propHook for "elements" to filter or add form elements
-			var elements = jQuery.prop( this, "elements" );
-			return elements ? jQuery.makeArray( elements ) : this;
-		})
-		.filter(function() {
-			var type = this.type;
-			// Use .is(":disabled") so that fieldset[disabled] works
-			return this.name && !jQuery( this ).is( ":disabled" ) &&
-				rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
-				( this.checked || !rcheckableType.test( type ) );
-		})
-		.map(function( i, elem ) {
-			var val = jQuery( this ).val();
-
-			return val == null ?
-				null :
-				jQuery.isArray( val ) ?
-					jQuery.map( val, function( val ) {
-						return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
-					}) :
-					{ name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
-		}).get();
-	}
-});
-
-
-// Create the request object
-// (This is still attached to ajaxSettings for backward compatibility)
-jQuery.ajaxSettings.xhr = window.ActiveXObject !== undefined ?
-	// Support: IE6+
-	function() {
-
-		// XHR cannot access local files, always use ActiveX for that case
-		return !this.isLocal &&
-
-			// Support: IE7-8
-			// oldIE XHR does not support non-RFC2616 methods (#13240)
-			// See http://msdn.microsoft.com/en-us/library/ie/ms536648(v=vs.85).aspx
-			// and http://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html#sec9
-			// Although this check for six methods instead of eight
-			// since IE also does not support "trace" and "connect"
-			/^(get|post|head|put|delete|options)$/i.test( this.type ) &&
-
-			createStandardXHR() || createActiveXHR();
-	} :
-	// For all other browsers, use the standard XMLHttpRequest object
-	createStandardXHR;
-
-var xhrId = 0,
-	xhrCallbacks = {},
-	xhrSupported = jQuery.ajaxSettings.xhr();
-
-// Support: IE<10
-// Open requests must be manually aborted on unload (#5280)
-if ( window.ActiveXObject ) {
-	jQuery( window ).on( "unload", function() {
-		for ( var key in xhrCallbacks ) {
-			xhrCallbacks[ key ]( undefined, true );
-		}
-	});
-}
-
-// Determine support properties
-support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
-xhrSupported = support.ajax = !!xhrSupported;
-
-// Create transport if the browser can provide an xhr
-if ( xhrSupported ) {
-
-	jQuery.ajaxTransport(function( options ) {
-		// Cross domain only allowed if supported through XMLHttpRequest
-		if ( !options.crossDomain || support.cors ) {
-
-			var callback;
-
-			return {
-				send: function( headers, complete ) {
-					var i,
-						xhr = options.xhr(),
-						id = ++xhrId;
-
-					// Open the socket
-					xhr.open( options.type, options.url, options.async, options.username, options.password );
-
-					// Apply custom fields if provided
-					if ( options.xhrFields ) {
-						for ( i in options.xhrFields ) {
-							xhr[ i ] = options.xhrFields[ i ];
-						}
-					}
-
-					// Override mime type if needed
-					if ( options.mimeType && xhr.overrideMimeType ) {
-						xhr.overrideMimeType( options.mimeType );
-					}
-
-					// X-Requested-With header
-					// For cross-domain requests, seeing as conditions for a preflight are
-					// akin to a jigsaw puzzle, we simply never set it to be sure.
-					// (it can always be set on a per-request basis or even using ajaxSetup)
-					// For same-domain requests, won't change header if already provided.
-					if ( !options.crossDomain && !headers["X-Requested-With"] ) {
-						headers["X-Requested-With"] = "XMLHttpRequest";
-					}
-
-					// Set headers
-					for ( i in headers ) {
-						// Support: IE<9
-						// IE's ActiveXObject throws a 'Type Mismatch' exception when setting
-						// request header to a null-value.
-						//
-						// To keep consistent with other XHR implementations, cast the value
-						// to string and ignore `undefined`.
-						if ( headers[ i ] !== undefined ) {
-							xhr.setRequestHeader( i, headers[ i ] + "" );
-						}
-					}
-
-					// Do send the request
-					// This may raise an exception which is actually
-					// handled in jQuery.ajax (so no try/catch here)
-					xhr.send( ( options.hasContent && options.data ) || null );
-
-					// Listener
-					callback = function( _, isAbort ) {
-						var status, statusText, responses;
-
-						// Was never called and is aborted or complete
-						if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
-							// Clean up
-							delete xhrCallbacks[ id ];
-							callback = undefined;
-							xhr.onreadystatechange = jQuery.noop;
-
-							// Abort manually if needed
-							if ( isAbort ) {
-								if ( xhr.readyState !== 4 ) {
-									xhr.abort();
-								}
-							} else {
-								responses = {};
-								status = xhr.status;
-
-								// Support: IE<10
-								// Accessing binary-data responseText throws an exception
-								// (#11426)
-								if ( typeof xhr.responseText === "string" ) {
-									responses.text = xhr.responseText;
-								}
-
-								// Firefox throws an exception when accessing
-								// statusText for faulty cross-domain requests
-								try {
-									statusText = xhr.statusText;
-								} catch( e ) {
-									// We normalize with Webkit giving an empty statusText
-									statusText = "";
-								}
-
-								// Filter status for non standard behaviors
-
-								// If the request is local and we have data: assume a success
-								// (success with no data won't get notified, that's the best we
-								// can do given current implementations)
-								if ( !status && options.isLocal && !options.crossDomain ) {
-									status = responses.text ? 200 : 404;
-								// IE - #1450: sometimes returns 1223 when it should be 204
-								} else if ( status === 1223 ) {
-									status = 204;
-								}
-							}
-						}
-
-						// Call complete if needed
-						if ( responses ) {
-							complete( status, statusText, responses, xhr.getAllResponseHeaders() );
-						}
-					};
-
-					if ( !options.async ) {
-						// if we're in sync mode we fire the callback
-						callback();
-					} else if ( xhr.readyState === 4 ) {
-						// (IE6 & IE7) if it's in cache and has been
-						// retrieved directly we need to fire the callback
-						setTimeout( callback );
-					} else {
-						// Add to the list of active xhr callbacks
-						xhr.onreadystatechange = xhrCallbacks[ id ] = callback;
-					}
-				},
-
-				abort: function() {
-					if ( callback ) {
-						callback( undefined, true );
-					}
-				}
-			};
-		}
-	});
-}
-
-// Functions to create xhrs
-function createStandardXHR() {
-	try {
-		return new window.XMLHttpRequest();
-	} catch( e ) {}
-}
-
-function createActiveXHR() {
-	try {
-		return new window.ActiveXObject( "Microsoft.XMLHTTP" );
-	} catch( e ) {}
-}
-
-
-
-
-// Install script dataType
-jQuery.ajaxSetup({
-	accepts: {
-		script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
-	},
-	contents: {
-		script: /(?:java|ecma)script/
-	},
-	converters: {
-		"text script": function( text ) {
-			jQuery.globalEval( text );
-			return text;
-		}
-	}
-});
-
-// Handle cache's special case and global
-jQuery.ajaxPrefilter( "script", function( s ) {
-	if ( s.cache === undefined ) {
-		s.cache = false;
-	}
-	if ( s.crossDomain ) {
-		s.type = "GET";
-		s.global = false;
-	}
-});
-
-// Bind script tag hack transport
-jQuery.ajaxTransport( "script", function(s) {
-
-	// This transport only deals with cross domain requests
-	if ( s.crossDomain ) {
-
-		var script,
-			head = document.head || jQuery("head")[0] || document.documentElement;
-
-		return {
-
-			send: function( _, callback ) {
-
-				script = document.createElement("script");
-
-				script.async = true;
-
-				if ( s.scriptCharset ) {
-					script.charset = s.scriptCharset;
-				}
-
-				script.src = s.url;
-
-				// Attach handlers for all browsers
-				script.onload = script.onreadystatechange = function( _, isAbort ) {
-
-					if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
-
-						// Handle memory leak in IE
-						script.onload = script.onreadystatechange = null;
-
-						// Remove the script
-						if ( script.parentNode ) {
-							script.parentNode.removeChild( script );
-						}
-
-						// Dereference the script
-						script = null;
-
-						// Callback if not abort
-						if ( !isAbort ) {
-							callback( 200, "success" );
-						}
-					}
-				};
-
-				// Circumvent IE6 bugs with base elements (#2709 and #4378) by prepending
-				// Use native DOM manipulation to avoid our domManip AJAX trickery
-				head.insertBefore( script, head.firstChild );
-			},
-
-			abort: function() {
-				if ( script ) {
-					script.onload( undefined, true );
-				}
-			}
-		};
-	}
-});
-
-
-
-
-var oldCallbacks = [],
-	rjsonp = /(=)\?(?=&|$)|\?\?/;
-
-// Default jsonp settings
-jQuery.ajaxSetup({
-	jsonp: "callback",
-	jsonpCallback: function() {
-		var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
-		this[ callback ] = true;
-		return callback;
-	}
-});
-
-// Detect, normalize options and install callbacks for jsonp requests
-jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
-
-	var callbackName, overwritten, responseContainer,
-		jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
-			"url" :
-			typeof s.data === "string" && !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") && rjsonp.test( s.data ) && "data"
-		);
-
-	// Handle iff the expected data type is "jsonp" or we have a parameter to set
-	if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
-
-		// Get callback name, remembering preexisting value associated with it
-		callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ?
-			s.jsonpCallback() :
-			s.jsonpCallback;
-
-		// Insert callback into url or form data
-		if ( jsonProp ) {
-			s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
-		} else if ( s.jsonp !== false ) {
-			s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
-		}
-
-		// Use data converter to retrieve json after script execution
-		s.converters["script json"] = function() {
-			if ( !responseContainer ) {
-				jQuery.error( callbackName + " was not called" );
-			}
-			return responseContainer[ 0 ];
-		};
-
-		// force json dataType
-		s.dataTypes[ 0 ] = "json";
-
-		// Install callback
-		overwritten = window[ callbackName ];
-		window[ callbackName ] = function() {
-			responseContainer = arguments;
-		};
-
-		// Clean-up function (fires after converters)
-		jqXHR.always(function() {
-			// Restore preexisting value
-			window[ callbackName ] = overwritten;
-
-			// Save back as free
-			if ( s[ callbackName ] ) {
-				// make sure that re-using the options doesn't screw things around
-				s.jsonpCallback = originalSettings.jsonpCallback;
-
-				// save the callback name for future use
-				oldCallbacks.push( callbackName );
-			}
-
-			// Call if it was a function and we have a response
-			if ( responseContainer && jQuery.isFunction( overwritten ) ) {
-				overwritten( responseContainer[ 0 ] );
-			}
-
-			responseContainer = overwritten = undefined;
-		});
-
-		// Delegate to script
-		return "script";
-	}
-});
-
-
-
-
-// data: string of html
-// context (optional): If specified, the fragment will be created in this context, defaults to document
-// keepScripts (optional): If true, will include scripts passed in the html string
-jQuery.parseHTML = function( data, context, keepScripts ) {
-	if ( !data || typeof data !== "string" ) {
-		return null;
-	}
-	if ( typeof context === "boolean" ) {
-		keepScripts = context;
-		context = false;
-	}
-	context = context || document;
-
-	var parsed = rsingleTag.exec( data ),
-		scripts = !keepScripts && [];
-
-	// Single tag
-	if ( parsed ) {
-		return [ context.createElement( parsed[1] ) ];
-	}
-
-	parsed = jQuery.buildFragment( [ data ], context, scripts );
-
-	if ( scripts && scripts.length ) {
-		jQuery( scripts ).remove();
-	}
-
-	return jQuery.merge( [], parsed.childNodes );
-};
-
-
-// Keep a copy of the old load method
-var _load = jQuery.fn.load;
-
-/**
- * Load a url into a page
- */
-jQuery.fn.load = function( url, params, callback ) {
-	if ( typeof url !== "string" && _load ) {
-		return _load.apply( this, arguments );
-	}
-
-	var selector, response, type,
-		self = this,
-		off = url.indexOf(" ");
-
-	if ( off >= 0 ) {
-		selector = jQuery.trim( url.slice( off, url.length ) );
-		url = url.slice( 0, off );
-	}
-
-	// If it's a function
-	if ( jQuery.isFunction( params ) ) {
-
-		// We assume that it's the callback
-		callback = params;
-		params = undefined;
-
-	// Otherwise, build a param string
-	} else if ( params && typeof params === "object" ) {
-		type = "POST";
-	}
-
-	// If we have elements to modify, make the request
-	if ( self.length > 0 ) {
-		jQuery.ajax({
-			url: url,
-
-			// if "type" variable is undefined, then "GET" method will be used
-			type: type,
-			dataType: "html",
-			data: params
-		}).done(function( responseText ) {
-
-			// Save response for use in complete callback
-			response = arguments;
-
-			self.html( selector ?
-
-				// If a selector was specified, locate the right elements in a dummy div
-				// Exclude scripts to avoid IE 'Permission Denied' errors
-				jQuery("<div>").append( jQuery.parseHTML( responseText ) ).find( selector ) :
-
-				// Otherwise use the full result
-				responseText );
-
-		}).complete( callback && function( jqXHR, status ) {
-			self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] );
-		});
-	}
-
-	return this;
-};
-
-
-
-
-jQuery.expr.filters.animated = function( elem ) {
-	return jQuery.grep(jQuery.timers, function( fn ) {
-		return elem === fn.elem;
-	}).length;
-};
-
-
-
-
-
-var docElem = window.document.documentElement;
-
-/**
- * Gets a window from an element
- */
-function getWindow( elem ) {
-	return jQuery.isWindow( elem ) ?
-		elem :
-		elem.nodeType === 9 ?
-			elem.defaultView || elem.parentWindow :
-			false;
-}
-
-jQuery.offset = {
-	setOffset: function( elem, options, i ) {
-		var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition,
-			position = jQuery.css( elem, "position" ),
-			curElem = jQuery( elem ),
-			props = {};
-
-		// set position first, in-case top/left are set even on static elem
-		if ( position === "static" ) {
-			elem.style.position = "relative";
-		}
-
-		curOffset = curElem.offset();
-		curCSSTop = jQuery.css( elem, "top" );
-		curCSSLeft = jQuery.css( elem, "left" );
-		calculatePosition = ( position === "absolute" || position === "fixed" ) &&
-			jQuery.inArray("auto", [ curCSSTop, curCSSLeft ] ) > -1;
-
-		// need to be able to calculate position if either top or left is auto and position is either absolute or fixed
-		if ( calculatePosition ) {
-			curPosition = curElem.position();
-			curTop = curPosition.top;
-			curLeft = curPosition.left;
-		} else {
-			curTop = parseFloat( curCSSTop ) || 0;
-			curLeft = parseFloat( curCSSLeft ) || 0;
-		}
-
-		if ( jQuery.isFunction( options ) ) {
-			options = options.call( elem, i, curOffset );
-		}
-
-		if ( options.top != null ) {
-			props.top = ( options.top - curOffset.top ) + curTop;
-		}
-		if ( options.left != null ) {
-			props.left = ( options.left - curOffset.left ) + curLeft;
-		}
-
-		if ( "using" in options ) {
-			options.using.call( elem, props );
-		} else {
-			curElem.css( props );
-		}
-	}
-};
-
-jQuery.fn.extend({
-	offset: function( options ) {
-		if ( arguments.length ) {
-			return options === undefined ?
-				this :
-				this.each(function( i ) {
-					jQuery.offset.setOffset( this, options, i );
-				});
-		}
-
-		var docElem, win,
-			box = { top: 0, left: 0 },
-			elem = this[ 0 ],
-			doc = elem && elem.ownerDocument;
-
-		if ( !doc ) {
-			return;
-		}
-
-		docElem = doc.documentElement;
-
-		// Make sure it's not a disconnected DOM node
-		if ( !jQuery.contains( docElem, elem ) ) {
-			return box;
-		}
-
-		// If we don't have gBCR, just use 0,0 rather than error
-		// BlackBerry 5, iOS 3 (original iPhone)
-		if ( typeof elem.getBoundingClientRect !== strundefined ) {
-			box = elem.getBoundingClientRect();
-		}
-		win = getWindow( doc );
-		return {
-			top: box.top  + ( win.pageYOffset || docElem.scrollTop )  - ( docElem.clientTop  || 0 ),
-			left: box.left + ( win.pageXOffset || docElem.scrollLeft ) - ( docElem.clientLeft || 0 )
-		};
-	},
-
-	position: function() {
-		if ( !this[ 0 ] ) {
-			return;
-		}
-
-		var offsetParent, offset,
-			parentOffset = { top: 0, left: 0 },
-			elem = this[ 0 ];
-
-		// fixed elements are offset from window (parentOffset = {top:0, left: 0}, because it is its only offset parent
-		if ( jQuery.css( elem, "position" ) === "fixed" ) {
-			// we assume that getBoundingClientRect is available when computed position is fixed
-			offset = elem.getBoundingClientRect();
-		} else {
-			// Get *real* offsetParent
-			offsetParent = this.offsetParent();
-
-			// Get correct offsets
-			offset = this.offset();
-			if ( !jQuery.nodeName( offsetParent[ 0 ], "html" ) ) {
-				parentOffset = offsetParent.offset();
-			}
-
-			// Add offsetParent borders
-			parentOffset.top  += jQuery.css( offsetParent[ 0 ], "borderTopWidth", true );
-			parentOffset.left += jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true );
-		}
-
-		// Subtract parent offsets and element margins
-		// note: when an element has margin: auto the offsetLeft and marginLeft
-		// are the same in Safari causing offset.left to incorrectly be 0
-		return {
-			top:  offset.top  - parentOffset.top - jQuery.css( elem, "marginTop", true ),
-			left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true)
-		};
-	},
-
-	offsetParent: function() {
-		return this.map(function() {
-			var offsetParent = this.offsetParent || docElem;
-
-			while ( offsetParent && ( !jQuery.nodeName( offsetParent, "html" ) && jQuery.css( offsetParent, "position" ) === "static" ) ) {
-				offsetParent = offsetParent.offsetParent;
-			}
-			return offsetParent || docElem;
-		});
-	}
-});
-
-// Create scrollLeft and scrollTop methods
-jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
-	var top = /Y/.test( prop );
-
-	jQuery.fn[ method ] = function( val ) {
-		return access( this, function( elem, method, val ) {
-			var win = getWindow( elem );
-
-			if ( val === undefined ) {
-				return win ? (prop in win) ? win[ prop ] :
-					win.document.documentElement[ method ] :
-					elem[ method ];
-			}
-
-			if ( win ) {
-				win.scrollTo(
-					!top ? val : jQuery( win ).scrollLeft(),
-					top ? val : jQuery( win ).scrollTop()
-				);
-
-			} else {
-				elem[ method ] = val;
-			}
-		}, method, val, arguments.length, null );
-	};
-});
-
-// Add the top/left cssHooks using jQuery.fn.position
-// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
-// getComputedStyle returns percent when specified for top/left/bottom/right
-// rather than make the css module depend on the offset module, we just check for it here
-jQuery.each( [ "top", "left" ], function( i, prop ) {
-	jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
-		function( elem, computed ) {
-			if ( computed ) {
-				computed = curCSS( elem, prop );
-				// if curCSS returns percentage, fallback to offset
-				return rnumnonpx.test( computed ) ?
-					jQuery( elem ).position()[ prop ] + "px" :
-					computed;
-			}
-		}
-	);
-});
-
-
-// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
-jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
-	jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {
-		// margin is only for outerHeight, outerWidth
-		jQuery.fn[ funcName ] = function( margin, value ) {
-			var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
-				extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
-
-			return access( this, function( elem, type, value ) {
-				var doc;
-
-				if ( jQuery.isWindow( elem ) ) {
-					// As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there
-					// isn't a whole lot we can do. See pull request at this URL for discussion:
-					// https://github.com/jquery/jquery/pull/764
-					return elem.document.documentElement[ "client" + name ];
-				}
-
-				// Get document width or height
-				if ( elem.nodeType === 9 ) {
-					doc = elem.documentElement;
-
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diff --git a/doc/html/_static/jquery.js b/doc/html/_static/jquery.js
index ab28a24729b320bffd3d2f60302af949db39ab85..415ff5100ca0b534d7c2d9a91a6b7cbf9c39c40f 100644
--- a/doc/html/_static/jquery.js
+++ b/doc/html/_static/jquery.js
@@ -1,4 +1,10351 @@
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+/*!
+ * jQuery JavaScript Library v1.11.3
+ * http://jquery.com/
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ *
+ * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2015-09-23T12:31Z
+ */
+
+(function( global, factory ) {
+
+	if ( typeof module === "object" && typeof module.exports === "object" ) {
+		// For CommonJS and CommonJS-like environments where a proper window is present,
+		// execute the factory and get jQuery
+		// For environments that do not inherently posses a window with a document
+		// (such as Node.js), expose a jQuery-making factory as module.exports
+		// This accentuates the need for the creation of a real window
+		// e.g. var jQuery = require("jquery")(window);
+		// See ticket #14549 for more info
+		module.exports = global.document ?
+			factory( global, true ) :
+			function( w ) {
+				if ( !w.document ) {
+					throw new Error( "jQuery requires a window with a document" );
+				}
+				return factory( w );
+			};
+	} else {
+		factory( global );
+	}
+
+// Pass this if window is not defined yet
+}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
+
+// Can't do this because several apps including ASP.NET trace
+// the stack via arguments.caller.callee and Firefox dies if
+// you try to trace through "use strict" call chains. (#13335)
+// Support: Firefox 18+
+//
+var deletedIds = [];
+
+var slice = deletedIds.slice;
+
+var concat = deletedIds.concat;
+
+var push = deletedIds.push;
+
+var indexOf = deletedIds.indexOf;
+
+var class2type = {};
+
+var toString = class2type.toString;
+
+var hasOwn = class2type.hasOwnProperty;
+
+var support = {};
+
+
+
+var
+	version = "1.11.3",
+
+	// Define a local copy of jQuery
+	jQuery = function( selector, context ) {
+		// The jQuery object is actually just the init constructor 'enhanced'
+		// Need init if jQuery is called (just allow error to be thrown if not included)
+		return new jQuery.fn.init( selector, context );
+	},
+
+	// Support: Android<4.1, IE<9
+	// Make sure we trim BOM and NBSP
+	rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
+
+	// Matches dashed string for camelizing
+	rmsPrefix = /^-ms-/,
+	rdashAlpha = /-([\da-z])/gi,
+
+	// Used by jQuery.camelCase as callback to replace()
+	fcamelCase = function( all, letter ) {
+		return letter.toUpperCase();
+	};
+
+jQuery.fn = jQuery.prototype = {
+	// The current version of jQuery being used
+	jquery: version,
+
+	constructor: jQuery,
+
+	// Start with an empty selector
+	selector: "",
+
+	// The default length of a jQuery object is 0
+	length: 0,
+
+	toArray: function() {
+		return slice.call( this );
+	},
+
+	// Get the Nth element in the matched element set OR
+	// Get the whole matched element set as a clean array
+	get: function( num ) {
+		return num != null ?
+
+			// Return just the one element from the set
+			( num < 0 ? this[ num + this.length ] : this[ num ] ) :
+
+			// Return all the elements in a clean array
+			slice.call( this );
+	},
+
+	// Take an array of elements and push it onto the stack
+	// (returning the new matched element set)
+	pushStack: function( elems ) {
+
+		// Build a new jQuery matched element set
+		var ret = jQuery.merge( this.constructor(), elems );
+
+		// Add the old object onto the stack (as a reference)
+		ret.prevObject = this;
+		ret.context = this.context;
+
+		// Return the newly-formed element set
+		return ret;
+	},
+
+	// Execute a callback for every element in the matched set.
+	// (You can seed the arguments with an array of args, but this is
+	// only used internally.)
+	each: function( callback, args ) {
+		return jQuery.each( this, callback, args );
+	},
+
+	map: function( callback ) {
+		return this.pushStack( jQuery.map(this, function( elem, i ) {
+			return callback.call( elem, i, elem );
+		}));
+	},
+
+	slice: function() {
+		return this.pushStack( slice.apply( this, arguments ) );
+	},
+
+	first: function() {
+		return this.eq( 0 );
+	},
+
+	last: function() {
+		return this.eq( -1 );
+	},
+
+	eq: function( i ) {
+		var len = this.length,
+			j = +i + ( i < 0 ? len : 0 );
+		return this.pushStack( j >= 0 && j < len ? [ this[j] ] : [] );
+	},
+
+	end: function() {
+		return this.prevObject || this.constructor(null);
+	},
+
+	// For internal use only.
+	// Behaves like an Array's method, not like a jQuery method.
+	push: push,
+	sort: deletedIds.sort,
+	splice: deletedIds.splice
+};
+
+jQuery.extend = jQuery.fn.extend = function() {
+	var src, copyIsArray, copy, name, options, clone,
+		target = arguments[0] || {},
+		i = 1,
+		length = arguments.length,
+		deep = false;
+
+	// Handle a deep copy situation
+	if ( typeof target === "boolean" ) {
+		deep = target;
+
+		// skip the boolean and the target
+		target = arguments[ i ] || {};
+		i++;
+	}
+
+	// Handle case when target is a string or something (possible in deep copy)
+	if ( typeof target !== "object" && !jQuery.isFunction(target) ) {
+		target = {};
+	}
+
+	// extend jQuery itself if only one argument is passed
+	if ( i === length ) {
+		target = this;
+		i--;
+	}
+
+	for ( ; i < length; i++ ) {
+		// Only deal with non-null/undefined values
+		if ( (options = arguments[ i ]) != null ) {
+			// Extend the base object
+			for ( name in options ) {
+				src = target[ name ];
+				copy = options[ name ];
+
+				// Prevent never-ending loop
+				if ( target === copy ) {
+					continue;
+				}
+
+				// Recurse if we're merging plain objects or arrays
+				if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) {
+					if ( copyIsArray ) {
+						copyIsArray = false;
+						clone = src && jQuery.isArray(src) ? src : [];
+
+					} else {
+						clone = src && jQuery.isPlainObject(src) ? src : {};
+					}
+
+					// Never move original objects, clone them
+					target[ name ] = jQuery.extend( deep, clone, copy );
+
+				// Don't bring in undefined values
+				} else if ( copy !== undefined ) {
+					target[ name ] = copy;
+				}
+			}
+		}
+	}
+
+	// Return the modified object
+	return target;
+};
+
+jQuery.extend({
+	// Unique for each copy of jQuery on the page
+	expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
+
+	// Assume jQuery is ready without the ready module
+	isReady: true,
+
+	error: function( msg ) {
+		throw new Error( msg );
+	},
+
+	noop: function() {},
+
+	// See test/unit/core.js for details concerning isFunction.
+	// Since version 1.3, DOM methods and functions like alert
+	// aren't supported. They return false on IE (#2968).
+	isFunction: function( obj ) {
+		return jQuery.type(obj) === "function";
+	},
+
+	isArray: Array.isArray || function( obj ) {
+		return jQuery.type(obj) === "array";
+	},
+
+	isWindow: function( obj ) {
+		/* jshint eqeqeq: false */
+		return obj != null && obj == obj.window;
+	},
+
+	isNumeric: function( obj ) {
+		// parseFloat NaNs numeric-cast false positives (null|true|false|"")
+		// ...but misinterprets leading-number strings, particularly hex literals ("0x...")
+		// subtraction forces infinities to NaN
+		// adding 1 corrects loss of precision from parseFloat (#15100)
+		return !jQuery.isArray( obj ) && (obj - parseFloat( obj ) + 1) >= 0;
+	},
+
+	isEmptyObject: function( obj ) {
+		var name;
+		for ( name in obj ) {
+			return false;
+		}
+		return true;
+	},
+
+	isPlainObject: function( obj ) {
+		var key;
+
+		// Must be an Object.
+		// Because of IE, we also have to check the presence of the constructor property.
+		// Make sure that DOM nodes and window objects don't pass through, as well
+		if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) {
+			return false;
+		}
+
+		try {
+			// Not own constructor property must be Object
+			if ( obj.constructor &&
+				!hasOwn.call(obj, "constructor") &&
+				!hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
+				return false;
+			}
+		} catch ( e ) {
+			// IE8,9 Will throw exceptions on certain host objects #9897
+			return false;
+		}
+
+		// Support: IE<9
+		// Handle iteration over inherited properties before own properties.
+		if ( support.ownLast ) {
+			for ( key in obj ) {
+				return hasOwn.call( obj, key );
+			}
+		}
+
+		// Own properties are enumerated firstly, so to speed up,
+		// if last one is own, then all properties are own.
+		for ( key in obj ) {}
+
+		return key === undefined || hasOwn.call( obj, key );
+	},
+
+	type: function( obj ) {
+		if ( obj == null ) {
+			return obj + "";
+		}
+		return typeof obj === "object" || typeof obj === "function" ?
+			class2type[ toString.call(obj) ] || "object" :
+			typeof obj;
+	},
+
+	// Evaluates a script in a global context
+	// Workarounds based on findings by Jim Driscoll
+	// http://weblogs.java.net/blog/driscoll/archive/2009/09/08/eval-javascript-global-context
+	globalEval: function( data ) {
+		if ( data && jQuery.trim( data ) ) {
+			// We use execScript on Internet Explorer
+			// We use an anonymous function so that context is window
+			// rather than jQuery in Firefox
+			( window.execScript || function( data ) {
+				window[ "eval" ].call( window, data );
+			} )( data );
+		}
+	},
+
+	// Convert dashed to camelCase; used by the css and data modules
+	// Microsoft forgot to hump their vendor prefix (#9572)
+	camelCase: function( string ) {
+		return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
+	},
+
+	nodeName: function( elem, name ) {
+		return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+	},
+
+	// args is for internal usage only
+	each: function( obj, callback, args ) {
+		var value,
+			i = 0,
+			length = obj.length,
+			isArray = isArraylike( obj );
+
+		if ( args ) {
+			if ( isArray ) {
+				for ( ; i < length; i++ ) {
+					value = callback.apply( obj[ i ], args );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			} else {
+				for ( i in obj ) {
+					value = callback.apply( obj[ i ], args );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			}
+
+		// A special, fast, case for the most common use of each
+		} else {
+			if ( isArray ) {
+				for ( ; i < length; i++ ) {
+					value = callback.call( obj[ i ], i, obj[ i ] );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			} else {
+				for ( i in obj ) {
+					value = callback.call( obj[ i ], i, obj[ i ] );
+
+					if ( value === false ) {
+						break;
+					}
+				}
+			}
+		}
+
+		return obj;
+	},
+
+	// Support: Android<4.1, IE<9
+	trim: function( text ) {
+		return text == null ?
+			"" :
+			( text + "" ).replace( rtrim, "" );
+	},
+
+	// results is for internal usage only
+	makeArray: function( arr, results ) {
+		var ret = results || [];
+
+		if ( arr != null ) {
+			if ( isArraylike( Object(arr) ) ) {
+				jQuery.merge( ret,
+					typeof arr === "string" ?
+					[ arr ] : arr
+				);
+			} else {
+				push.call( ret, arr );
+			}
+		}
+
+		return ret;
+	},
+
+	inArray: function( elem, arr, i ) {
+		var len;
+
+		if ( arr ) {
+			if ( indexOf ) {
+				return indexOf.call( arr, elem, i );
+			}
+
+			len = arr.length;
+			i = i ? i < 0 ? Math.max( 0, len + i ) : i : 0;
+
+			for ( ; i < len; i++ ) {
+				// Skip accessing in sparse arrays
+				if ( i in arr && arr[ i ] === elem ) {
+					return i;
+				}
+			}
+		}
+
+		return -1;
+	},
+
+	merge: function( first, second ) {
+		var len = +second.length,
+			j = 0,
+			i = first.length;
+
+		while ( j < len ) {
+			first[ i++ ] = second[ j++ ];
+		}
+
+		// Support: IE<9
+		// Workaround casting of .length to NaN on otherwise arraylike objects (e.g., NodeLists)
+		if ( len !== len ) {
+			while ( second[j] !== undefined ) {
+				first[ i++ ] = second[ j++ ];
+			}
+		}
+
+		first.length = i;
+
+		return first;
+	},
+
+	grep: function( elems, callback, invert ) {
+		var callbackInverse,
+			matches = [],
+			i = 0,
+			length = elems.length,
+			callbackExpect = !invert;
+
+		// Go through the array, only saving the items
+		// that pass the validator function
+		for ( ; i < length; i++ ) {
+			callbackInverse = !callback( elems[ i ], i );
+			if ( callbackInverse !== callbackExpect ) {
+				matches.push( elems[ i ] );
+			}
+		}
+
+		return matches;
+	},
+
+	// arg is for internal usage only
+	map: function( elems, callback, arg ) {
+		var value,
+			i = 0,
+			length = elems.length,
+			isArray = isArraylike( elems ),
+			ret = [];
+
+		// Go through the array, translating each of the items to their new values
+		if ( isArray ) {
+			for ( ; i < length; i++ ) {
+				value = callback( elems[ i ], i, arg );
+
+				if ( value != null ) {
+					ret.push( value );
+				}
+			}
+
+		// Go through every key on the object,
+		} else {
+			for ( i in elems ) {
+				value = callback( elems[ i ], i, arg );
+
+				if ( value != null ) {
+					ret.push( value );
+				}
+			}
+		}
+
+		// Flatten any nested arrays
+		return concat.apply( [], ret );
+	},
+
+	// A global GUID counter for objects
+	guid: 1,
+
+	// Bind a function to a context, optionally partially applying any
+	// arguments.
+	proxy: function( fn, context ) {
+		var args, proxy, tmp;
+
+		if ( typeof context === "string" ) {
+			tmp = fn[ context ];
+			context = fn;
+			fn = tmp;
+		}
+
+		// Quick check to determine if target is callable, in the spec
+		// this throws a TypeError, but we will just return undefined.
+		if ( !jQuery.isFunction( fn ) ) {
+			return undefined;
+		}
+
+		// Simulated bind
+		args = slice.call( arguments, 2 );
+		proxy = function() {
+			return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
+		};
+
+		// Set the guid of unique handler to the same of original handler, so it can be removed
+		proxy.guid = fn.guid = fn.guid || jQuery.guid++;
+
+		return proxy;
+	},
+
+	now: function() {
+		return +( new Date() );
+	},
+
+	// jQuery.support is not used in Core but other projects attach their
+	// properties to it so it needs to exist.
+	support: support
+});
+
+// Populate the class2type map
+jQuery.each("Boolean Number String Function Array Date RegExp Object Error".split(" "), function(i, name) {
+	class2type[ "[object " + name + "]" ] = name.toLowerCase();
+});
+
+function isArraylike( obj ) {
+
+	// Support: iOS 8.2 (not reproducible in simulator)
+	// `in` check used to prevent JIT error (gh-2145)
+	// hasOwn isn't used here due to false negatives
+	// regarding Nodelist length in IE
+	var length = "length" in obj && obj.length,
+		type = jQuery.type( obj );
+
+	if ( type === "function" || jQuery.isWindow( obj ) ) {
+		return false;
+	}
+
+	if ( obj.nodeType === 1 && length ) {
+		return true;
+	}
+
+	return type === "array" || length === 0 ||
+		typeof length === "number" && length > 0 && ( length - 1 ) in obj;
+}
+var Sizzle =
+/*!
+ * Sizzle CSS Selector Engine v2.2.0-pre
+ * http://sizzlejs.com/
+ *
+ * Copyright 2008, 2014 jQuery Foundation, Inc. and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2014-12-16
+ */
+(function( window ) {
+
+var i,
+	support,
+	Expr,
+	getText,
+	isXML,
+	tokenize,
+	compile,
+	select,
+	outermostContext,
+	sortInput,
+	hasDuplicate,
+
+	// Local document vars
+	setDocument,
+	document,
+	docElem,
+	documentIsHTML,
+	rbuggyQSA,
+	rbuggyMatches,
+	matches,
+	contains,
+
+	// Instance-specific data
+	expando = "sizzle" + 1 * new Date(),
+	preferredDoc = window.document,
+	dirruns = 0,
+	done = 0,
+	classCache = createCache(),
+	tokenCache = createCache(),
+	compilerCache = createCache(),
+	sortOrder = function( a, b ) {
+		if ( a === b ) {
+			hasDuplicate = true;
+		}
+		return 0;
+	},
+
+	// General-purpose constants
+	MAX_NEGATIVE = 1 << 31,
+
+	// Instance methods
+	hasOwn = ({}).hasOwnProperty,
+	arr = [],
+	pop = arr.pop,
+	push_native = arr.push,
+	push = arr.push,
+	slice = arr.slice,
+	// Use a stripped-down indexOf as it's faster than native
+	// http://jsperf.com/thor-indexof-vs-for/5
+	indexOf = function( list, elem ) {
+		var i = 0,
+			len = list.length;
+		for ( ; i < len; i++ ) {
+			if ( list[i] === elem ) {
+				return i;
+			}
+		}
+		return -1;
+	},
+
+	booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
+
+	// Regular expressions
+
+	// Whitespace characters http://www.w3.org/TR/css3-selectors/#whitespace
+	whitespace = "[\\x20\\t\\r\\n\\f]",
+	// http://www.w3.org/TR/css3-syntax/#characters
+	characterEncoding = "(?:\\\\.|[\\w-]|[^\\x00-\\xa0])+",
+
+	// Loosely modeled on CSS identifier characters
+	// An unquoted value should be a CSS identifier http://www.w3.org/TR/css3-selectors/#attribute-selectors
+	// Proper syntax: http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
+	identifier = characterEncoding.replace( "w", "w#" ),
+
+	// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
+	attributes = "\\[" + whitespace + "*(" + characterEncoding + ")(?:" + whitespace +
+		// Operator (capture 2)
+		"*([*^$|!~]?=)" + whitespace +
+		// "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
+		"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
+		"*\\]",
+
+	pseudos = ":(" + characterEncoding + ")(?:\\((" +
+		// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
+		// 1. quoted (capture 3; capture 4 or capture 5)
+		"('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
+		// 2. simple (capture 6)
+		"((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
+		// 3. anything else (capture 2)
+		".*" +
+		")\\)|)",
+
+	// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
+	rwhitespace = new RegExp( whitespace + "+", "g" ),
+	rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
+
+	rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
+	rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
+
+	rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ),
+
+	rpseudo = new RegExp( pseudos ),
+	ridentifier = new RegExp( "^" + identifier + "$" ),
+
+	matchExpr = {
+		"ID": new RegExp( "^#(" + characterEncoding + ")" ),
+		"CLASS": new RegExp( "^\\.(" + characterEncoding + ")" ),
+		"TAG": new RegExp( "^(" + characterEncoding.replace( "w", "w*" ) + ")" ),
+		"ATTR": new RegExp( "^" + attributes ),
+		"PSEUDO": new RegExp( "^" + pseudos ),
+		"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
+			"*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
+			"*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
+		"bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
+		// For use in libraries implementing .is()
+		// We use this for POS matching in `select`
+		"needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
+			whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
+	},
+
+	rinputs = /^(?:input|select|textarea|button)$/i,
+	rheader = /^h\d$/i,
+
+	rnative = /^[^{]+\{\s*\[native \w/,
+
+	// Easily-parseable/retrievable ID or TAG or CLASS selectors
+	rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
+
+	rsibling = /[+~]/,
+	rescape = /'|\\/g,
+
+	// CSS escapes http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
+	runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
+	funescape = function( _, escaped, escapedWhitespace ) {
+		var high = "0x" + escaped - 0x10000;
+		// NaN means non-codepoint
+		// Support: Firefox<24
+		// Workaround erroneous numeric interpretation of +"0x"
+		return high !== high || escapedWhitespace ?
+			escaped :
+			high < 0 ?
+				// BMP codepoint
+				String.fromCharCode( high + 0x10000 ) :
+				// Supplemental Plane codepoint (surrogate pair)
+				String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
+	},
+
+	// Used for iframes
+	// See setDocument()
+	// Removing the function wrapper causes a "Permission Denied"
+	// error in IE
+	unloadHandler = function() {
+		setDocument();
+	};
+
+// Optimize for push.apply( _, NodeList )
+try {
+	push.apply(
+		(arr = slice.call( preferredDoc.childNodes )),
+		preferredDoc.childNodes
+	);
+	// Support: Android<4.0
+	// Detect silently failing push.apply
+	arr[ preferredDoc.childNodes.length ].nodeType;
+} catch ( e ) {
+	push = { apply: arr.length ?
+
+		// Leverage slice if possible
+		function( target, els ) {
+			push_native.apply( target, slice.call(els) );
+		} :
+
+		// Support: IE<9
+		// Otherwise append directly
+		function( target, els ) {
+			var j = target.length,
+				i = 0;
+			// Can't trust NodeList.length
+			while ( (target[j++] = els[i++]) ) {}
+			target.length = j - 1;
+		}
+	};
+}
+
+function Sizzle( selector, context, results, seed ) {
+	var match, elem, m, nodeType,
+		// QSA vars
+		i, groups, old, nid, newContext, newSelector;
+
+	if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
+		setDocument( context );
+	}
+
+	context = context || document;
+	results = results || [];
+	nodeType = context.nodeType;
+
+	if ( typeof selector !== "string" || !selector ||
+		nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
+
+		return results;
+	}
+
+	if ( !seed && documentIsHTML ) {
+
+		// Try to shortcut find operations when possible (e.g., not under DocumentFragment)
+		if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {
+			// Speed-up: Sizzle("#ID")
+			if ( (m = match[1]) ) {
+				if ( nodeType === 9 ) {
+					elem = context.getElementById( m );
+					// Check parentNode to catch when Blackberry 4.6 returns
+					// nodes that are no longer in the document (jQuery #6963)
+					if ( elem && elem.parentNode ) {
+						// Handle the case where IE, Opera, and Webkit return items
+						// by name instead of ID
+						if ( elem.id === m ) {
+							results.push( elem );
+							return results;
+						}
+					} else {
+						return results;
+					}
+				} else {
+					// Context is not a document
+					if ( context.ownerDocument && (elem = context.ownerDocument.getElementById( m )) &&
+						contains( context, elem ) && elem.id === m ) {
+						results.push( elem );
+						return results;
+					}
+				}
+
+			// Speed-up: Sizzle("TAG")
+			} else if ( match[2] ) {
+				push.apply( results, context.getElementsByTagName( selector ) );
+				return results;
+
+			// Speed-up: Sizzle(".CLASS")
+			} else if ( (m = match[3]) && support.getElementsByClassName ) {
+				push.apply( results, context.getElementsByClassName( m ) );
+				return results;
+			}
+		}
+
+		// QSA path
+		if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
+			nid = old = expando;
+			newContext = context;
+			newSelector = nodeType !== 1 && selector;
+
+			// qSA works strangely on Element-rooted queries
+			// We can work around this by specifying an extra ID on the root
+			// and working up from there (Thanks to Andrew Dupont for the technique)
+			// IE 8 doesn't work on object elements
+			if ( nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
+				groups = tokenize( selector );
+
+				if ( (old = context.getAttribute("id")) ) {
+					nid = old.replace( rescape, "\\$&" );
+				} else {
+					context.setAttribute( "id", nid );
+				}
+				nid = "[id='" + nid + "'] ";
+
+				i = groups.length;
+				while ( i-- ) {
+					groups[i] = nid + toSelector( groups[i] );
+				}
+				newContext = rsibling.test( selector ) && testContext( context.parentNode ) || context;
+				newSelector = groups.join(",");
+			}
+
+			if ( newSelector ) {
+				try {
+					push.apply( results,
+						newContext.querySelectorAll( newSelector )
+					);
+					return results;
+				} catch(qsaError) {
+				} finally {
+					if ( !old ) {
+						context.removeAttribute("id");
+					}
+				}
+			}
+		}
+	}
+
+	// All others
+	return select( selector.replace( rtrim, "$1" ), context, results, seed );
+}
+
+/**
+ * Create key-value caches of limited size
+ * @returns {Function(string, Object)} Returns the Object data after storing it on itself with
+ *	property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
+ *	deleting the oldest entry
+ */
+function createCache() {
+	var keys = [];
+
+	function cache( key, value ) {
+		// Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
+		if ( keys.push( key + " " ) > Expr.cacheLength ) {
+			// Only keep the most recent entries
+			delete cache[ keys.shift() ];
+		}
+		return (cache[ key + " " ] = value);
+	}
+	return cache;
+}
+
+/**
+ * Mark a function for special use by Sizzle
+ * @param {Function} fn The function to mark
+ */
+function markFunction( fn ) {
+	fn[ expando ] = true;
+	return fn;
+}
+
+/**
+ * Support testing using an element
+ * @param {Function} fn Passed the created div and expects a boolean result
+ */
+function assert( fn ) {
+	var div = document.createElement("div");
+
+	try {
+		return !!fn( div );
+	} catch (e) {
+		return false;
+	} finally {
+		// Remove from its parent by default
+		if ( div.parentNode ) {
+			div.parentNode.removeChild( div );
+		}
+		// release memory in IE
+		div = null;
+	}
+}
+
+/**
+ * Adds the same handler for all of the specified attrs
+ * @param {String} attrs Pipe-separated list of attributes
+ * @param {Function} handler The method that will be applied
+ */
+function addHandle( attrs, handler ) {
+	var arr = attrs.split("|"),
+		i = attrs.length;
+
+	while ( i-- ) {
+		Expr.attrHandle[ arr[i] ] = handler;
+	}
+}
+
+/**
+ * Checks document order of two siblings
+ * @param {Element} a
+ * @param {Element} b
+ * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
+ */
+function siblingCheck( a, b ) {
+	var cur = b && a,
+		diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
+			( ~b.sourceIndex || MAX_NEGATIVE ) -
+			( ~a.sourceIndex || MAX_NEGATIVE );
+
+	// Use IE sourceIndex if available on both nodes
+	if ( diff ) {
+		return diff;
+	}
+
+	// Check if b follows a
+	if ( cur ) {
+		while ( (cur = cur.nextSibling) ) {
+			if ( cur === b ) {
+				return -1;
+			}
+		}
+	}
+
+	return a ? 1 : -1;
+}
+
+/**
+ * Returns a function to use in pseudos for input types
+ * @param {String} type
+ */
+function createInputPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return name === "input" && elem.type === type;
+	};
+}
+
+/**
+ * Returns a function to use in pseudos for buttons
+ * @param {String} type
+ */
+function createButtonPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return (name === "input" || name === "button") && elem.type === type;
+	};
+}
+
+/**
+ * Returns a function to use in pseudos for positionals
+ * @param {Function} fn
+ */
+function createPositionalPseudo( fn ) {
+	return markFunction(function( argument ) {
+		argument = +argument;
+		return markFunction(function( seed, matches ) {
+			var j,
+				matchIndexes = fn( [], seed.length, argument ),
+				i = matchIndexes.length;
+
+			// Match elements found at the specified indexes
+			while ( i-- ) {
+				if ( seed[ (j = matchIndexes[i]) ] ) {
+					seed[j] = !(matches[j] = seed[j]);
+				}
+			}
+		});
+	});
+}
+
+/**
+ * Checks a node for validity as a Sizzle context
+ * @param {Element|Object=} context
+ * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
+ */
+function testContext( context ) {
+	return context && typeof context.getElementsByTagName !== "undefined" && context;
+}
+
+// Expose support vars for convenience
+support = Sizzle.support = {};
+
+/**
+ * Detects XML nodes
+ * @param {Element|Object} elem An element or a document
+ * @returns {Boolean} True iff elem is a non-HTML XML node
+ */
+isXML = Sizzle.isXML = function( elem ) {
+	// documentElement is verified for cases where it doesn't yet exist
+	// (such as loading iframes in IE - #4833)
+	var documentElement = elem && (elem.ownerDocument || elem).documentElement;
+	return documentElement ? documentElement.nodeName !== "HTML" : false;
+};
+
+/**
+ * Sets document-related variables once based on the current document
+ * @param {Element|Object} [doc] An element or document object to use to set the document
+ * @returns {Object} Returns the current document
+ */
+setDocument = Sizzle.setDocument = function( node ) {
+	var hasCompare, parent,
+		doc = node ? node.ownerDocument || node : preferredDoc;
+
+	// If no document and documentElement is available, return
+	if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
+		return document;
+	}
+
+	// Set our document
+	document = doc;
+	docElem = doc.documentElement;
+	parent = doc.defaultView;
+
+	// Support: IE>8
+	// If iframe document is assigned to "document" variable and if iframe has been reloaded,
+	// IE will throw "permission denied" error when accessing "document" variable, see jQuery #13936
+	// IE6-8 do not support the defaultView property so parent will be undefined
+	if ( parent && parent !== parent.top ) {
+		// IE11 does not have attachEvent, so all must suffer
+		if ( parent.addEventListener ) {
+			parent.addEventListener( "unload", unloadHandler, false );
+		} else if ( parent.attachEvent ) {
+			parent.attachEvent( "onunload", unloadHandler );
+		}
+	}
+
+	/* Support tests
+	---------------------------------------------------------------------- */
+	documentIsHTML = !isXML( doc );
+
+	/* Attributes
+	---------------------------------------------------------------------- */
+
+	// Support: IE<8
+	// Verify that getAttribute really returns attributes and not properties
+	// (excepting IE8 booleans)
+	support.attributes = assert(function( div ) {
+		div.className = "i";
+		return !div.getAttribute("className");
+	});
+
+	/* getElement(s)By*
+	---------------------------------------------------------------------- */
+
+	// Check if getElementsByTagName("*") returns only elements
+	support.getElementsByTagName = assert(function( div ) {
+		div.appendChild( doc.createComment("") );
+		return !div.getElementsByTagName("*").length;
+	});
+
+	// Support: IE<9
+	support.getElementsByClassName = rnative.test( doc.getElementsByClassName );
+
+	// Support: IE<10
+	// Check if getElementById returns elements by name
+	// The broken getElementById methods don't pick up programatically-set names,
+	// so use a roundabout getElementsByName test
+	support.getById = assert(function( div ) {
+		docElem.appendChild( div ).id = expando;
+		return !doc.getElementsByName || !doc.getElementsByName( expando ).length;
+	});
+
+	// ID find and filter
+	if ( support.getById ) {
+		Expr.find["ID"] = function( id, context ) {
+			if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+				var m = context.getElementById( id );
+				// Check parentNode to catch when Blackberry 4.6 returns
+				// nodes that are no longer in the document #6963
+				return m && m.parentNode ? [ m ] : [];
+			}
+		};
+		Expr.filter["ID"] = function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				return elem.getAttribute("id") === attrId;
+			};
+		};
+	} else {
+		// Support: IE6/7
+		// getElementById is not reliable as a find shortcut
+		delete Expr.find["ID"];
+
+		Expr.filter["ID"] =  function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id");
+				return node && node.value === attrId;
+			};
+		};
+	}
+
+	// Tag
+	Expr.find["TAG"] = support.getElementsByTagName ?
+		function( tag, context ) {
+			if ( typeof context.getElementsByTagName !== "undefined" ) {
+				return context.getElementsByTagName( tag );
+
+			// DocumentFragment nodes don't have gEBTN
+			} else if ( support.qsa ) {
+				return context.querySelectorAll( tag );
+			}
+		} :
+
+		function( tag, context ) {
+			var elem,
+				tmp = [],
+				i = 0,
+				// By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
+				results = context.getElementsByTagName( tag );
+
+			// Filter out possible comments
+			if ( tag === "*" ) {
+				while ( (elem = results[i++]) ) {
+					if ( elem.nodeType === 1 ) {
+						tmp.push( elem );
+					}
+				}
+
+				return tmp;
+			}
+			return results;
+		};
+
+	// Class
+	Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
+		if ( documentIsHTML ) {
+			return context.getElementsByClassName( className );
+		}
+	};
+
+	/* QSA/matchesSelector
+	---------------------------------------------------------------------- */
+
+	// QSA and matchesSelector support
+
+	// matchesSelector(:active) reports false when true (IE9/Opera 11.5)
+	rbuggyMatches = [];
+
+	// qSa(:focus) reports false when true (Chrome 21)
+	// We allow this because of a bug in IE8/9 that throws an error
+	// whenever `document.activeElement` is accessed on an iframe
+	// So, we allow :focus to pass through QSA all the time to avoid the IE error
+	// See http://bugs.jquery.com/ticket/13378
+	rbuggyQSA = [];
+
+	if ( (support.qsa = rnative.test( doc.querySelectorAll )) ) {
+		// Build QSA regex
+		// Regex strategy adopted from Diego Perini
+		assert(function( div ) {
+			// Select is set to empty string on purpose
+			// This is to test IE's treatment of not explicitly
+			// setting a boolean content attribute,
+			// since its presence should be enough
+			// http://bugs.jquery.com/ticket/12359
+			docElem.appendChild( div ).innerHTML = "<a id='" + expando + "'></a>" +
+				"<select id='" + expando + "-\f]' msallowcapture=''>" +
+				"<option selected=''></option></select>";
+
+			// Support: IE8, Opera 11-12.16
+			// Nothing should be selected when empty strings follow ^= or $= or *=
+			// The test attribute must be unknown in Opera but "safe" for WinRT
+			// http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
+			if ( div.querySelectorAll("[msallowcapture^='']").length ) {
+				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
+			}
+
+			// Support: IE8
+			// Boolean attributes and "value" are not treated correctly
+			if ( !div.querySelectorAll("[selected]").length ) {
+				rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
+			}
+
+			// Support: Chrome<29, Android<4.2+, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.7+
+			if ( !div.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
+				rbuggyQSA.push("~=");
+			}
+
+			// Webkit/Opera - :checked should return selected option elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			// IE8 throws error here and will not see later tests
+			if ( !div.querySelectorAll(":checked").length ) {
+				rbuggyQSA.push(":checked");
+			}
+
+			// Support: Safari 8+, iOS 8+
+			// https://bugs.webkit.org/show_bug.cgi?id=136851
+			// In-page `selector#id sibing-combinator selector` fails
+			if ( !div.querySelectorAll( "a#" + expando + "+*" ).length ) {
+				rbuggyQSA.push(".#.+[+~]");
+			}
+		});
+
+		assert(function( div ) {
+			// Support: Windows 8 Native Apps
+			// The type and name attributes are restricted during .innerHTML assignment
+			var input = doc.createElement("input");
+			input.setAttribute( "type", "hidden" );
+			div.appendChild( input ).setAttribute( "name", "D" );
+
+			// Support: IE8
+			// Enforce case-sensitivity of name attribute
+			if ( div.querySelectorAll("[name=d]").length ) {
+				rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
+			}
+
+			// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
+			// IE8 throws error here and will not see later tests
+			if ( !div.querySelectorAll(":enabled").length ) {
+				rbuggyQSA.push( ":enabled", ":disabled" );
+			}
+
+			// Opera 10-11 does not throw on post-comma invalid pseudos
+			div.querySelectorAll("*,:x");
+			rbuggyQSA.push(",.*:");
+		});
+	}
+
+	if ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||
+		docElem.webkitMatchesSelector ||
+		docElem.mozMatchesSelector ||
+		docElem.oMatchesSelector ||
+		docElem.msMatchesSelector) )) ) {
+
+		assert(function( div ) {
+			// Check to see if it's possible to do matchesSelector
+			// on a disconnected node (IE 9)
+			support.disconnectedMatch = matches.call( div, "div" );
+
+			// This should fail with an exception
+			// Gecko does not error, returns false instead
+			matches.call( div, "[s!='']:x" );
+			rbuggyMatches.push( "!=", pseudos );
+		});
+	}
+
+	rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") );
+	rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") );
+
+	/* Contains
+	---------------------------------------------------------------------- */
+	hasCompare = rnative.test( docElem.compareDocumentPosition );
+
+	// Element contains another
+	// Purposefully does not implement inclusive descendent
+	// As in, an element does not contain itself
+	contains = hasCompare || rnative.test( docElem.contains ) ?
+		function( a, b ) {
+			var adown = a.nodeType === 9 ? a.documentElement : a,
+				bup = b && b.parentNode;
+			return a === bup || !!( bup && bup.nodeType === 1 && (
+				adown.contains ?
+					adown.contains( bup ) :
+					a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
+			));
+		} :
+		function( a, b ) {
+			if ( b ) {
+				while ( (b = b.parentNode) ) {
+					if ( b === a ) {
+						return true;
+					}
+				}
+			}
+			return false;
+		};
+
+	/* Sorting
+	---------------------------------------------------------------------- */
+
+	// Document order sorting
+	sortOrder = hasCompare ?
+	function( a, b ) {
+
+		// Flag for duplicate removal
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
+		}
+
+		// Sort on method existence if only one input has compareDocumentPosition
+		var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
+		if ( compare ) {
+			return compare;
+		}
+
+		// Calculate position if both inputs belong to the same document
+		compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?
+			a.compareDocumentPosition( b ) :
+
+			// Otherwise we know they are disconnected
+			1;
+
+		// Disconnected nodes
+		if ( compare & 1 ||
+			(!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
+
+			// Choose the first element that is related to our preferred document
+			if ( a === doc || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
+				return -1;
+			}
+			if ( b === doc || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
+				return 1;
+			}
+
+			// Maintain original order
+			return sortInput ?
+				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+				0;
+		}
+
+		return compare & 4 ? -1 : 1;
+	} :
+	function( a, b ) {
+		// Exit early if the nodes are identical
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
+		}
+
+		var cur,
+			i = 0,
+			aup = a.parentNode,
+			bup = b.parentNode,
+			ap = [ a ],
+			bp = [ b ];
+
+		// Parentless nodes are either documents or disconnected
+		if ( !aup || !bup ) {
+			return a === doc ? -1 :
+				b === doc ? 1 :
+				aup ? -1 :
+				bup ? 1 :
+				sortInput ?
+				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+				0;
+
+		// If the nodes are siblings, we can do a quick check
+		} else if ( aup === bup ) {
+			return siblingCheck( a, b );
+		}
+
+		// Otherwise we need full lists of their ancestors for comparison
+		cur = a;
+		while ( (cur = cur.parentNode) ) {
+			ap.unshift( cur );
+		}
+		cur = b;
+		while ( (cur = cur.parentNode) ) {
+			bp.unshift( cur );
+		}
+
+		// Walk down the tree looking for a discrepancy
+		while ( ap[i] === bp[i] ) {
+			i++;
+		}
+
+		return i ?
+			// Do a sibling check if the nodes have a common ancestor
+			siblingCheck( ap[i], bp[i] ) :
+
+			// Otherwise nodes in our document sort first
+			ap[i] === preferredDoc ? -1 :
+			bp[i] === preferredDoc ? 1 :
+			0;
+	};
+
+	return doc;
+};
+
+Sizzle.matches = function( expr, elements ) {
+	return Sizzle( expr, null, null, elements );
+};
+
+Sizzle.matchesSelector = function( elem, expr ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
+	}
+
+	// Make sure that attribute selectors are quoted
+	expr = expr.replace( rattributeQuotes, "='$1']" );
+
+	if ( support.matchesSelector && documentIsHTML &&
+		( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
+		( !rbuggyQSA     || !rbuggyQSA.test( expr ) ) ) {
+
+		try {
+			var ret = matches.call( elem, expr );
+
+			// IE 9's matchesSelector returns false on disconnected nodes
+			if ( ret || support.disconnectedMatch ||
+					// As well, disconnected nodes are said to be in a document
+					// fragment in IE 9
+					elem.document && elem.document.nodeType !== 11 ) {
+				return ret;
+			}
+		} catch (e) {}
+	}
+
+	return Sizzle( expr, document, null, [ elem ] ).length > 0;
+};
+
+Sizzle.contains = function( context, elem ) {
+	// Set document vars if needed
+	if ( ( context.ownerDocument || context ) !== document ) {
+		setDocument( context );
+	}
+	return contains( context, elem );
+};
+
+Sizzle.attr = function( elem, name ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
+	}
+
+	var fn = Expr.attrHandle[ name.toLowerCase() ],
+		// Don't get fooled by Object.prototype properties (jQuery #13807)
+		val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
+			fn( elem, name, !documentIsHTML ) :
+			undefined;
+
+	return val !== undefined ?
+		val :
+		support.attributes || !documentIsHTML ?
+			elem.getAttribute( name ) :
+			(val = elem.getAttributeNode(name)) && val.specified ?
+				val.value :
+				null;
+};
+
+Sizzle.error = function( msg ) {
+	throw new Error( "Syntax error, unrecognized expression: " + msg );
+};
+
+/**
+ * Document sorting and removing duplicates
+ * @param {ArrayLike} results
+ */
+Sizzle.uniqueSort = function( results ) {
+	var elem,
+		duplicates = [],
+		j = 0,
+		i = 0;
+
+	// Unless we *know* we can detect duplicates, assume their presence
+	hasDuplicate = !support.detectDuplicates;
+	sortInput = !support.sortStable && results.slice( 0 );
+	results.sort( sortOrder );
+
+	if ( hasDuplicate ) {
+		while ( (elem = results[i++]) ) {
+			if ( elem === results[ i ] ) {
+				j = duplicates.push( i );
+			}
+		}
+		while ( j-- ) {
+			results.splice( duplicates[ j ], 1 );
+		}
+	}
+
+	// Clear input after sorting to release objects
+	// See https://github.com/jquery/sizzle/pull/225
+	sortInput = null;
+
+	return results;
+};
+
+/**
+ * Utility function for retrieving the text value of an array of DOM nodes
+ * @param {Array|Element} elem
+ */
+getText = Sizzle.getText = function( elem ) {
+	var node,
+		ret = "",
+		i = 0,
+		nodeType = elem.nodeType;
+
+	if ( !nodeType ) {
+		// If no nodeType, this is expected to be an array
+		while ( (node = elem[i++]) ) {
+			// Do not traverse comment nodes
+			ret += getText( node );
+		}
+	} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
+		// Use textContent for elements
+		// innerText usage removed for consistency of new lines (jQuery #11153)
+		if ( typeof elem.textContent === "string" ) {
+			return elem.textContent;
+		} else {
+			// Traverse its children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				ret += getText( elem );
+			}
+		}
+	} else if ( nodeType === 3 || nodeType === 4 ) {
+		return elem.nodeValue;
+	}
+	// Do not include comment or processing instruction nodes
+
+	return ret;
+};
+
+Expr = Sizzle.selectors = {
+
+	// Can be adjusted by the user
+	cacheLength: 50,
+
+	createPseudo: markFunction,
+
+	match: matchExpr,
+
+	attrHandle: {},
+
+	find: {},
+
+	relative: {
+		">": { dir: "parentNode", first: true },
+		" ": { dir: "parentNode" },
+		"+": { dir: "previousSibling", first: true },
+		"~": { dir: "previousSibling" }
+	},
+
+	preFilter: {
+		"ATTR": function( match ) {
+			match[1] = match[1].replace( runescape, funescape );
+
+			// Move the given value to match[3] whether quoted or unquoted
+			match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape );
+
+			if ( match[2] === "~=" ) {
+				match[3] = " " + match[3] + " ";
+			}
+
+			return match.slice( 0, 4 );
+		},
+
+		"CHILD": function( match ) {
+			/* matches from matchExpr["CHILD"]
+				1 type (only|nth|...)
+				2 what (child|of-type)
+				3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
+				4 xn-component of xn+y argument ([+-]?\d*n|)
+				5 sign of xn-component
+				6 x of xn-component
+				7 sign of y-component
+				8 y of y-component
+			*/
+			match[1] = match[1].toLowerCase();
+
+			if ( match[1].slice( 0, 3 ) === "nth" ) {
+				// nth-* requires argument
+				if ( !match[3] ) {
+					Sizzle.error( match[0] );
+				}
+
+				// numeric x and y parameters for Expr.filter.CHILD
+				// remember that false/true cast respectively to 0/1
+				match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
+				match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
+
+			// other types prohibit arguments
+			} else if ( match[3] ) {
+				Sizzle.error( match[0] );
+			}
+
+			return match;
+		},
+
+		"PSEUDO": function( match ) {
+			var excess,
+				unquoted = !match[6] && match[2];
+
+			if ( matchExpr["CHILD"].test( match[0] ) ) {
+				return null;
+			}
+
+			// Accept quoted arguments as-is
+			if ( match[3] ) {
+				match[2] = match[4] || match[5] || "";
+
+			// Strip excess characters from unquoted arguments
+			} else if ( unquoted && rpseudo.test( unquoted ) &&
+				// Get excess from tokenize (recursively)
+				(excess = tokenize( unquoted, true )) &&
+				// advance to the next closing parenthesis
+				(excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
+
+				// excess is a negative index
+				match[0] = match[0].slice( 0, excess );
+				match[2] = unquoted.slice( 0, excess );
+			}
+
+			// Return only captures needed by the pseudo filter method (type and argument)
+			return match.slice( 0, 3 );
+		}
+	},
+
+	filter: {
+
+		"TAG": function( nodeNameSelector ) {
+			var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
+			return nodeNameSelector === "*" ?
+				function() { return true; } :
+				function( elem ) {
+					return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
+				};
+		},
+
+		"CLASS": function( className ) {
+			var pattern = classCache[ className + " " ];
+
+			return pattern ||
+				(pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
+				classCache( className, function( elem ) {
+					return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" );
+				});
+		},
+
+		"ATTR": function( name, operator, check ) {
+			return function( elem ) {
+				var result = Sizzle.attr( elem, name );
+
+				if ( result == null ) {
+					return operator === "!=";
+				}
+				if ( !operator ) {
+					return true;
+				}
+
+				result += "";
+
+				return operator === "=" ? result === check :
+					operator === "!=" ? result !== check :
+					operator === "^=" ? check && result.indexOf( check ) === 0 :
+					operator === "*=" ? check && result.indexOf( check ) > -1 :
+					operator === "$=" ? check && result.slice( -check.length ) === check :
+					operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 :
+					operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
+					false;
+			};
+		},
+
+		"CHILD": function( type, what, argument, first, last ) {
+			var simple = type.slice( 0, 3 ) !== "nth",
+				forward = type.slice( -4 ) !== "last",
+				ofType = what === "of-type";
+
+			return first === 1 && last === 0 ?
+
+				// Shortcut for :nth-*(n)
+				function( elem ) {
+					return !!elem.parentNode;
+				} :
+
+				function( elem, context, xml ) {
+					var cache, outerCache, node, diff, nodeIndex, start,
+						dir = simple !== forward ? "nextSibling" : "previousSibling",
+						parent = elem.parentNode,
+						name = ofType && elem.nodeName.toLowerCase(),
+						useCache = !xml && !ofType;
+
+					if ( parent ) {
+
+						// :(first|last|only)-(child|of-type)
+						if ( simple ) {
+							while ( dir ) {
+								node = elem;
+								while ( (node = node[ dir ]) ) {
+									if ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) {
+										return false;
+									}
+								}
+								// Reverse direction for :only-* (if we haven't yet done so)
+								start = dir = type === "only" && !start && "nextSibling";
+							}
+							return true;
+						}
+
+						start = [ forward ? parent.firstChild : parent.lastChild ];
+
+						// non-xml :nth-child(...) stores cache data on `parent`
+						if ( forward && useCache ) {
+							// Seek `elem` from a previously-cached index
+							outerCache = parent[ expando ] || (parent[ expando ] = {});
+							cache = outerCache[ type ] || [];
+							nodeIndex = cache[0] === dirruns && cache[1];
+							diff = cache[0] === dirruns && cache[2];
+							node = nodeIndex && parent.childNodes[ nodeIndex ];
+
+							while ( (node = ++nodeIndex && node && node[ dir ] ||
+
+								// Fallback to seeking `elem` from the start
+								(diff = nodeIndex = 0) || start.pop()) ) {
+
+								// When found, cache indexes on `parent` and break
+								if ( node.nodeType === 1 && ++diff && node === elem ) {
+									outerCache[ type ] = [ dirruns, nodeIndex, diff ];
+									break;
+								}
+							}
+
+						// Use previously-cached element index if available
+						} else if ( useCache && (cache = (elem[ expando ] || (elem[ expando ] = {}))[ type ]) && cache[0] === dirruns ) {
+							diff = cache[1];
+
+						// xml :nth-child(...) or :nth-last-child(...) or :nth(-last)?-of-type(...)
+						} else {
+							// Use the same loop as above to seek `elem` from the start
+							while ( (node = ++nodeIndex && node && node[ dir ] ||
+								(diff = nodeIndex = 0) || start.pop()) ) {
+
+								if ( ( ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1 ) && ++diff ) {
+									// Cache the index of each encountered element
+									if ( useCache ) {
+										(node[ expando ] || (node[ expando ] = {}))[ type ] = [ dirruns, diff ];
+									}
+
+									if ( node === elem ) {
+										break;
+									}
+								}
+							}
+						}
+
+						// Incorporate the offset, then check against cycle size
+						diff -= last;
+						return diff === first || ( diff % first === 0 && diff / first >= 0 );
+					}
+				};
+		},
+
+		"PSEUDO": function( pseudo, argument ) {
+			// pseudo-class names are case-insensitive
+			// http://www.w3.org/TR/selectors/#pseudo-classes
+			// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
+			// Remember that setFilters inherits from pseudos
+			var args,
+				fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
+					Sizzle.error( "unsupported pseudo: " + pseudo );
+
+			// The user may use createPseudo to indicate that
+			// arguments are needed to create the filter function
+			// just as Sizzle does
+			if ( fn[ expando ] ) {
+				return fn( argument );
+			}
+
+			// But maintain support for old signatures
+			if ( fn.length > 1 ) {
+				args = [ pseudo, pseudo, "", argument ];
+				return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
+					markFunction(function( seed, matches ) {
+						var idx,
+							matched = fn( seed, argument ),
+							i = matched.length;
+						while ( i-- ) {
+							idx = indexOf( seed, matched[i] );
+							seed[ idx ] = !( matches[ idx ] = matched[i] );
+						}
+					}) :
+					function( elem ) {
+						return fn( elem, 0, args );
+					};
+			}
+
+			return fn;
+		}
+	},
+
+	pseudos: {
+		// Potentially complex pseudos
+		"not": markFunction(function( selector ) {
+			// Trim the selector passed to compile
+			// to avoid treating leading and trailing
+			// spaces as combinators
+			var input = [],
+				results = [],
+				matcher = compile( selector.replace( rtrim, "$1" ) );
+
+			return matcher[ expando ] ?
+				markFunction(function( seed, matches, context, xml ) {
+					var elem,
+						unmatched = matcher( seed, null, xml, [] ),
+						i = seed.length;
+
+					// Match elements unmatched by `matcher`
+					while ( i-- ) {
+						if ( (elem = unmatched[i]) ) {
+							seed[i] = !(matches[i] = elem);
+						}
+					}
+				}) :
+				function( elem, context, xml ) {
+					input[0] = elem;
+					matcher( input, null, xml, results );
+					// Don't keep the element (issue #299)
+					input[0] = null;
+					return !results.pop();
+				};
+		}),
+
+		"has": markFunction(function( selector ) {
+			return function( elem ) {
+				return Sizzle( selector, elem ).length > 0;
+			};
+		}),
+
+		"contains": markFunction(function( text ) {
+			text = text.replace( runescape, funescape );
+			return function( elem ) {
+				return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
+			};
+		}),
+
+		// "Whether an element is represented by a :lang() selector
+		// is based solely on the element's language value
+		// being equal to the identifier C,
+		// or beginning with the identifier C immediately followed by "-".
+		// The matching of C against the element's language value is performed case-insensitively.
+		// The identifier C does not have to be a valid language name."
+		// http://www.w3.org/TR/selectors/#lang-pseudo
+		"lang": markFunction( function( lang ) {
+			// lang value must be a valid identifier
+			if ( !ridentifier.test(lang || "") ) {
+				Sizzle.error( "unsupported lang: " + lang );
+			}
+			lang = lang.replace( runescape, funescape ).toLowerCase();
+			return function( elem ) {
+				var elemLang;
+				do {
+					if ( (elemLang = documentIsHTML ?
+						elem.lang :
+						elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) {
+
+						elemLang = elemLang.toLowerCase();
+						return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
+					}
+				} while ( (elem = elem.parentNode) && elem.nodeType === 1 );
+				return false;
+			};
+		}),
+
+		// Miscellaneous
+		"target": function( elem ) {
+			var hash = window.location && window.location.hash;
+			return hash && hash.slice( 1 ) === elem.id;
+		},
+
+		"root": function( elem ) {
+			return elem === docElem;
+		},
+
+		"focus": function( elem ) {
+			return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
+		},
+
+		// Boolean properties
+		"enabled": function( elem ) {
+			return elem.disabled === false;
+		},
+
+		"disabled": function( elem ) {
+			return elem.disabled === true;
+		},
+
+		"checked": function( elem ) {
+			// In CSS3, :checked should return both checked and selected elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			var nodeName = elem.nodeName.toLowerCase();
+			return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
+		},
+
+		"selected": function( elem ) {
+			// Accessing this property makes selected-by-default
+			// options in Safari work properly
+			if ( elem.parentNode ) {
+				elem.parentNode.selectedIndex;
+			}
+
+			return elem.selected === true;
+		},
+
+		// Contents
+		"empty": function( elem ) {
+			// http://www.w3.org/TR/selectors/#empty-pseudo
+			// :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
+			//   but not by others (comment: 8; processing instruction: 7; etc.)
+			// nodeType < 6 works because attributes (2) do not appear as children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				if ( elem.nodeType < 6 ) {
+					return false;
+				}
+			}
+			return true;
+		},
+
+		"parent": function( elem ) {
+			return !Expr.pseudos["empty"]( elem );
+		},
+
+		// Element/input types
+		"header": function( elem ) {
+			return rheader.test( elem.nodeName );
+		},
+
+		"input": function( elem ) {
+			return rinputs.test( elem.nodeName );
+		},
+
+		"button": function( elem ) {
+			var name = elem.nodeName.toLowerCase();
+			return name === "input" && elem.type === "button" || name === "button";
+		},
+
+		"text": function( elem ) {
+			var attr;
+			return elem.nodeName.toLowerCase() === "input" &&
+				elem.type === "text" &&
+
+				// Support: IE<8
+				// New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
+				( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" );
+		},
+
+		// Position-in-collection
+		"first": createPositionalPseudo(function() {
+			return [ 0 ];
+		}),
+
+		"last": createPositionalPseudo(function( matchIndexes, length ) {
+			return [ length - 1 ];
+		}),
+
+		"eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			return [ argument < 0 ? argument + length : argument ];
+		}),
+
+		"even": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 0;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"odd": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 1;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ? argument + length : argument;
+			for ( ; --i >= 0; ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ? argument + length : argument;
+			for ( ; ++i < length; ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		})
+	}
+};
+
+Expr.pseudos["nth"] = Expr.pseudos["eq"];
+
+// Add button/input type pseudos
+for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
+	Expr.pseudos[ i ] = createInputPseudo( i );
+}
+for ( i in { submit: true, reset: true } ) {
+	Expr.pseudos[ i ] = createButtonPseudo( i );
+}
+
+// Easy API for creating new setFilters
+function setFilters() {}
+setFilters.prototype = Expr.filters = Expr.pseudos;
+Expr.setFilters = new setFilters();
+
+tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
+	var matched, match, tokens, type,
+		soFar, groups, preFilters,
+		cached = tokenCache[ selector + " " ];
+
+	if ( cached ) {
+		return parseOnly ? 0 : cached.slice( 0 );
+	}
+
+	soFar = selector;
+	groups = [];
+	preFilters = Expr.preFilter;
+
+	while ( soFar ) {
+
+		// Comma and first run
+		if ( !matched || (match = rcomma.exec( soFar )) ) {
+			if ( match ) {
+				// Don't consume trailing commas as valid
+				soFar = soFar.slice( match[0].length ) || soFar;
+			}
+			groups.push( (tokens = []) );
+		}
+
+		matched = false;
+
+		// Combinators
+		if ( (match = rcombinators.exec( soFar )) ) {
+			matched = match.shift();
+			tokens.push({
+				value: matched,
+				// Cast descendant combinators to space
+				type: match[0].replace( rtrim, " " )
+			});
+			soFar = soFar.slice( matched.length );
+		}
+
+		// Filters
+		for ( type in Expr.filter ) {
+			if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
+				(match = preFilters[ type ]( match ))) ) {
+				matched = match.shift();
+				tokens.push({
+					value: matched,
+					type: type,
+					matches: match
+				});
+				soFar = soFar.slice( matched.length );
+			}
+		}
+
+		if ( !matched ) {
+			break;
+		}
+	}
+
+	// Return the length of the invalid excess
+	// if we're just parsing
+	// Otherwise, throw an error or return tokens
+	return parseOnly ?
+		soFar.length :
+		soFar ?
+			Sizzle.error( selector ) :
+			// Cache the tokens
+			tokenCache( selector, groups ).slice( 0 );
+};
+
+function toSelector( tokens ) {
+	var i = 0,
+		len = tokens.length,
+		selector = "";
+	for ( ; i < len; i++ ) {
+		selector += tokens[i].value;
+	}
+	return selector;
+}
+
+function addCombinator( matcher, combinator, base ) {
+	var dir = combinator.dir,
+		checkNonElements = base && dir === "parentNode",
+		doneName = done++;
+
+	return combinator.first ?
+		// Check against closest ancestor/preceding element
+		function( elem, context, xml ) {
+			while ( (elem = elem[ dir ]) ) {
+				if ( elem.nodeType === 1 || checkNonElements ) {
+					return matcher( elem, context, xml );
+				}
+			}
+		} :
+
+		// Check against all ancestor/preceding elements
+		function( elem, context, xml ) {
+			var oldCache, outerCache,
+				newCache = [ dirruns, doneName ];
+
+			// We can't set arbitrary data on XML nodes, so they don't benefit from dir caching
+			if ( xml ) {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						if ( matcher( elem, context, xml ) ) {
+							return true;
+						}
+					}
+				}
+			} else {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						outerCache = elem[ expando ] || (elem[ expando ] = {});
+						if ( (oldCache = outerCache[ dir ]) &&
+							oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
+
+							// Assign to newCache so results back-propagate to previous elements
+							return (newCache[ 2 ] = oldCache[ 2 ]);
+						} else {
+							// Reuse newcache so results back-propagate to previous elements
+							outerCache[ dir ] = newCache;
+
+							// A match means we're done; a fail means we have to keep checking
+							if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
+								return true;
+							}
+						}
+					}
+				}
+			}
+		};
+}
+
+function elementMatcher( matchers ) {
+	return matchers.length > 1 ?
+		function( elem, context, xml ) {
+			var i = matchers.length;
+			while ( i-- ) {
+				if ( !matchers[i]( elem, context, xml ) ) {
+					return false;
+				}
+			}
+			return true;
+		} :
+		matchers[0];
+}
+
+function multipleContexts( selector, contexts, results ) {
+	var i = 0,
+		len = contexts.length;
+	for ( ; i < len; i++ ) {
+		Sizzle( selector, contexts[i], results );
+	}
+	return results;
+}
+
+function condense( unmatched, map, filter, context, xml ) {
+	var elem,
+		newUnmatched = [],
+		i = 0,
+		len = unmatched.length,
+		mapped = map != null;
+
+	for ( ; i < len; i++ ) {
+		if ( (elem = unmatched[i]) ) {
+			if ( !filter || filter( elem, context, xml ) ) {
+				newUnmatched.push( elem );
+				if ( mapped ) {
+					map.push( i );
+				}
+			}
+		}
+	}
+
+	return newUnmatched;
+}
+
+function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
+	if ( postFilter && !postFilter[ expando ] ) {
+		postFilter = setMatcher( postFilter );
+	}
+	if ( postFinder && !postFinder[ expando ] ) {
+		postFinder = setMatcher( postFinder, postSelector );
+	}
+	return markFunction(function( seed, results, context, xml ) {
+		var temp, i, elem,
+			preMap = [],
+			postMap = [],
+			preexisting = results.length,
+
+			// Get initial elements from seed or context
+			elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
+
+			// Prefilter to get matcher input, preserving a map for seed-results synchronization
+			matcherIn = preFilter && ( seed || !selector ) ?
+				condense( elems, preMap, preFilter, context, xml ) :
+				elems,
+
+			matcherOut = matcher ?
+				// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
+				postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
+
+					// ...intermediate processing is necessary
+					[] :
+
+					// ...otherwise use results directly
+					results :
+				matcherIn;
+
+		// Find primary matches
+		if ( matcher ) {
+			matcher( matcherIn, matcherOut, context, xml );
+		}
+
+		// Apply postFilter
+		if ( postFilter ) {
+			temp = condense( matcherOut, postMap );
+			postFilter( temp, [], context, xml );
+
+			// Un-match failing elements by moving them back to matcherIn
+			i = temp.length;
+			while ( i-- ) {
+				if ( (elem = temp[i]) ) {
+					matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
+				}
+			}
+		}
+
+		if ( seed ) {
+			if ( postFinder || preFilter ) {
+				if ( postFinder ) {
+					// Get the final matcherOut by condensing this intermediate into postFinder contexts
+					temp = [];
+					i = matcherOut.length;
+					while ( i-- ) {
+						if ( (elem = matcherOut[i]) ) {
+							// Restore matcherIn since elem is not yet a final match
+							temp.push( (matcherIn[i] = elem) );
+						}
+					}
+					postFinder( null, (matcherOut = []), temp, xml );
+				}
+
+				// Move matched elements from seed to results to keep them synchronized
+				i = matcherOut.length;
+				while ( i-- ) {
+					if ( (elem = matcherOut[i]) &&
+						(temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) {
+
+						seed[temp] = !(results[temp] = elem);
+					}
+				}
+			}
+
+		// Add elements to results, through postFinder if defined
+		} else {
+			matcherOut = condense(
+				matcherOut === results ?
+					matcherOut.splice( preexisting, matcherOut.length ) :
+					matcherOut
+			);
+			if ( postFinder ) {
+				postFinder( null, results, matcherOut, xml );
+			} else {
+				push.apply( results, matcherOut );
+			}
+		}
+	});
+}
+
+function matcherFromTokens( tokens ) {
+	var checkContext, matcher, j,
+		len = tokens.length,
+		leadingRelative = Expr.relative[ tokens[0].type ],
+		implicitRelative = leadingRelative || Expr.relative[" "],
+		i = leadingRelative ? 1 : 0,
+
+		// The foundational matcher ensures that elements are reachable from top-level context(s)
+		matchContext = addCombinator( function( elem ) {
+			return elem === checkContext;
+		}, implicitRelative, true ),
+		matchAnyContext = addCombinator( function( elem ) {
+			return indexOf( checkContext, elem ) > -1;
+		}, implicitRelative, true ),
+		matchers = [ function( elem, context, xml ) {
+			var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
+				(checkContext = context).nodeType ?
+					matchContext( elem, context, xml ) :
+					matchAnyContext( elem, context, xml ) );
+			// Avoid hanging onto element (issue #299)
+			checkContext = null;
+			return ret;
+		} ];
+
+	for ( ; i < len; i++ ) {
+		if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
+			matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
+		} else {
+			matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
+
+			// Return special upon seeing a positional matcher
+			if ( matcher[ expando ] ) {
+				// Find the next relative operator (if any) for proper handling
+				j = ++i;
+				for ( ; j < len; j++ ) {
+					if ( Expr.relative[ tokens[j].type ] ) {
+						break;
+					}
+				}
+				return setMatcher(
+					i > 1 && elementMatcher( matchers ),
+					i > 1 && toSelector(
+						// If the preceding token was a descendant combinator, insert an implicit any-element `*`
+						tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" })
+					).replace( rtrim, "$1" ),
+					matcher,
+					i < j && matcherFromTokens( tokens.slice( i, j ) ),
+					j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
+					j < len && toSelector( tokens )
+				);
+			}
+			matchers.push( matcher );
+		}
+	}
+
+	return elementMatcher( matchers );
+}
+
+function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
+	var bySet = setMatchers.length > 0,
+		byElement = elementMatchers.length > 0,
+		superMatcher = function( seed, context, xml, results, outermost ) {
+			var elem, j, matcher,
+				matchedCount = 0,
+				i = "0",
+				unmatched = seed && [],
+				setMatched = [],
+				contextBackup = outermostContext,
+				// We must always have either seed elements or outermost context
+				elems = seed || byElement && Expr.find["TAG"]( "*", outermost ),
+				// Use integer dirruns iff this is the outermost matcher
+				dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),
+				len = elems.length;
+
+			if ( outermost ) {
+				outermostContext = context !== document && context;
+			}
+
+			// Add elements passing elementMatchers directly to results
+			// Keep `i` a string if there are no elements so `matchedCount` will be "00" below
+			// Support: IE<9, Safari
+			// Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
+			for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
+				if ( byElement && elem ) {
+					j = 0;
+					while ( (matcher = elementMatchers[j++]) ) {
+						if ( matcher( elem, context, xml ) ) {
+							results.push( elem );
+							break;
+						}
+					}
+					if ( outermost ) {
+						dirruns = dirrunsUnique;
+					}
+				}
+
+				// Track unmatched elements for set filters
+				if ( bySet ) {
+					// They will have gone through all possible matchers
+					if ( (elem = !matcher && elem) ) {
+						matchedCount--;
+					}
+
+					// Lengthen the array for every element, matched or not
+					if ( seed ) {
+						unmatched.push( elem );
+					}
+				}
+			}
+
+			// Apply set filters to unmatched elements
+			matchedCount += i;
+			if ( bySet && i !== matchedCount ) {
+				j = 0;
+				while ( (matcher = setMatchers[j++]) ) {
+					matcher( unmatched, setMatched, context, xml );
+				}
+
+				if ( seed ) {
+					// Reintegrate element matches to eliminate the need for sorting
+					if ( matchedCount > 0 ) {
+						while ( i-- ) {
+							if ( !(unmatched[i] || setMatched[i]) ) {
+								setMatched[i] = pop.call( results );
+							}
+						}
+					}
+
+					// Discard index placeholder values to get only actual matches
+					setMatched = condense( setMatched );
+				}
+
+				// Add matches to results
+				push.apply( results, setMatched );
+
+				// Seedless set matches succeeding multiple successful matchers stipulate sorting
+				if ( outermost && !seed && setMatched.length > 0 &&
+					( matchedCount + setMatchers.length ) > 1 ) {
+
+					Sizzle.uniqueSort( results );
+				}
+			}
+
+			// Override manipulation of globals by nested matchers
+			if ( outermost ) {
+				dirruns = dirrunsUnique;
+				outermostContext = contextBackup;
+			}
+
+			return unmatched;
+		};
+
+	return bySet ?
+		markFunction( superMatcher ) :
+		superMatcher;
+}
+
+compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
+	var i,
+		setMatchers = [],
+		elementMatchers = [],
+		cached = compilerCache[ selector + " " ];
+
+	if ( !cached ) {
+		// Generate a function of recursive functions that can be used to check each element
+		if ( !match ) {
+			match = tokenize( selector );
+		}
+		i = match.length;
+		while ( i-- ) {
+			cached = matcherFromTokens( match[i] );
+			if ( cached[ expando ] ) {
+				setMatchers.push( cached );
+			} else {
+				elementMatchers.push( cached );
+			}
+		}
+
+		// Cache the compiled function
+		cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
+
+		// Save selector and tokenization
+		cached.selector = selector;
+	}
+	return cached;
+};
+
+/**
+ * A low-level selection function that works with Sizzle's compiled
+ *  selector functions
+ * @param {String|Function} selector A selector or a pre-compiled
+ *  selector function built with Sizzle.compile
+ * @param {Element} context
+ * @param {Array} [results]
+ * @param {Array} [seed] A set of elements to match against
+ */
+select = Sizzle.select = function( selector, context, results, seed ) {
+	var i, tokens, token, type, find,
+		compiled = typeof selector === "function" && selector,
+		match = !seed && tokenize( (selector = compiled.selector || selector) );
+
+	results = results || [];
+
+	// Try to minimize operations if there is no seed and only one group
+	if ( match.length === 1 ) {
+
+		// Take a shortcut and set the context if the root selector is an ID
+		tokens = match[0] = match[0].slice( 0 );
+		if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
+				support.getById && context.nodeType === 9 && documentIsHTML &&
+				Expr.relative[ tokens[1].type ] ) {
+
+			context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
+			if ( !context ) {
+				return results;
+
+			// Precompiled matchers will still verify ancestry, so step up a level
+			} else if ( compiled ) {
+				context = context.parentNode;
+			}
+
+			selector = selector.slice( tokens.shift().value.length );
+		}
+
+		// Fetch a seed set for right-to-left matching
+		i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
+		while ( i-- ) {
+			token = tokens[i];
+
+			// Abort if we hit a combinator
+			if ( Expr.relative[ (type = token.type) ] ) {
+				break;
+			}
+			if ( (find = Expr.find[ type ]) ) {
+				// Search, expanding context for leading sibling combinators
+				if ( (seed = find(
+					token.matches[0].replace( runescape, funescape ),
+					rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
+				)) ) {
+
+					// If seed is empty or no tokens remain, we can return early
+					tokens.splice( i, 1 );
+					selector = seed.length && toSelector( tokens );
+					if ( !selector ) {
+						push.apply( results, seed );
+						return results;
+					}
+
+					break;
+				}
+			}
+		}
+	}
+
+	// Compile and execute a filtering function if one is not provided
+	// Provide `match` to avoid retokenization if we modified the selector above
+	( compiled || compile( selector, match ) )(
+		seed,
+		context,
+		!documentIsHTML,
+		results,
+		rsibling.test( selector ) && testContext( context.parentNode ) || context
+	);
+	return results;
+};
+
+// One-time assignments
+
+// Sort stability
+support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
+
+// Support: Chrome 14-35+
+// Always assume duplicates if they aren't passed to the comparison function
+support.detectDuplicates = !!hasDuplicate;
+
+// Initialize against the default document
+setDocument();
+
+// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
+// Detached nodes confoundingly follow *each other*
+support.sortDetached = assert(function( div1 ) {
+	// Should return 1, but returns 4 (following)
+	return div1.compareDocumentPosition( document.createElement("div") ) & 1;
+});
+
+// Support: IE<8
+// Prevent attribute/property "interpolation"
+// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !assert(function( div ) {
+	div.innerHTML = "<a href='#'></a>";
+	return div.firstChild.getAttribute("href") === "#" ;
+}) ) {
+	addHandle( "type|href|height|width", function( elem, name, isXML ) {
+		if ( !isXML ) {
+			return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
+		}
+	});
+}
+
+// Support: IE<9
+// Use defaultValue in place of getAttribute("value")
+if ( !support.attributes || !assert(function( div ) {
+	div.innerHTML = "<input/>";
+	div.firstChild.setAttribute( "value", "" );
+	return div.firstChild.getAttribute( "value" ) === "";
+}) ) {
+	addHandle( "value", function( elem, name, isXML ) {
+		if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
+			return elem.defaultValue;
+		}
+	});
+}
+
+// Support: IE<9
+// Use getAttributeNode to fetch booleans when getAttribute lies
+if ( !assert(function( div ) {
+	return div.getAttribute("disabled") == null;
+}) ) {
+	addHandle( booleans, function( elem, name, isXML ) {
+		var val;
+		if ( !isXML ) {
+			return elem[ name ] === true ? name.toLowerCase() :
+					(val = elem.getAttributeNode( name )) && val.specified ?
+					val.value :
+				null;
+		}
+	});
+}
+
+return Sizzle;
+
+})( window );
+
+
+
+jQuery.find = Sizzle;
+jQuery.expr = Sizzle.selectors;
+jQuery.expr[":"] = jQuery.expr.pseudos;
+jQuery.unique = Sizzle.uniqueSort;
+jQuery.text = Sizzle.getText;
+jQuery.isXMLDoc = Sizzle.isXML;
+jQuery.contains = Sizzle.contains;
+
+
+
+var rneedsContext = jQuery.expr.match.needsContext;
+
+var rsingleTag = (/^<(\w+)\s*\/?>(?:<\/\1>|)$/);
+
+
+
+var risSimple = /^.[^:#\[\.,]*$/;
+
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, not ) {
+	if ( jQuery.isFunction( qualifier ) ) {
+		return jQuery.grep( elements, function( elem, i ) {
+			/* jshint -W018 */
+			return !!qualifier.call( elem, i, elem ) !== not;
+		});
+
+	}
+
+	if ( qualifier.nodeType ) {
+		return jQuery.grep( elements, function( elem ) {
+			return ( elem === qualifier ) !== not;
+		});
+
+	}
+
+	if ( typeof qualifier === "string" ) {
+		if ( risSimple.test( qualifier ) ) {
+			return jQuery.filter( qualifier, elements, not );
+		}
+
+		qualifier = jQuery.filter( qualifier, elements );
+	}
+
+	return jQuery.grep( elements, function( elem ) {
+		return ( jQuery.inArray( elem, qualifier ) >= 0 ) !== not;
+	});
+}
+
+jQuery.filter = function( expr, elems, not ) {
+	var elem = elems[ 0 ];
+
+	if ( not ) {
+		expr = ":not(" + expr + ")";
+	}
+
+	return elems.length === 1 && elem.nodeType === 1 ?
+		jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [] :
+		jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
+			return elem.nodeType === 1;
+		}));
+};
+
+jQuery.fn.extend({
+	find: function( selector ) {
+		var i,
+			ret = [],
+			self = this,
+			len = self.length;
+
+		if ( typeof selector !== "string" ) {
+			return this.pushStack( jQuery( selector ).filter(function() {
+				for ( i = 0; i < len; i++ ) {
+					if ( jQuery.contains( self[ i ], this ) ) {
+						return true;
+					}
+				}
+			}) );
+		}
+
+		for ( i = 0; i < len; i++ ) {
+			jQuery.find( selector, self[ i ], ret );
+		}
+
+		// Needed because $( selector, context ) becomes $( context ).find( selector )
+		ret = this.pushStack( len > 1 ? jQuery.unique( ret ) : ret );
+		ret.selector = this.selector ? this.selector + " " + selector : selector;
+		return ret;
+	},
+	filter: function( selector ) {
+		return this.pushStack( winnow(this, selector || [], false) );
+	},
+	not: function( selector ) {
+		return this.pushStack( winnow(this, selector || [], true) );
+	},
+	is: function( selector ) {
+		return !!winnow(
+			this,
+
+			// If this is a positional/relative selector, check membership in the returned set
+			// so $("p:first").is("p:last") won't return true for a doc with two "p".
+			typeof selector === "string" && rneedsContext.test( selector ) ?
+				jQuery( selector ) :
+				selector || [],
+			false
+		).length;
+	}
+});
+
+
+// Initialize a jQuery object
+
+
+// A central reference to the root jQuery(document)
+var rootjQuery,
+
+	// Use the correct document accordingly with window argument (sandbox)
+	document = window.document,
+
+	// A simple way to check for HTML strings
+	// Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
+	// Strict HTML recognition (#11290: must start with <)
+	rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,
+
+	init = jQuery.fn.init = function( selector, context ) {
+		var match, elem;
+
+		// HANDLE: $(""), $(null), $(undefined), $(false)
+		if ( !selector ) {
+			return this;
+		}
+
+		// Handle HTML strings
+		if ( typeof selector === "string" ) {
+			if ( selector.charAt(0) === "<" && selector.charAt( selector.length - 1 ) === ">" && selector.length >= 3 ) {
+				// Assume that strings that start and end with <> are HTML and skip the regex check
+				match = [ null, selector, null ];
+
+			} else {
+				match = rquickExpr.exec( selector );
+			}
+
+			// Match html or make sure no context is specified for #id
+			if ( match && (match[1] || !context) ) {
+
+				// HANDLE: $(html) -> $(array)
+				if ( match[1] ) {
+					context = context instanceof jQuery ? context[0] : context;
+
+					// scripts is true for back-compat
+					// Intentionally let the error be thrown if parseHTML is not present
+					jQuery.merge( this, jQuery.parseHTML(
+						match[1],
+						context && context.nodeType ? context.ownerDocument || context : document,
+						true
+					) );
+
+					// HANDLE: $(html, props)
+					if ( rsingleTag.test( match[1] ) && jQuery.isPlainObject( context ) ) {
+						for ( match in context ) {
+							// Properties of context are called as methods if possible
+							if ( jQuery.isFunction( this[ match ] ) ) {
+								this[ match ]( context[ match ] );
+
+							// ...and otherwise set as attributes
+							} else {
+								this.attr( match, context[ match ] );
+							}
+						}
+					}
+
+					return this;
+
+				// HANDLE: $(#id)
+				} else {
+					elem = document.getElementById( match[2] );
+
+					// Check parentNode to catch when Blackberry 4.6 returns
+					// nodes that are no longer in the document #6963
+					if ( elem && elem.parentNode ) {
+						// Handle the case where IE and Opera return items
+						// by name instead of ID
+						if ( elem.id !== match[2] ) {
+							return rootjQuery.find( selector );
+						}
+
+						// Otherwise, we inject the element directly into the jQuery object
+						this.length = 1;
+						this[0] = elem;
+					}
+
+					this.context = document;
+					this.selector = selector;
+					return this;
+				}
+
+			// HANDLE: $(expr, $(...))
+			} else if ( !context || context.jquery ) {
+				return ( context || rootjQuery ).find( selector );
+
+			// HANDLE: $(expr, context)
+			// (which is just equivalent to: $(context).find(expr)
+			} else {
+				return this.constructor( context ).find( selector );
+			}
+
+		// HANDLE: $(DOMElement)
+		} else if ( selector.nodeType ) {
+			this.context = this[0] = selector;
+			this.length = 1;
+			return this;
+
+		// HANDLE: $(function)
+		// Shortcut for document ready
+		} else if ( jQuery.isFunction( selector ) ) {
+			return typeof rootjQuery.ready !== "undefined" ?
+				rootjQuery.ready( selector ) :
+				// Execute immediately if ready is not present
+				selector( jQuery );
+		}
+
+		if ( selector.selector !== undefined ) {
+			this.selector = selector.selector;
+			this.context = selector.context;
+		}
+
+		return jQuery.makeArray( selector, this );
+	};
+
+// Give the init function the jQuery prototype for later instantiation
+init.prototype = jQuery.fn;
+
+// Initialize central reference
+rootjQuery = jQuery( document );
+
+
+var rparentsprev = /^(?:parents|prev(?:Until|All))/,
+	// methods guaranteed to produce a unique set when starting from a unique set
+	guaranteedUnique = {
+		children: true,
+		contents: true,
+		next: true,
+		prev: true
+	};
+
+jQuery.extend({
+	dir: function( elem, dir, until ) {
+		var matched = [],
+			cur = elem[ dir ];
+
+		while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
+			if ( cur.nodeType === 1 ) {
+				matched.push( cur );
+			}
+			cur = cur[dir];
+		}
+		return matched;
+	},
+
+	sibling: function( n, elem ) {
+		var r = [];
+
+		for ( ; n; n = n.nextSibling ) {
+			if ( n.nodeType === 1 && n !== elem ) {
+				r.push( n );
+			}
+		}
+
+		return r;
+	}
+});
+
+jQuery.fn.extend({
+	has: function( target ) {
+		var i,
+			targets = jQuery( target, this ),
+			len = targets.length;
+
+		return this.filter(function() {
+			for ( i = 0; i < len; i++ ) {
+				if ( jQuery.contains( this, targets[i] ) ) {
+					return true;
+				}
+			}
+		});
+	},
+
+	closest: function( selectors, context ) {
+		var cur,
+			i = 0,
+			l = this.length,
+			matched = [],
+			pos = rneedsContext.test( selectors ) || typeof selectors !== "string" ?
+				jQuery( selectors, context || this.context ) :
+				0;
+
+		for ( ; i < l; i++ ) {
+			for ( cur = this[i]; cur && cur !== context; cur = cur.parentNode ) {
+				// Always skip document fragments
+				if ( cur.nodeType < 11 && (pos ?
+					pos.index(cur) > -1 :
+
+					// Don't pass non-elements to Sizzle
+					cur.nodeType === 1 &&
+						jQuery.find.matchesSelector(cur, selectors)) ) {
+
+					matched.push( cur );
+					break;
+				}
+			}
+		}
+
+		return this.pushStack( matched.length > 1 ? jQuery.unique( matched ) : matched );
+	},
+
+	// Determine the position of an element within
+	// the matched set of elements
+	index: function( elem ) {
+
+		// No argument, return index in parent
+		if ( !elem ) {
+			return ( this[0] && this[0].parentNode ) ? this.first().prevAll().length : -1;
+		}
+
+		// index in selector
+		if ( typeof elem === "string" ) {
+			return jQuery.inArray( this[0], jQuery( elem ) );
+		}
+
+		// Locate the position of the desired element
+		return jQuery.inArray(
+			// If it receives a jQuery object, the first element is used
+			elem.jquery ? elem[0] : elem, this );
+	},
+
+	add: function( selector, context ) {
+		return this.pushStack(
+			jQuery.unique(
+				jQuery.merge( this.get(), jQuery( selector, context ) )
+			)
+		);
+	},
+
+	addBack: function( selector ) {
+		return this.add( selector == null ?
+			this.prevObject : this.prevObject.filter(selector)
+		);
+	}
+});
+
+function sibling( cur, dir ) {
+	do {
+		cur = cur[ dir ];
+	} while ( cur && cur.nodeType !== 1 );
+
+	return cur;
+}
+
+jQuery.each({
+	parent: function( elem ) {
+		var parent = elem.parentNode;
+		return parent && parent.nodeType !== 11 ? parent : null;
+	},
+	parents: function( elem ) {
+		return jQuery.dir( elem, "parentNode" );
+	},
+	parentsUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "parentNode", until );
+	},
+	next: function( elem ) {
+		return sibling( elem, "nextSibling" );
+	},
+	prev: function( elem ) {
+		return sibling( elem, "previousSibling" );
+	},
+	nextAll: function( elem ) {
+		return jQuery.dir( elem, "nextSibling" );
+	},
+	prevAll: function( elem ) {
+		return jQuery.dir( elem, "previousSibling" );
+	},
+	nextUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "nextSibling", until );
+	},
+	prevUntil: function( elem, i, until ) {
+		return jQuery.dir( elem, "previousSibling", until );
+	},
+	siblings: function( elem ) {
+		return jQuery.sibling( ( elem.parentNode || {} ).firstChild, elem );
+	},
+	children: function( elem ) {
+		return jQuery.sibling( elem.firstChild );
+	},
+	contents: function( elem ) {
+		return jQuery.nodeName( elem, "iframe" ) ?
+			elem.contentDocument || elem.contentWindow.document :
+			jQuery.merge( [], elem.childNodes );
+	}
+}, function( name, fn ) {
+	jQuery.fn[ name ] = function( until, selector ) {
+		var ret = jQuery.map( this, fn, until );
+
+		if ( name.slice( -5 ) !== "Until" ) {
+			selector = until;
+		}
+
+		if ( selector && typeof selector === "string" ) {
+			ret = jQuery.filter( selector, ret );
+		}
+
+		if ( this.length > 1 ) {
+			// Remove duplicates
+			if ( !guaranteedUnique[ name ] ) {
+				ret = jQuery.unique( ret );
+			}
+
+			// Reverse order for parents* and prev-derivatives
+			if ( rparentsprev.test( name ) ) {
+				ret = ret.reverse();
+			}
+		}
+
+		return this.pushStack( ret );
+	};
+});
+var rnotwhite = (/\S+/g);
+
+
+
+// String to Object options format cache
+var optionsCache = {};
+
+// Convert String-formatted options into Object-formatted ones and store in cache
+function createOptions( options ) {
+	var object = optionsCache[ options ] = {};
+	jQuery.each( options.match( rnotwhite ) || [], function( _, flag ) {
+		object[ flag ] = true;
+	});
+	return object;
+}
+
+/*
+ * Create a callback list using the following parameters:
+ *
+ *	options: an optional list of space-separated options that will change how
+ *			the callback list behaves or a more traditional option object
+ *
+ * By default a callback list will act like an event callback list and can be
+ * "fired" multiple times.
+ *
+ * Possible options:
+ *
+ *	once:			will ensure the callback list can only be fired once (like a Deferred)
+ *
+ *	memory:			will keep track of previous values and will call any callback added
+ *					after the list has been fired right away with the latest "memorized"
+ *					values (like a Deferred)
+ *
+ *	unique:			will ensure a callback can only be added once (no duplicate in the list)
+ *
+ *	stopOnFalse:	interrupt callings when a callback returns false
+ *
+ */
+jQuery.Callbacks = function( options ) {
+
+	// Convert options from String-formatted to Object-formatted if needed
+	// (we check in cache first)
+	options = typeof options === "string" ?
+		( optionsCache[ options ] || createOptions( options ) ) :
+		jQuery.extend( {}, options );
+
+	var // Flag to know if list is currently firing
+		firing,
+		// Last fire value (for non-forgettable lists)
+		memory,
+		// Flag to know if list was already fired
+		fired,
+		// End of the loop when firing
+		firingLength,
+		// Index of currently firing callback (modified by remove if needed)
+		firingIndex,
+		// First callback to fire (used internally by add and fireWith)
+		firingStart,
+		// Actual callback list
+		list = [],
+		// Stack of fire calls for repeatable lists
+		stack = !options.once && [],
+		// Fire callbacks
+		fire = function( data ) {
+			memory = options.memory && data;
+			fired = true;
+			firingIndex = firingStart || 0;
+			firingStart = 0;
+			firingLength = list.length;
+			firing = true;
+			for ( ; list && firingIndex < firingLength; firingIndex++ ) {
+				if ( list[ firingIndex ].apply( data[ 0 ], data[ 1 ] ) === false && options.stopOnFalse ) {
+					memory = false; // To prevent further calls using add
+					break;
+				}
+			}
+			firing = false;
+			if ( list ) {
+				if ( stack ) {
+					if ( stack.length ) {
+						fire( stack.shift() );
+					}
+				} else if ( memory ) {
+					list = [];
+				} else {
+					self.disable();
+				}
+			}
+		},
+		// Actual Callbacks object
+		self = {
+			// Add a callback or a collection of callbacks to the list
+			add: function() {
+				if ( list ) {
+					// First, we save the current length
+					var start = list.length;
+					(function add( args ) {
+						jQuery.each( args, function( _, arg ) {
+							var type = jQuery.type( arg );
+							if ( type === "function" ) {
+								if ( !options.unique || !self.has( arg ) ) {
+									list.push( arg );
+								}
+							} else if ( arg && arg.length && type !== "string" ) {
+								// Inspect recursively
+								add( arg );
+							}
+						});
+					})( arguments );
+					// Do we need to add the callbacks to the
+					// current firing batch?
+					if ( firing ) {
+						firingLength = list.length;
+					// With memory, if we're not firing then
+					// we should call right away
+					} else if ( memory ) {
+						firingStart = start;
+						fire( memory );
+					}
+				}
+				return this;
+			},
+			// Remove a callback from the list
+			remove: function() {
+				if ( list ) {
+					jQuery.each( arguments, function( _, arg ) {
+						var index;
+						while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
+							list.splice( index, 1 );
+							// Handle firing indexes
+							if ( firing ) {
+								if ( index <= firingLength ) {
+									firingLength--;
+								}
+								if ( index <= firingIndex ) {
+									firingIndex--;
+								}
+							}
+						}
+					});
+				}
+				return this;
+			},
+			// Check if a given callback is in the list.
+			// If no argument is given, return whether or not list has callbacks attached.
+			has: function( fn ) {
+				return fn ? jQuery.inArray( fn, list ) > -1 : !!( list && list.length );
+			},
+			// Remove all callbacks from the list
+			empty: function() {
+				list = [];
+				firingLength = 0;
+				return this;
+			},
+			// Have the list do nothing anymore
+			disable: function() {
+				list = stack = memory = undefined;
+				return this;
+			},
+			// Is it disabled?
+			disabled: function() {
+				return !list;
+			},
+			// Lock the list in its current state
+			lock: function() {
+				stack = undefined;
+				if ( !memory ) {
+					self.disable();
+				}
+				return this;
+			},
+			// Is it locked?
+			locked: function() {
+				return !stack;
+			},
+			// Call all callbacks with the given context and arguments
+			fireWith: function( context, args ) {
+				if ( list && ( !fired || stack ) ) {
+					args = args || [];
+					args = [ context, args.slice ? args.slice() : args ];
+					if ( firing ) {
+						stack.push( args );
+					} else {
+						fire( args );
+					}
+				}
+				return this;
+			},
+			// Call all the callbacks with the given arguments
+			fire: function() {
+				self.fireWith( this, arguments );
+				return this;
+			},
+			// To know if the callbacks have already been called at least once
+			fired: function() {
+				return !!fired;
+			}
+		};
+
+	return self;
+};
+
+
+jQuery.extend({
+
+	Deferred: function( func ) {
+		var tuples = [
+				// action, add listener, listener list, final state
+				[ "resolve", "done", jQuery.Callbacks("once memory"), "resolved" ],
+				[ "reject", "fail", jQuery.Callbacks("once memory"), "rejected" ],
+				[ "notify", "progress", jQuery.Callbacks("memory") ]
+			],
+			state = "pending",
+			promise = {
+				state: function() {
+					return state;
+				},
+				always: function() {
+					deferred.done( arguments ).fail( arguments );
+					return this;
+				},
+				then: function( /* fnDone, fnFail, fnProgress */ ) {
+					var fns = arguments;
+					return jQuery.Deferred(function( newDefer ) {
+						jQuery.each( tuples, function( i, tuple ) {
+							var fn = jQuery.isFunction( fns[ i ] ) && fns[ i ];
+							// deferred[ done | fail | progress ] for forwarding actions to newDefer
+							deferred[ tuple[1] ](function() {
+								var returned = fn && fn.apply( this, arguments );
+								if ( returned && jQuery.isFunction( returned.promise ) ) {
+									returned.promise()
+										.done( newDefer.resolve )
+										.fail( newDefer.reject )
+										.progress( newDefer.notify );
+								} else {
+									newDefer[ tuple[ 0 ] + "With" ]( this === promise ? newDefer.promise() : this, fn ? [ returned ] : arguments );
+								}
+							});
+						});
+						fns = null;
+					}).promise();
+				},
+				// Get a promise for this deferred
+				// If obj is provided, the promise aspect is added to the object
+				promise: function( obj ) {
+					return obj != null ? jQuery.extend( obj, promise ) : promise;
+				}
+			},
+			deferred = {};
+
+		// Keep pipe for back-compat
+		promise.pipe = promise.then;
+
+		// Add list-specific methods
+		jQuery.each( tuples, function( i, tuple ) {
+			var list = tuple[ 2 ],
+				stateString = tuple[ 3 ];
+
+			// promise[ done | fail | progress ] = list.add
+			promise[ tuple[1] ] = list.add;
+
+			// Handle state
+			if ( stateString ) {
+				list.add(function() {
+					// state = [ resolved | rejected ]
+					state = stateString;
+
+				// [ reject_list | resolve_list ].disable; progress_list.lock
+				}, tuples[ i ^ 1 ][ 2 ].disable, tuples[ 2 ][ 2 ].lock );
+			}
+
+			// deferred[ resolve | reject | notify ]
+			deferred[ tuple[0] ] = function() {
+				deferred[ tuple[0] + "With" ]( this === deferred ? promise : this, arguments );
+				return this;
+			};
+			deferred[ tuple[0] + "With" ] = list.fireWith;
+		});
+
+		// Make the deferred a promise
+		promise.promise( deferred );
+
+		// Call given func if any
+		if ( func ) {
+			func.call( deferred, deferred );
+		}
+
+		// All done!
+		return deferred;
+	},
+
+	// Deferred helper
+	when: function( subordinate /* , ..., subordinateN */ ) {
+		var i = 0,
+			resolveValues = slice.call( arguments ),
+			length = resolveValues.length,
+
+			// the count of uncompleted subordinates
+			remaining = length !== 1 || ( subordinate && jQuery.isFunction( subordinate.promise ) ) ? length : 0,
+
+			// the master Deferred. If resolveValues consist of only a single Deferred, just use that.
+			deferred = remaining === 1 ? subordinate : jQuery.Deferred(),
+
+			// Update function for both resolve and progress values
+			updateFunc = function( i, contexts, values ) {
+				return function( value ) {
+					contexts[ i ] = this;
+					values[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
+					if ( values === progressValues ) {
+						deferred.notifyWith( contexts, values );
+
+					} else if ( !(--remaining) ) {
+						deferred.resolveWith( contexts, values );
+					}
+				};
+			},
+
+			progressValues, progressContexts, resolveContexts;
+
+		// add listeners to Deferred subordinates; treat others as resolved
+		if ( length > 1 ) {
+			progressValues = new Array( length );
+			progressContexts = new Array( length );
+			resolveContexts = new Array( length );
+			for ( ; i < length; i++ ) {
+				if ( resolveValues[ i ] && jQuery.isFunction( resolveValues[ i ].promise ) ) {
+					resolveValues[ i ].promise()
+						.done( updateFunc( i, resolveContexts, resolveValues ) )
+						.fail( deferred.reject )
+						.progress( updateFunc( i, progressContexts, progressValues ) );
+				} else {
+					--remaining;
+				}
+			}
+		}
+
+		// if we're not waiting on anything, resolve the master
+		if ( !remaining ) {
+			deferred.resolveWith( resolveContexts, resolveValues );
+		}
+
+		return deferred.promise();
+	}
+});
+
+
+// The deferred used on DOM ready
+var readyList;
+
+jQuery.fn.ready = function( fn ) {
+	// Add the callback
+	jQuery.ready.promise().done( fn );
+
+	return this;
+};
+
+jQuery.extend({
+	// Is the DOM ready to be used? Set to true once it occurs.
+	isReady: false,
+
+	// A counter to track how many items to wait for before
+	// the ready event fires. See #6781
+	readyWait: 1,
+
+	// Hold (or release) the ready event
+	holdReady: function( hold ) {
+		if ( hold ) {
+			jQuery.readyWait++;
+		} else {
+			jQuery.ready( true );
+		}
+	},
+
+	// Handle when the DOM is ready
+	ready: function( wait ) {
+
+		// Abort if there are pending holds or we're already ready
+		if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
+			return;
+		}
+
+		// Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
+		if ( !document.body ) {
+			return setTimeout( jQuery.ready );
+		}
+
+		// Remember that the DOM is ready
+		jQuery.isReady = true;
+
+		// If a normal DOM Ready event fired, decrement, and wait if need be
+		if ( wait !== true && --jQuery.readyWait > 0 ) {
+			return;
+		}
+
+		// If there are functions bound, to execute
+		readyList.resolveWith( document, [ jQuery ] );
+
+		// Trigger any bound ready events
+		if ( jQuery.fn.triggerHandler ) {
+			jQuery( document ).triggerHandler( "ready" );
+			jQuery( document ).off( "ready" );
+		}
+	}
+});
+
+/**
+ * Clean-up method for dom ready events
+ */
+function detach() {
+	if ( document.addEventListener ) {
+		document.removeEventListener( "DOMContentLoaded", completed, false );
+		window.removeEventListener( "load", completed, false );
+
+	} else {
+		document.detachEvent( "onreadystatechange", completed );
+		window.detachEvent( "onload", completed );
+	}
+}
+
+/**
+ * The ready event handler and self cleanup method
+ */
+function completed() {
+	// readyState === "complete" is good enough for us to call the dom ready in oldIE
+	if ( document.addEventListener || event.type === "load" || document.readyState === "complete" ) {
+		detach();
+		jQuery.ready();
+	}
+}
+
+jQuery.ready.promise = function( obj ) {
+	if ( !readyList ) {
+
+		readyList = jQuery.Deferred();
+
+		// Catch cases where $(document).ready() is called after the browser event has already occurred.
+		// we once tried to use readyState "interactive" here, but it caused issues like the one
+		// discovered by ChrisS here: http://bugs.jquery.com/ticket/12282#comment:15
+		if ( document.readyState === "complete" ) {
+			// Handle it asynchronously to allow scripts the opportunity to delay ready
+			setTimeout( jQuery.ready );
+
+		// Standards-based browsers support DOMContentLoaded
+		} else if ( document.addEventListener ) {
+			// Use the handy event callback
+			document.addEventListener( "DOMContentLoaded", completed, false );
+
+			// A fallback to window.onload, that will always work
+			window.addEventListener( "load", completed, false );
+
+		// If IE event model is used
+		} else {
+			// Ensure firing before onload, maybe late but safe also for iframes
+			document.attachEvent( "onreadystatechange", completed );
+
+			// A fallback to window.onload, that will always work
+			window.attachEvent( "onload", completed );
+
+			// If IE and not a frame
+			// continually check to see if the document is ready
+			var top = false;
+
+			try {
+				top = window.frameElement == null && document.documentElement;
+			} catch(e) {}
+
+			if ( top && top.doScroll ) {
+				(function doScrollCheck() {
+					if ( !jQuery.isReady ) {
+
+						try {
+							// Use the trick by Diego Perini
+							// http://javascript.nwbox.com/IEContentLoaded/
+							top.doScroll("left");
+						} catch(e) {
+							return setTimeout( doScrollCheck, 50 );
+						}
+
+						// detach all dom ready events
+						detach();
+
+						// and execute any waiting functions
+						jQuery.ready();
+					}
+				})();
+			}
+		}
+	}
+	return readyList.promise( obj );
+};
+
+
+var strundefined = typeof undefined;
+
+
+
+// Support: IE<9
+// Iteration over object's inherited properties before its own
+var i;
+for ( i in jQuery( support ) ) {
+	break;
+}
+support.ownLast = i !== "0";
+
+// Note: most support tests are defined in their respective modules.
+// false until the test is run
+support.inlineBlockNeedsLayout = false;
+
+// Execute ASAP in case we need to set body.style.zoom
+jQuery(function() {
+	// Minified: var a,b,c,d
+	var val, div, body, container;
+
+	body = document.getElementsByTagName( "body" )[ 0 ];
+	if ( !body || !body.style ) {
+		// Return for frameset docs that don't have a body
+		return;
+	}
+
+	// Setup
+	div = document.createElement( "div" );
+	container = document.createElement( "div" );
+	container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+	body.appendChild( container ).appendChild( div );
+
+	if ( typeof div.style.zoom !== strundefined ) {
+		// Support: IE<8
+		// Check if natively block-level elements act like inline-block
+		// elements when setting their display to 'inline' and giving
+		// them layout
+		div.style.cssText = "display:inline;margin:0;border:0;padding:1px;width:1px;zoom:1";
+
+		support.inlineBlockNeedsLayout = val = div.offsetWidth === 3;
+		if ( val ) {
+			// Prevent IE 6 from affecting layout for positioned elements #11048
+			// Prevent IE from shrinking the body in IE 7 mode #12869
+			// Support: IE<8
+			body.style.zoom = 1;
+		}
+	}
+
+	body.removeChild( container );
+});
+
+
+
+
+(function() {
+	var div = document.createElement( "div" );
+
+	// Execute the test only if not already executed in another module.
+	if (support.deleteExpando == null) {
+		// Support: IE<9
+		support.deleteExpando = true;
+		try {
+			delete div.test;
+		} catch( e ) {
+			support.deleteExpando = false;
+		}
+	}
+
+	// Null elements to avoid leaks in IE.
+	div = null;
+})();
+
+
+/**
+ * Determines whether an object can have data
+ */
+jQuery.acceptData = function( elem ) {
+	var noData = jQuery.noData[ (elem.nodeName + " ").toLowerCase() ],
+		nodeType = +elem.nodeType || 1;
+
+	// Do not set data on non-element DOM nodes because it will not be cleared (#8335).
+	return nodeType !== 1 && nodeType !== 9 ?
+		false :
+
+		// Nodes accept data unless otherwise specified; rejection can be conditional
+		!noData || noData !== true && elem.getAttribute("classid") === noData;
+};
+
+
+var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
+	rmultiDash = /([A-Z])/g;
+
+function dataAttr( elem, key, data ) {
+	// If nothing was found internally, try to fetch any
+	// data from the HTML5 data-* attribute
+	if ( data === undefined && elem.nodeType === 1 ) {
+
+		var name = "data-" + key.replace( rmultiDash, "-$1" ).toLowerCase();
+
+		data = elem.getAttribute( name );
+
+		if ( typeof data === "string" ) {
+			try {
+				data = data === "true" ? true :
+					data === "false" ? false :
+					data === "null" ? null :
+					// Only convert to a number if it doesn't change the string
+					+data + "" === data ? +data :
+					rbrace.test( data ) ? jQuery.parseJSON( data ) :
+					data;
+			} catch( e ) {}
+
+			// Make sure we set the data so it isn't changed later
+			jQuery.data( elem, key, data );
+
+		} else {
+			data = undefined;
+		}
+	}
+
+	return data;
+}
+
+// checks a cache object for emptiness
+function isEmptyDataObject( obj ) {
+	var name;
+	for ( name in obj ) {
+
+		// if the public data object is empty, the private is still empty
+		if ( name === "data" && jQuery.isEmptyObject( obj[name] ) ) {
+			continue;
+		}
+		if ( name !== "toJSON" ) {
+			return false;
+		}
+	}
+
+	return true;
+}
+
+function internalData( elem, name, data, pvt /* Internal Use Only */ ) {
+	if ( !jQuery.acceptData( elem ) ) {
+		return;
+	}
+
+	var ret, thisCache,
+		internalKey = jQuery.expando,
+
+		// We have to handle DOM nodes and JS objects differently because IE6-7
+		// can't GC object references properly across the DOM-JS boundary
+		isNode = elem.nodeType,
+
+		// Only DOM nodes need the global jQuery cache; JS object data is
+		// attached directly to the object so GC can occur automatically
+		cache = isNode ? jQuery.cache : elem,
+
+		// Only defining an ID for JS objects if its cache already exists allows
+		// the code to shortcut on the same path as a DOM node with no cache
+		id = isNode ? elem[ internalKey ] : elem[ internalKey ] && internalKey;
+
+	// Avoid doing any more work than we need to when trying to get data on an
+	// object that has no data at all
+	if ( (!id || !cache[id] || (!pvt && !cache[id].data)) && data === undefined && typeof name === "string" ) {
+		return;
+	}
+
+	if ( !id ) {
+		// Only DOM nodes need a new unique ID for each element since their data
+		// ends up in the global cache
+		if ( isNode ) {
+			id = elem[ internalKey ] = deletedIds.pop() || jQuery.guid++;
+		} else {
+			id = internalKey;
+		}
+	}
+
+	if ( !cache[ id ] ) {
+		// Avoid exposing jQuery metadata on plain JS objects when the object
+		// is serialized using JSON.stringify
+		cache[ id ] = isNode ? {} : { toJSON: jQuery.noop };
+	}
+
+	// An object can be passed to jQuery.data instead of a key/value pair; this gets
+	// shallow copied over onto the existing cache
+	if ( typeof name === "object" || typeof name === "function" ) {
+		if ( pvt ) {
+			cache[ id ] = jQuery.extend( cache[ id ], name );
+		} else {
+			cache[ id ].data = jQuery.extend( cache[ id ].data, name );
+		}
+	}
+
+	thisCache = cache[ id ];
+
+	// jQuery data() is stored in a separate object inside the object's internal data
+	// cache in order to avoid key collisions between internal data and user-defined
+	// data.
+	if ( !pvt ) {
+		if ( !thisCache.data ) {
+			thisCache.data = {};
+		}
+
+		thisCache = thisCache.data;
+	}
+
+	if ( data !== undefined ) {
+		thisCache[ jQuery.camelCase( name ) ] = data;
+	}
+
+	// Check for both converted-to-camel and non-converted data property names
+	// If a data property was specified
+	if ( typeof name === "string" ) {
+
+		// First Try to find as-is property data
+		ret = thisCache[ name ];
+
+		// Test for null|undefined property data
+		if ( ret == null ) {
+
+			// Try to find the camelCased property
+			ret = thisCache[ jQuery.camelCase( name ) ];
+		}
+	} else {
+		ret = thisCache;
+	}
+
+	return ret;
+}
+
+function internalRemoveData( elem, name, pvt ) {
+	if ( !jQuery.acceptData( elem ) ) {
+		return;
+	}
+
+	var thisCache, i,
+		isNode = elem.nodeType,
+
+		// See jQuery.data for more information
+		cache = isNode ? jQuery.cache : elem,
+		id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
+
+	// If there is already no cache entry for this object, there is no
+	// purpose in continuing
+	if ( !cache[ id ] ) {
+		return;
+	}
+
+	if ( name ) {
+
+		thisCache = pvt ? cache[ id ] : cache[ id ].data;
+
+		if ( thisCache ) {
+
+			// Support array or space separated string names for data keys
+			if ( !jQuery.isArray( name ) ) {
+
+				// try the string as a key before any manipulation
+				if ( name in thisCache ) {
+					name = [ name ];
+				} else {
+
+					// split the camel cased version by spaces unless a key with the spaces exists
+					name = jQuery.camelCase( name );
+					if ( name in thisCache ) {
+						name = [ name ];
+					} else {
+						name = name.split(" ");
+					}
+				}
+			} else {
+				// If "name" is an array of keys...
+				// When data is initially created, via ("key", "val") signature,
+				// keys will be converted to camelCase.
+				// Since there is no way to tell _how_ a key was added, remove
+				// both plain key and camelCase key. #12786
+				// This will only penalize the array argument path.
+				name = name.concat( jQuery.map( name, jQuery.camelCase ) );
+			}
+
+			i = name.length;
+			while ( i-- ) {
+				delete thisCache[ name[i] ];
+			}
+
+			// If there is no data left in the cache, we want to continue
+			// and let the cache object itself get destroyed
+			if ( pvt ? !isEmptyDataObject(thisCache) : !jQuery.isEmptyObject(thisCache) ) {
+				return;
+			}
+		}
+	}
+
+	// See jQuery.data for more information
+	if ( !pvt ) {
+		delete cache[ id ].data;
+
+		// Don't destroy the parent cache unless the internal data object
+		// had been the only thing left in it
+		if ( !isEmptyDataObject( cache[ id ] ) ) {
+			return;
+		}
+	}
+
+	// Destroy the cache
+	if ( isNode ) {
+		jQuery.cleanData( [ elem ], true );
+
+	// Use delete when supported for expandos or `cache` is not a window per isWindow (#10080)
+	/* jshint eqeqeq: false */
+	} else if ( support.deleteExpando || cache != cache.window ) {
+		/* jshint eqeqeq: true */
+		delete cache[ id ];
+
+	// When all else fails, null
+	} else {
+		cache[ id ] = null;
+	}
+}
+
+jQuery.extend({
+	cache: {},
+
+	// The following elements (space-suffixed to avoid Object.prototype collisions)
+	// throw uncatchable exceptions if you attempt to set expando properties
+	noData: {
+		"applet ": true,
+		"embed ": true,
+		// ...but Flash objects (which have this classid) *can* handle expandos
+		"object ": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
+	},
+
+	hasData: function( elem ) {
+		elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
+		return !!elem && !isEmptyDataObject( elem );
+	},
+
+	data: function( elem, name, data ) {
+		return internalData( elem, name, data );
+	},
+
+	removeData: function( elem, name ) {
+		return internalRemoveData( elem, name );
+	},
+
+	// For internal use only.
+	_data: function( elem, name, data ) {
+		return internalData( elem, name, data, true );
+	},
+
+	_removeData: function( elem, name ) {
+		return internalRemoveData( elem, name, true );
+	}
+});
+
+jQuery.fn.extend({
+	data: function( key, value ) {
+		var i, name, data,
+			elem = this[0],
+			attrs = elem && elem.attributes;
+
+		// Special expections of .data basically thwart jQuery.access,
+		// so implement the relevant behavior ourselves
+
+		// Gets all values
+		if ( key === undefined ) {
+			if ( this.length ) {
+				data = jQuery.data( elem );
+
+				if ( elem.nodeType === 1 && !jQuery._data( elem, "parsedAttrs" ) ) {
+					i = attrs.length;
+					while ( i-- ) {
+
+						// Support: IE11+
+						// The attrs elements can be null (#14894)
+						if ( attrs[ i ] ) {
+							name = attrs[ i ].name;
+							if ( name.indexOf( "data-" ) === 0 ) {
+								name = jQuery.camelCase( name.slice(5) );
+								dataAttr( elem, name, data[ name ] );
+							}
+						}
+					}
+					jQuery._data( elem, "parsedAttrs", true );
+				}
+			}
+
+			return data;
+		}
+
+		// Sets multiple values
+		if ( typeof key === "object" ) {
+			return this.each(function() {
+				jQuery.data( this, key );
+			});
+		}
+
+		return arguments.length > 1 ?
+
+			// Sets one value
+			this.each(function() {
+				jQuery.data( this, key, value );
+			}) :
+
+			// Gets one value
+			// Try to fetch any internally stored data first
+			elem ? dataAttr( elem, key, jQuery.data( elem, key ) ) : undefined;
+	},
+
+	removeData: function( key ) {
+		return this.each(function() {
+			jQuery.removeData( this, key );
+		});
+	}
+});
+
+
+jQuery.extend({
+	queue: function( elem, type, data ) {
+		var queue;
+
+		if ( elem ) {
+			type = ( type || "fx" ) + "queue";
+			queue = jQuery._data( elem, type );
+
+			// Speed up dequeue by getting out quickly if this is just a lookup
+			if ( data ) {
+				if ( !queue || jQuery.isArray(data) ) {
+					queue = jQuery._data( elem, type, jQuery.makeArray(data) );
+				} else {
+					queue.push( data );
+				}
+			}
+			return queue || [];
+		}
+	},
+
+	dequeue: function( elem, type ) {
+		type = type || "fx";
+
+		var queue = jQuery.queue( elem, type ),
+			startLength = queue.length,
+			fn = queue.shift(),
+			hooks = jQuery._queueHooks( elem, type ),
+			next = function() {
+				jQuery.dequeue( elem, type );
+			};
+
+		// If the fx queue is dequeued, always remove the progress sentinel
+		if ( fn === "inprogress" ) {
+			fn = queue.shift();
+			startLength--;
+		}
+
+		if ( fn ) {
+
+			// Add a progress sentinel to prevent the fx queue from being
+			// automatically dequeued
+			if ( type === "fx" ) {
+				queue.unshift( "inprogress" );
+			}
+
+			// clear up the last queue stop function
+			delete hooks.stop;
+			fn.call( elem, next, hooks );
+		}
+
+		if ( !startLength && hooks ) {
+			hooks.empty.fire();
+		}
+	},
+
+	// not intended for public consumption - generates a queueHooks object, or returns the current one
+	_queueHooks: function( elem, type ) {
+		var key = type + "queueHooks";
+		return jQuery._data( elem, key ) || jQuery._data( elem, key, {
+			empty: jQuery.Callbacks("once memory").add(function() {
+				jQuery._removeData( elem, type + "queue" );
+				jQuery._removeData( elem, key );
+			})
+		});
+	}
+});
+
+jQuery.fn.extend({
+	queue: function( type, data ) {
+		var setter = 2;
+
+		if ( typeof type !== "string" ) {
+			data = type;
+			type = "fx";
+			setter--;
+		}
+
+		if ( arguments.length < setter ) {
+			return jQuery.queue( this[0], type );
+		}
+
+		return data === undefined ?
+			this :
+			this.each(function() {
+				var queue = jQuery.queue( this, type, data );
+
+				// ensure a hooks for this queue
+				jQuery._queueHooks( this, type );
+
+				if ( type === "fx" && queue[0] !== "inprogress" ) {
+					jQuery.dequeue( this, type );
+				}
+			});
+	},
+	dequeue: function( type ) {
+		return this.each(function() {
+			jQuery.dequeue( this, type );
+		});
+	},
+	clearQueue: function( type ) {
+		return this.queue( type || "fx", [] );
+	},
+	// Get a promise resolved when queues of a certain type
+	// are emptied (fx is the type by default)
+	promise: function( type, obj ) {
+		var tmp,
+			count = 1,
+			defer = jQuery.Deferred(),
+			elements = this,
+			i = this.length,
+			resolve = function() {
+				if ( !( --count ) ) {
+					defer.resolveWith( elements, [ elements ] );
+				}
+			};
+
+		if ( typeof type !== "string" ) {
+			obj = type;
+			type = undefined;
+		}
+		type = type || "fx";
+
+		while ( i-- ) {
+			tmp = jQuery._data( elements[ i ], type + "queueHooks" );
+			if ( tmp && tmp.empty ) {
+				count++;
+				tmp.empty.add( resolve );
+			}
+		}
+		resolve();
+		return defer.promise( obj );
+	}
+});
+var pnum = (/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/).source;
+
+var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
+
+var isHidden = function( elem, el ) {
+		// isHidden might be called from jQuery#filter function;
+		// in that case, element will be second argument
+		elem = el || elem;
+		return jQuery.css( elem, "display" ) === "none" || !jQuery.contains( elem.ownerDocument, elem );
+	};
+
+
+
+// Multifunctional method to get and set values of a collection
+// The value/s can optionally be executed if it's a function
+var access = jQuery.access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
+	var i = 0,
+		length = elems.length,
+		bulk = key == null;
+
+	// Sets many values
+	if ( jQuery.type( key ) === "object" ) {
+		chainable = true;
+		for ( i in key ) {
+			jQuery.access( elems, fn, i, key[i], true, emptyGet, raw );
+		}
+
+	// Sets one value
+	} else if ( value !== undefined ) {
+		chainable = true;
+
+		if ( !jQuery.isFunction( value ) ) {
+			raw = true;
+		}
+
+		if ( bulk ) {
+			// Bulk operations run against the entire set
+			if ( raw ) {
+				fn.call( elems, value );
+				fn = null;
+
+			// ...except when executing function values
+			} else {
+				bulk = fn;
+				fn = function( elem, key, value ) {
+					return bulk.call( jQuery( elem ), value );
+				};
+			}
+		}
+
+		if ( fn ) {
+			for ( ; i < length; i++ ) {
+				fn( elems[i], key, raw ? value : value.call( elems[i], i, fn( elems[i], key ) ) );
+			}
+		}
+	}
+
+	return chainable ?
+		elems :
+
+		// Gets
+		bulk ?
+			fn.call( elems ) :
+			length ? fn( elems[0], key ) : emptyGet;
+};
+var rcheckableType = (/^(?:checkbox|radio)$/i);
+
+
+
+(function() {
+	// Minified: var a,b,c
+	var input = document.createElement( "input" ),
+		div = document.createElement( "div" ),
+		fragment = document.createDocumentFragment();
+
+	// Setup
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+
+	// IE strips leading whitespace when .innerHTML is used
+	support.leadingWhitespace = div.firstChild.nodeType === 3;
+
+	// Make sure that tbody elements aren't automatically inserted
+	// IE will insert them into empty tables
+	support.tbody = !div.getElementsByTagName( "tbody" ).length;
+
+	// Make sure that link elements get serialized correctly by innerHTML
+	// This requires a wrapper element in IE
+	support.htmlSerialize = !!div.getElementsByTagName( "link" ).length;
+
+	// Makes sure cloning an html5 element does not cause problems
+	// Where outerHTML is undefined, this still works
+	support.html5Clone =
+		document.createElement( "nav" ).cloneNode( true ).outerHTML !== "<:nav></:nav>";
+
+	// Check if a disconnected checkbox will retain its checked
+	// value of true after appended to the DOM (IE6/7)
+	input.type = "checkbox";
+	input.checked = true;
+	fragment.appendChild( input );
+	support.appendChecked = input.checked;
+
+	// Make sure textarea (and checkbox) defaultValue is properly cloned
+	// Support: IE6-IE11+
+	div.innerHTML = "<textarea>x</textarea>";
+	support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
+
+	// #11217 - WebKit loses check when the name is after the checked attribute
+	fragment.appendChild( div );
+	div.innerHTML = "<input type='radio' checked='checked' name='t'/>";
+
+	// Support: Safari 5.1, iOS 5.1, Android 4.x, Android 2.3
+	// old WebKit doesn't clone checked state correctly in fragments
+	support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
+
+	// Support: IE<9
+	// Opera does not clone events (and typeof div.attachEvent === undefined).
+	// IE9-10 clones events bound via attachEvent, but they don't trigger with .click()
+	support.noCloneEvent = true;
+	if ( div.attachEvent ) {
+		div.attachEvent( "onclick", function() {
+			support.noCloneEvent = false;
+		});
+
+		div.cloneNode( true ).click();
+	}
+
+	// Execute the test only if not already executed in another module.
+	if (support.deleteExpando == null) {
+		// Support: IE<9
+		support.deleteExpando = true;
+		try {
+			delete div.test;
+		} catch( e ) {
+			support.deleteExpando = false;
+		}
+	}
+})();
+
+
+(function() {
+	var i, eventName,
+		div = document.createElement( "div" );
+
+	// Support: IE<9 (lack submit/change bubble), Firefox 23+ (lack focusin event)
+	for ( i in { submit: true, change: true, focusin: true }) {
+		eventName = "on" + i;
+
+		if ( !(support[ i + "Bubbles" ] = eventName in window) ) {
+			// Beware of CSP restrictions (https://developer.mozilla.org/en/Security/CSP)
+			div.setAttribute( eventName, "t" );
+			support[ i + "Bubbles" ] = div.attributes[ eventName ].expando === false;
+		}
+	}
+
+	// Null elements to avoid leaks in IE.
+	div = null;
+})();
+
+
+var rformElems = /^(?:input|select|textarea)$/i,
+	rkeyEvent = /^key/,
+	rmouseEvent = /^(?:mouse|pointer|contextmenu)|click/,
+	rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
+	rtypenamespace = /^([^.]*)(?:\.(.+)|)$/;
+
+function returnTrue() {
+	return true;
+}
+
+function returnFalse() {
+	return false;
+}
+
+function safeActiveElement() {
+	try {
+		return document.activeElement;
+	} catch ( err ) { }
+}
+
+/*
+ * Helper functions for managing events -- not part of the public interface.
+ * Props to Dean Edwards' addEvent library for many of the ideas.
+ */
+jQuery.event = {
+
+	global: {},
+
+	add: function( elem, types, handler, data, selector ) {
+		var tmp, events, t, handleObjIn,
+			special, eventHandle, handleObj,
+			handlers, type, namespaces, origType,
+			elemData = jQuery._data( elem );
+
+		// Don't attach events to noData or text/comment nodes (but allow plain objects)
+		if ( !elemData ) {
+			return;
+		}
+
+		// Caller can pass in an object of custom data in lieu of the handler
+		if ( handler.handler ) {
+			handleObjIn = handler;
+			handler = handleObjIn.handler;
+			selector = handleObjIn.selector;
+		}
+
+		// Make sure that the handler has a unique ID, used to find/remove it later
+		if ( !handler.guid ) {
+			handler.guid = jQuery.guid++;
+		}
+
+		// Init the element's event structure and main handler, if this is the first
+		if ( !(events = elemData.events) ) {
+			events = elemData.events = {};
+		}
+		if ( !(eventHandle = elemData.handle) ) {
+			eventHandle = elemData.handle = function( e ) {
+				// Discard the second event of a jQuery.event.trigger() and
+				// when an event is called after a page has unloaded
+				return typeof jQuery !== strundefined && (!e || jQuery.event.triggered !== e.type) ?
+					jQuery.event.dispatch.apply( eventHandle.elem, arguments ) :
+					undefined;
+			};
+			// Add elem as a property of the handle fn to prevent a memory leak with IE non-native events
+			eventHandle.elem = elem;
+		}
+
+		// Handle multiple events separated by a space
+		types = ( types || "" ).match( rnotwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[t] ) || [];
+			type = origType = tmp[1];
+			namespaces = ( tmp[2] || "" ).split( "." ).sort();
+
+			// There *must* be a type, no attaching namespace-only handlers
+			if ( !type ) {
+				continue;
+			}
+
+			// If event changes its type, use the special event handlers for the changed type
+			special = jQuery.event.special[ type ] || {};
+
+			// If selector defined, determine special event api type, otherwise given type
+			type = ( selector ? special.delegateType : special.bindType ) || type;
+
+			// Update special based on newly reset type
+			special = jQuery.event.special[ type ] || {};
+
+			// handleObj is passed to all event handlers
+			handleObj = jQuery.extend({
+				type: type,
+				origType: origType,
+				data: data,
+				handler: handler,
+				guid: handler.guid,
+				selector: selector,
+				needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
+				namespace: namespaces.join(".")
+			}, handleObjIn );
+
+			// Init the event handler queue if we're the first
+			if ( !(handlers = events[ type ]) ) {
+				handlers = events[ type ] = [];
+				handlers.delegateCount = 0;
+
+				// Only use addEventListener/attachEvent if the special events handler returns false
+				if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
+					// Bind the global event handler to the element
+					if ( elem.addEventListener ) {
+						elem.addEventListener( type, eventHandle, false );
+
+					} else if ( elem.attachEvent ) {
+						elem.attachEvent( "on" + type, eventHandle );
+					}
+				}
+			}
+
+			if ( special.add ) {
+				special.add.call( elem, handleObj );
+
+				if ( !handleObj.handler.guid ) {
+					handleObj.handler.guid = handler.guid;
+				}
+			}
+
+			// Add to the element's handler list, delegates in front
+			if ( selector ) {
+				handlers.splice( handlers.delegateCount++, 0, handleObj );
+			} else {
+				handlers.push( handleObj );
+			}
+
+			// Keep track of which events have ever been used, for event optimization
+			jQuery.event.global[ type ] = true;
+		}
+
+		// Nullify elem to prevent memory leaks in IE
+		elem = null;
+	},
+
+	// Detach an event or set of events from an element
+	remove: function( elem, types, handler, selector, mappedTypes ) {
+		var j, handleObj, tmp,
+			origCount, t, events,
+			special, handlers, type,
+			namespaces, origType,
+			elemData = jQuery.hasData( elem ) && jQuery._data( elem );
+
+		if ( !elemData || !(events = elemData.events) ) {
+			return;
+		}
+
+		// Once for each type.namespace in types; type may be omitted
+		types = ( types || "" ).match( rnotwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[t] ) || [];
+			type = origType = tmp[1];
+			namespaces = ( tmp[2] || "" ).split( "." ).sort();
+
+			// Unbind all events (on this namespace, if provided) for the element
+			if ( !type ) {
+				for ( type in events ) {
+					jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
+				}
+				continue;
+			}
+
+			special = jQuery.event.special[ type ] || {};
+			type = ( selector ? special.delegateType : special.bindType ) || type;
+			handlers = events[ type ] || [];
+			tmp = tmp[2] && new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" );
+
+			// Remove matching events
+			origCount = j = handlers.length;
+			while ( j-- ) {
+				handleObj = handlers[ j ];
+
+				if ( ( mappedTypes || origType === handleObj.origType ) &&
+					( !handler || handler.guid === handleObj.guid ) &&
+					( !tmp || tmp.test( handleObj.namespace ) ) &&
+					( !selector || selector === handleObj.selector || selector === "**" && handleObj.selector ) ) {
+					handlers.splice( j, 1 );
+
+					if ( handleObj.selector ) {
+						handlers.delegateCount--;
+					}
+					if ( special.remove ) {
+						special.remove.call( elem, handleObj );
+					}
+				}
+			}
+
+			// Remove generic event handler if we removed something and no more handlers exist
+			// (avoids potential for endless recursion during removal of special event handlers)
+			if ( origCount && !handlers.length ) {
+				if ( !special.teardown || special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+					jQuery.removeEvent( elem, type, elemData.handle );
+				}
+
+				delete events[ type ];
+			}
+		}
+
+		// Remove the expando if it's no longer used
+		if ( jQuery.isEmptyObject( events ) ) {
+			delete elemData.handle;
+
+			// removeData also checks for emptiness and clears the expando if empty
+			// so use it instead of delete
+			jQuery._removeData( elem, "events" );
+		}
+	},
+
+	trigger: function( event, data, elem, onlyHandlers ) {
+		var handle, ontype, cur,
+			bubbleType, special, tmp, i,
+			eventPath = [ elem || document ],
+			type = hasOwn.call( event, "type" ) ? event.type : event,
+			namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split(".") : [];
+
+		cur = tmp = elem = elem || document;
+
+		// Don't do events on text and comment nodes
+		if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
+			return;
+		}
+
+		// focus/blur morphs to focusin/out; ensure we're not firing them right now
+		if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
+			return;
+		}
+
+		if ( type.indexOf(".") >= 0 ) {
+			// Namespaced trigger; create a regexp to match event type in handle()
+			namespaces = type.split(".");
+			type = namespaces.shift();
+			namespaces.sort();
+		}
+		ontype = type.indexOf(":") < 0 && "on" + type;
+
+		// Caller can pass in a jQuery.Event object, Object, or just an event type string
+		event = event[ jQuery.expando ] ?
+			event :
+			new jQuery.Event( type, typeof event === "object" && event );
+
+		// Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
+		event.isTrigger = onlyHandlers ? 2 : 3;
+		event.namespace = namespaces.join(".");
+		event.namespace_re = event.namespace ?
+			new RegExp( "(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)" ) :
+			null;
+
+		// Clean up the event in case it is being reused
+		event.result = undefined;
+		if ( !event.target ) {
+			event.target = elem;
+		}
+
+		// Clone any incoming data and prepend the event, creating the handler arg list
+		data = data == null ?
+			[ event ] :
+			jQuery.makeArray( data, [ event ] );
+
+		// Allow special events to draw outside the lines
+		special = jQuery.event.special[ type ] || {};
+		if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
+			return;
+		}
+
+		// Determine event propagation path in advance, per W3C events spec (#9951)
+		// Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
+		if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
+
+			bubbleType = special.delegateType || type;
+			if ( !rfocusMorph.test( bubbleType + type ) ) {
+				cur = cur.parentNode;
+			}
+			for ( ; cur; cur = cur.parentNode ) {
+				eventPath.push( cur );
+				tmp = cur;
+			}
+
+			// Only add window if we got to document (e.g., not plain obj or detached DOM)
+			if ( tmp === (elem.ownerDocument || document) ) {
+				eventPath.push( tmp.defaultView || tmp.parentWindow || window );
+			}
+		}
+
+		// Fire handlers on the event path
+		i = 0;
+		while ( (cur = eventPath[i++]) && !event.isPropagationStopped() ) {
+
+			event.type = i > 1 ?
+				bubbleType :
+				special.bindType || type;
+
+			// jQuery handler
+			handle = ( jQuery._data( cur, "events" ) || {} )[ event.type ] && jQuery._data( cur, "handle" );
+			if ( handle ) {
+				handle.apply( cur, data );
+			}
+
+			// Native handler
+			handle = ontype && cur[ ontype ];
+			if ( handle && handle.apply && jQuery.acceptData( cur ) ) {
+				event.result = handle.apply( cur, data );
+				if ( event.result === false ) {
+					event.preventDefault();
+				}
+			}
+		}
+		event.type = type;
+
+		// If nobody prevented the default action, do it now
+		if ( !onlyHandlers && !event.isDefaultPrevented() ) {
+
+			if ( (!special._default || special._default.apply( eventPath.pop(), data ) === false) &&
+				jQuery.acceptData( elem ) ) {
+
+				// Call a native DOM method on the target with the same name name as the event.
+				// Can't use an .isFunction() check here because IE6/7 fails that test.
+				// Don't do default actions on window, that's where global variables be (#6170)
+				if ( ontype && elem[ type ] && !jQuery.isWindow( elem ) ) {
+
+					// Don't re-trigger an onFOO event when we call its FOO() method
+					tmp = elem[ ontype ];
+
+					if ( tmp ) {
+						elem[ ontype ] = null;
+					}
+
+					// Prevent re-triggering of the same event, since we already bubbled it above
+					jQuery.event.triggered = type;
+					try {
+						elem[ type ]();
+					} catch ( e ) {
+						// IE<9 dies on focus/blur to hidden element (#1486,#12518)
+						// only reproducible on winXP IE8 native, not IE9 in IE8 mode
+					}
+					jQuery.event.triggered = undefined;
+
+					if ( tmp ) {
+						elem[ ontype ] = tmp;
+					}
+				}
+			}
+		}
+
+		return event.result;
+	},
+
+	dispatch: function( event ) {
+
+		// Make a writable jQuery.Event from the native event object
+		event = jQuery.event.fix( event );
+
+		var i, ret, handleObj, matched, j,
+			handlerQueue = [],
+			args = slice.call( arguments ),
+			handlers = ( jQuery._data( this, "events" ) || {} )[ event.type ] || [],
+			special = jQuery.event.special[ event.type ] || {};
+
+		// Use the fix-ed jQuery.Event rather than the (read-only) native event
+		args[0] = event;
+		event.delegateTarget = this;
+
+		// Call the preDispatch hook for the mapped type, and let it bail if desired
+		if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
+			return;
+		}
+
+		// Determine handlers
+		handlerQueue = jQuery.event.handlers.call( this, event, handlers );
+
+		// Run delegates first; they may want to stop propagation beneath us
+		i = 0;
+		while ( (matched = handlerQueue[ i++ ]) && !event.isPropagationStopped() ) {
+			event.currentTarget = matched.elem;
+
+			j = 0;
+			while ( (handleObj = matched.handlers[ j++ ]) && !event.isImmediatePropagationStopped() ) {
+
+				// Triggered event must either 1) have no namespace, or
+				// 2) have namespace(s) a subset or equal to those in the bound event (both can have no namespace).
+				if ( !event.namespace_re || event.namespace_re.test( handleObj.namespace ) ) {
+
+					event.handleObj = handleObj;
+					event.data = handleObj.data;
+
+					ret = ( (jQuery.event.special[ handleObj.origType ] || {}).handle || handleObj.handler )
+							.apply( matched.elem, args );
+
+					if ( ret !== undefined ) {
+						if ( (event.result = ret) === false ) {
+							event.preventDefault();
+							event.stopPropagation();
+						}
+					}
+				}
+			}
+		}
+
+		// Call the postDispatch hook for the mapped type
+		if ( special.postDispatch ) {
+			special.postDispatch.call( this, event );
+		}
+
+		return event.result;
+	},
+
+	handlers: function( event, handlers ) {
+		var sel, handleObj, matches, i,
+			handlerQueue = [],
+			delegateCount = handlers.delegateCount,
+			cur = event.target;
+
+		// Find delegate handlers
+		// Black-hole SVG <use> instance trees (#13180)
+		// Avoid non-left-click bubbling in Firefox (#3861)
+		if ( delegateCount && cur.nodeType && (!event.button || event.type !== "click") ) {
+
+			/* jshint eqeqeq: false */
+			for ( ; cur != this; cur = cur.parentNode || this ) {
+				/* jshint eqeqeq: true */
+
+				// Don't check non-elements (#13208)
+				// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
+				if ( cur.nodeType === 1 && (cur.disabled !== true || event.type !== "click") ) {
+					matches = [];
+					for ( i = 0; i < delegateCount; i++ ) {
+						handleObj = handlers[ i ];
+
+						// Don't conflict with Object.prototype properties (#13203)
+						sel = handleObj.selector + " ";
+
+						if ( matches[ sel ] === undefined ) {
+							matches[ sel ] = handleObj.needsContext ?
+								jQuery( sel, this ).index( cur ) >= 0 :
+								jQuery.find( sel, this, null, [ cur ] ).length;
+						}
+						if ( matches[ sel ] ) {
+							matches.push( handleObj );
+						}
+					}
+					if ( matches.length ) {
+						handlerQueue.push({ elem: cur, handlers: matches });
+					}
+				}
+			}
+		}
+
+		// Add the remaining (directly-bound) handlers
+		if ( delegateCount < handlers.length ) {
+			handlerQueue.push({ elem: this, handlers: handlers.slice( delegateCount ) });
+		}
+
+		return handlerQueue;
+	},
+
+	fix: function( event ) {
+		if ( event[ jQuery.expando ] ) {
+			return event;
+		}
+
+		// Create a writable copy of the event object and normalize some properties
+		var i, prop, copy,
+			type = event.type,
+			originalEvent = event,
+			fixHook = this.fixHooks[ type ];
+
+		if ( !fixHook ) {
+			this.fixHooks[ type ] = fixHook =
+				rmouseEvent.test( type ) ? this.mouseHooks :
+				rkeyEvent.test( type ) ? this.keyHooks :
+				{};
+		}
+		copy = fixHook.props ? this.props.concat( fixHook.props ) : this.props;
+
+		event = new jQuery.Event( originalEvent );
+
+		i = copy.length;
+		while ( i-- ) {
+			prop = copy[ i ];
+			event[ prop ] = originalEvent[ prop ];
+		}
+
+		// Support: IE<9
+		// Fix target property (#1925)
+		if ( !event.target ) {
+			event.target = originalEvent.srcElement || document;
+		}
+
+		// Support: Chrome 23+, Safari?
+		// Target should not be a text node (#504, #13143)
+		if ( event.target.nodeType === 3 ) {
+			event.target = event.target.parentNode;
+		}
+
+		// Support: IE<9
+		// For mouse/key events, metaKey==false if it's undefined (#3368, #11328)
+		event.metaKey = !!event.metaKey;
+
+		return fixHook.filter ? fixHook.filter( event, originalEvent ) : event;
+	},
+
+	// Includes some event props shared by KeyEvent and MouseEvent
+	props: "altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),
+
+	fixHooks: {},
+
+	keyHooks: {
+		props: "char charCode key keyCode".split(" "),
+		filter: function( event, original ) {
+
+			// Add which for key events
+			if ( event.which == null ) {
+				event.which = original.charCode != null ? original.charCode : original.keyCode;
+			}
+
+			return event;
+		}
+	},
+
+	mouseHooks: {
+		props: "button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),
+		filter: function( event, original ) {
+			var body, eventDoc, doc,
+				button = original.button,
+				fromElement = original.fromElement;
+
+			// Calculate pageX/Y if missing and clientX/Y available
+			if ( event.pageX == null && original.clientX != null ) {
+				eventDoc = event.target.ownerDocument || document;
+				doc = eventDoc.documentElement;
+				body = eventDoc.body;
+
+				event.pageX = original.clientX + ( doc && doc.scrollLeft || body && body.scrollLeft || 0 ) - ( doc && doc.clientLeft || body && body.clientLeft || 0 );
+				event.pageY = original.clientY + ( doc && doc.scrollTop  || body && body.scrollTop  || 0 ) - ( doc && doc.clientTop  || body && body.clientTop  || 0 );
+			}
+
+			// Add relatedTarget, if necessary
+			if ( !event.relatedTarget && fromElement ) {
+				event.relatedTarget = fromElement === event.target ? original.toElement : fromElement;
+			}
+
+			// Add which for click: 1 === left; 2 === middle; 3 === right
+			// Note: button is not normalized, so don't use it
+			if ( !event.which && button !== undefined ) {
+				event.which = ( button & 1 ? 1 : ( button & 2 ? 3 : ( button & 4 ? 2 : 0 ) ) );
+			}
+
+			return event;
+		}
+	},
+
+	special: {
+		load: {
+			// Prevent triggered image.load events from bubbling to window.load
+			noBubble: true
+		},
+		focus: {
+			// Fire native event if possible so blur/focus sequence is correct
+			trigger: function() {
+				if ( this !== safeActiveElement() && this.focus ) {
+					try {
+						this.focus();
+						return false;
+					} catch ( e ) {
+						// Support: IE<9
+						// If we error on focus to hidden element (#1486, #12518),
+						// let .trigger() run the handlers
+					}
+				}
+			},
+			delegateType: "focusin"
+		},
+		blur: {
+			trigger: function() {
+				if ( this === safeActiveElement() && this.blur ) {
+					this.blur();
+					return false;
+				}
+			},
+			delegateType: "focusout"
+		},
+		click: {
+			// For checkbox, fire native event so checked state will be right
+			trigger: function() {
+				if ( jQuery.nodeName( this, "input" ) && this.type === "checkbox" && this.click ) {
+					this.click();
+					return false;
+				}
+			},
+
+			// For cross-browser consistency, don't fire native .click() on links
+			_default: function( event ) {
+				return jQuery.nodeName( event.target, "a" );
+			}
+		},
+
+		beforeunload: {
+			postDispatch: function( event ) {
+
+				// Support: Firefox 20+
+				// Firefox doesn't alert if the returnValue field is not set.
+				if ( event.result !== undefined && event.originalEvent ) {
+					event.originalEvent.returnValue = event.result;
+				}
+			}
+		}
+	},
+
+	simulate: function( type, elem, event, bubble ) {
+		// Piggyback on a donor event to simulate a different one.
+		// Fake originalEvent to avoid donor's stopPropagation, but if the
+		// simulated event prevents default then we do the same on the donor.
+		var e = jQuery.extend(
+			new jQuery.Event(),
+			event,
+			{
+				type: type,
+				isSimulated: true,
+				originalEvent: {}
+			}
+		);
+		if ( bubble ) {
+			jQuery.event.trigger( e, null, elem );
+		} else {
+			jQuery.event.dispatch.call( elem, e );
+		}
+		if ( e.isDefaultPrevented() ) {
+			event.preventDefault();
+		}
+	}
+};
+
+jQuery.removeEvent = document.removeEventListener ?
+	function( elem, type, handle ) {
+		if ( elem.removeEventListener ) {
+			elem.removeEventListener( type, handle, false );
+		}
+	} :
+	function( elem, type, handle ) {
+		var name = "on" + type;
+
+		if ( elem.detachEvent ) {
+
+			// #8545, #7054, preventing memory leaks for custom events in IE6-8
+			// detachEvent needed property on element, by name of that event, to properly expose it to GC
+			if ( typeof elem[ name ] === strundefined ) {
+				elem[ name ] = null;
+			}
+
+			elem.detachEvent( name, handle );
+		}
+	};
+
+jQuery.Event = function( src, props ) {
+	// Allow instantiation without the 'new' keyword
+	if ( !(this instanceof jQuery.Event) ) {
+		return new jQuery.Event( src, props );
+	}
+
+	// Event object
+	if ( src && src.type ) {
+		this.originalEvent = src;
+		this.type = src.type;
+
+		// Events bubbling up the document may have been marked as prevented
+		// by a handler lower down the tree; reflect the correct value.
+		this.isDefaultPrevented = src.defaultPrevented ||
+				src.defaultPrevented === undefined &&
+				// Support: IE < 9, Android < 4.0
+				src.returnValue === false ?
+			returnTrue :
+			returnFalse;
+
+	// Event type
+	} else {
+		this.type = src;
+	}
+
+	// Put explicitly provided properties onto the event object
+	if ( props ) {
+		jQuery.extend( this, props );
+	}
+
+	// Create a timestamp if incoming event doesn't have one
+	this.timeStamp = src && src.timeStamp || jQuery.now();
+
+	// Mark it as fixed
+	this[ jQuery.expando ] = true;
+};
+
+// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
+// http://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
+jQuery.Event.prototype = {
+	isDefaultPrevented: returnFalse,
+	isPropagationStopped: returnFalse,
+	isImmediatePropagationStopped: returnFalse,
+
+	preventDefault: function() {
+		var e = this.originalEvent;
+
+		this.isDefaultPrevented = returnTrue;
+		if ( !e ) {
+			return;
+		}
+
+		// If preventDefault exists, run it on the original event
+		if ( e.preventDefault ) {
+			e.preventDefault();
+
+		// Support: IE
+		// Otherwise set the returnValue property of the original event to false
+		} else {
+			e.returnValue = false;
+		}
+	},
+	stopPropagation: function() {
+		var e = this.originalEvent;
+
+		this.isPropagationStopped = returnTrue;
+		if ( !e ) {
+			return;
+		}
+		// If stopPropagation exists, run it on the original event
+		if ( e.stopPropagation ) {
+			e.stopPropagation();
+		}
+
+		// Support: IE
+		// Set the cancelBubble property of the original event to true
+		e.cancelBubble = true;
+	},
+	stopImmediatePropagation: function() {
+		var e = this.originalEvent;
+
+		this.isImmediatePropagationStopped = returnTrue;
+
+		if ( e && e.stopImmediatePropagation ) {
+			e.stopImmediatePropagation();
+		}
+
+		this.stopPropagation();
+	}
+};
+
+// Create mouseenter/leave events using mouseover/out and event-time checks
+jQuery.each({
+	mouseenter: "mouseover",
+	mouseleave: "mouseout",
+	pointerenter: "pointerover",
+	pointerleave: "pointerout"
+}, function( orig, fix ) {
+	jQuery.event.special[ orig ] = {
+		delegateType: fix,
+		bindType: fix,
+
+		handle: function( event ) {
+			var ret,
+				target = this,
+				related = event.relatedTarget,
+				handleObj = event.handleObj;
+
+			// For mousenter/leave call the handler if related is outside the target.
+			// NB: No relatedTarget if the mouse left/entered the browser window
+			if ( !related || (related !== target && !jQuery.contains( target, related )) ) {
+				event.type = handleObj.origType;
+				ret = handleObj.handler.apply( this, arguments );
+				event.type = fix;
+			}
+			return ret;
+		}
+	};
+});
+
+// IE submit delegation
+if ( !support.submitBubbles ) {
+
+	jQuery.event.special.submit = {
+		setup: function() {
+			// Only need this for delegated form submit events
+			if ( jQuery.nodeName( this, "form" ) ) {
+				return false;
+			}
+
+			// Lazy-add a submit handler when a descendant form may potentially be submitted
+			jQuery.event.add( this, "click._submit keypress._submit", function( e ) {
+				// Node name check avoids a VML-related crash in IE (#9807)
+				var elem = e.target,
+					form = jQuery.nodeName( elem, "input" ) || jQuery.nodeName( elem, "button" ) ? elem.form : undefined;
+				if ( form && !jQuery._data( form, "submitBubbles" ) ) {
+					jQuery.event.add( form, "submit._submit", function( event ) {
+						event._submit_bubble = true;
+					});
+					jQuery._data( form, "submitBubbles", true );
+				}
+			});
+			// return undefined since we don't need an event listener
+		},
+
+		postDispatch: function( event ) {
+			// If form was submitted by the user, bubble the event up the tree
+			if ( event._submit_bubble ) {
+				delete event._submit_bubble;
+				if ( this.parentNode && !event.isTrigger ) {
+					jQuery.event.simulate( "submit", this.parentNode, event, true );
+				}
+			}
+		},
+
+		teardown: function() {
+			// Only need this for delegated form submit events
+			if ( jQuery.nodeName( this, "form" ) ) {
+				return false;
+			}
+
+			// Remove delegated handlers; cleanData eventually reaps submit handlers attached above
+			jQuery.event.remove( this, "._submit" );
+		}
+	};
+}
+
+// IE change delegation and checkbox/radio fix
+if ( !support.changeBubbles ) {
+
+	jQuery.event.special.change = {
+
+		setup: function() {
+
+			if ( rformElems.test( this.nodeName ) ) {
+				// IE doesn't fire change on a check/radio until blur; trigger it on click
+				// after a propertychange. Eat the blur-change in special.change.handle.
+				// This still fires onchange a second time for check/radio after blur.
+				if ( this.type === "checkbox" || this.type === "radio" ) {
+					jQuery.event.add( this, "propertychange._change", function( event ) {
+						if ( event.originalEvent.propertyName === "checked" ) {
+							this._just_changed = true;
+						}
+					});
+					jQuery.event.add( this, "click._change", function( event ) {
+						if ( this._just_changed && !event.isTrigger ) {
+							this._just_changed = false;
+						}
+						// Allow triggered, simulated change events (#11500)
+						jQuery.event.simulate( "change", this, event, true );
+					});
+				}
+				return false;
+			}
+			// Delegated event; lazy-add a change handler on descendant inputs
+			jQuery.event.add( this, "beforeactivate._change", function( e ) {
+				var elem = e.target;
+
+				if ( rformElems.test( elem.nodeName ) && !jQuery._data( elem, "changeBubbles" ) ) {
+					jQuery.event.add( elem, "change._change", function( event ) {
+						if ( this.parentNode && !event.isSimulated && !event.isTrigger ) {
+							jQuery.event.simulate( "change", this.parentNode, event, true );
+						}
+					});
+					jQuery._data( elem, "changeBubbles", true );
+				}
+			});
+		},
+
+		handle: function( event ) {
+			var elem = event.target;
+
+			// Swallow native change events from checkbox/radio, we already triggered them above
+			if ( this !== elem || event.isSimulated || event.isTrigger || (elem.type !== "radio" && elem.type !== "checkbox") ) {
+				return event.handleObj.handler.apply( this, arguments );
+			}
+		},
+
+		teardown: function() {
+			jQuery.event.remove( this, "._change" );
+
+			return !rformElems.test( this.nodeName );
+		}
+	};
+}
+
+// Create "bubbling" focus and blur events
+if ( !support.focusinBubbles ) {
+	jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) {
+
+		// Attach a single capturing handler on the document while someone wants focusin/focusout
+		var handler = function( event ) {
+				jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ), true );
+			};
+
+		jQuery.event.special[ fix ] = {
+			setup: function() {
+				var doc = this.ownerDocument || this,
+					attaches = jQuery._data( doc, fix );
+
+				if ( !attaches ) {
+					doc.addEventListener( orig, handler, true );
+				}
+				jQuery._data( doc, fix, ( attaches || 0 ) + 1 );
+			},
+			teardown: function() {
+				var doc = this.ownerDocument || this,
+					attaches = jQuery._data( doc, fix ) - 1;
+
+				if ( !attaches ) {
+					doc.removeEventListener( orig, handler, true );
+					jQuery._removeData( doc, fix );
+				} else {
+					jQuery._data( doc, fix, attaches );
+				}
+			}
+		};
+	});
+}
+
+jQuery.fn.extend({
+
+	on: function( types, selector, data, fn, /*INTERNAL*/ one ) {
+		var type, origFn;
+
+		// Types can be a map of types/handlers
+		if ( typeof types === "object" ) {
+			// ( types-Object, selector, data )
+			if ( typeof selector !== "string" ) {
+				// ( types-Object, data )
+				data = data || selector;
+				selector = undefined;
+			}
+			for ( type in types ) {
+				this.on( type, selector, data, types[ type ], one );
+			}
+			return this;
+		}
+
+		if ( data == null && fn == null ) {
+			// ( types, fn )
+			fn = selector;
+			data = selector = undefined;
+		} else if ( fn == null ) {
+			if ( typeof selector === "string" ) {
+				// ( types, selector, fn )
+				fn = data;
+				data = undefined;
+			} else {
+				// ( types, data, fn )
+				fn = data;
+				data = selector;
+				selector = undefined;
+			}
+		}
+		if ( fn === false ) {
+			fn = returnFalse;
+		} else if ( !fn ) {
+			return this;
+		}
+
+		if ( one === 1 ) {
+			origFn = fn;
+			fn = function( event ) {
+				// Can use an empty set, since event contains the info
+				jQuery().off( event );
+				return origFn.apply( this, arguments );
+			};
+			// Use same guid so caller can remove using origFn
+			fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
+		}
+		return this.each( function() {
+			jQuery.event.add( this, types, fn, data, selector );
+		});
+	},
+	one: function( types, selector, data, fn ) {
+		return this.on( types, selector, data, fn, 1 );
+	},
+	off: function( types, selector, fn ) {
+		var handleObj, type;
+		if ( types && types.preventDefault && types.handleObj ) {
+			// ( event )  dispatched jQuery.Event
+			handleObj = types.handleObj;
+			jQuery( types.delegateTarget ).off(
+				handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType,
+				handleObj.selector,
+				handleObj.handler
+			);
+			return this;
+		}
+		if ( typeof types === "object" ) {
+			// ( types-object [, selector] )
+			for ( type in types ) {
+				this.off( type, selector, types[ type ] );
+			}
+			return this;
+		}
+		if ( selector === false || typeof selector === "function" ) {
+			// ( types [, fn] )
+			fn = selector;
+			selector = undefined;
+		}
+		if ( fn === false ) {
+			fn = returnFalse;
+		}
+		return this.each(function() {
+			jQuery.event.remove( this, types, fn, selector );
+		});
+	},
+
+	trigger: function( type, data ) {
+		return this.each(function() {
+			jQuery.event.trigger( type, data, this );
+		});
+	},
+	triggerHandler: function( type, data ) {
+		var elem = this[0];
+		if ( elem ) {
+			return jQuery.event.trigger( type, data, elem, true );
+		}
+	}
+});
+
+
+function createSafeFragment( document ) {
+	var list = nodeNames.split( "|" ),
+		safeFrag = document.createDocumentFragment();
+
+	if ( safeFrag.createElement ) {
+		while ( list.length ) {
+			safeFrag.createElement(
+				list.pop()
+			);
+		}
+	}
+	return safeFrag;
+}
+
+var nodeNames = "abbr|article|aside|audio|bdi|canvas|data|datalist|details|figcaption|figure|footer|" +
+		"header|hgroup|mark|meter|nav|output|progress|section|summary|time|video",
+	rinlinejQuery = / jQuery\d+="(?:null|\d+)"/g,
+	rnoshimcache = new RegExp("<(?:" + nodeNames + ")[\\s/>]", "i"),
+	rleadingWhitespace = /^\s+/,
+	rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/gi,
+	rtagName = /<([\w:]+)/,
+	rtbody = /<tbody/i,
+	rhtml = /<|&#?\w+;/,
+	rnoInnerhtml = /<(?:script|style|link)/i,
+	// checked="checked" or checked
+	rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
+	rscriptType = /^$|\/(?:java|ecma)script/i,
+	rscriptTypeMasked = /^true\/(.*)/,
+	rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g,
+
+	// We have to close these tags to support XHTML (#13200)
+	wrapMap = {
+		option: [ 1, "<select multiple='multiple'>", "</select>" ],
+		legend: [ 1, "<fieldset>", "</fieldset>" ],
+		area: [ 1, "<map>", "</map>" ],
+		param: [ 1, "<object>", "</object>" ],
+		thead: [ 1, "<table>", "</table>" ],
+		tr: [ 2, "<table><tbody>", "</tbody></table>" ],
+		col: [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ],
+		td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
+
+		// IE6-8 can't serialize link, script, style, or any html5 (NoScope) tags,
+		// unless wrapped in a div with non-breaking characters in front of it.
+		_default: support.htmlSerialize ? [ 0, "", "" ] : [ 1, "X<div>", "</div>"  ]
+	},
+	safeFragment = createSafeFragment( document ),
+	fragmentDiv = safeFragment.appendChild( document.createElement("div") );
+
+wrapMap.optgroup = wrapMap.option;
+wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
+wrapMap.th = wrapMap.td;
+
+function getAll( context, tag ) {
+	var elems, elem,
+		i = 0,
+		found = typeof context.getElementsByTagName !== strundefined ? context.getElementsByTagName( tag || "*" ) :
+			typeof context.querySelectorAll !== strundefined ? context.querySelectorAll( tag || "*" ) :
+			undefined;
+
+	if ( !found ) {
+		for ( found = [], elems = context.childNodes || context; (elem = elems[i]) != null; i++ ) {
+			if ( !tag || jQuery.nodeName( elem, tag ) ) {
+				found.push( elem );
+			} else {
+				jQuery.merge( found, getAll( elem, tag ) );
+			}
+		}
+	}
+
+	return tag === undefined || tag && jQuery.nodeName( context, tag ) ?
+		jQuery.merge( [ context ], found ) :
+		found;
+}
+
+// Used in buildFragment, fixes the defaultChecked property
+function fixDefaultChecked( elem ) {
+	if ( rcheckableType.test( elem.type ) ) {
+		elem.defaultChecked = elem.checked;
+	}
+}
+
+// Support: IE<8
+// Manipulating tables requires a tbody
+function manipulationTarget( elem, content ) {
+	return jQuery.nodeName( elem, "table" ) &&
+		jQuery.nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ?
+
+		elem.getElementsByTagName("tbody")[0] ||
+			elem.appendChild( elem.ownerDocument.createElement("tbody") ) :
+		elem;
+}
+
+// Replace/restore the type attribute of script elements for safe DOM manipulation
+function disableScript( elem ) {
+	elem.type = (jQuery.find.attr( elem, "type" ) !== null) + "/" + elem.type;
+	return elem;
+}
+function restoreScript( elem ) {
+	var match = rscriptTypeMasked.exec( elem.type );
+	if ( match ) {
+		elem.type = match[1];
+	} else {
+		elem.removeAttribute("type");
+	}
+	return elem;
+}
+
+// Mark scripts as having already been evaluated
+function setGlobalEval( elems, refElements ) {
+	var elem,
+		i = 0;
+	for ( ; (elem = elems[i]) != null; i++ ) {
+		jQuery._data( elem, "globalEval", !refElements || jQuery._data( refElements[i], "globalEval" ) );
+	}
+}
+
+function cloneCopyEvent( src, dest ) {
+
+	if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) {
+		return;
+	}
+
+	var type, i, l,
+		oldData = jQuery._data( src ),
+		curData = jQuery._data( dest, oldData ),
+		events = oldData.events;
+
+	if ( events ) {
+		delete curData.handle;
+		curData.events = {};
+
+		for ( type in events ) {
+			for ( i = 0, l = events[ type ].length; i < l; i++ ) {
+				jQuery.event.add( dest, type, events[ type ][ i ] );
+			}
+		}
+	}
+
+	// make the cloned public data object a copy from the original
+	if ( curData.data ) {
+		curData.data = jQuery.extend( {}, curData.data );
+	}
+}
+
+function fixCloneNodeIssues( src, dest ) {
+	var nodeName, e, data;
+
+	// We do not need to do anything for non-Elements
+	if ( dest.nodeType !== 1 ) {
+		return;
+	}
+
+	nodeName = dest.nodeName.toLowerCase();
+
+	// IE6-8 copies events bound via attachEvent when using cloneNode.
+	if ( !support.noCloneEvent && dest[ jQuery.expando ] ) {
+		data = jQuery._data( dest );
+
+		for ( e in data.events ) {
+			jQuery.removeEvent( dest, e, data.handle );
+		}
+
+		// Event data gets referenced instead of copied if the expando gets copied too
+		dest.removeAttribute( jQuery.expando );
+	}
+
+	// IE blanks contents when cloning scripts, and tries to evaluate newly-set text
+	if ( nodeName === "script" && dest.text !== src.text ) {
+		disableScript( dest ).text = src.text;
+		restoreScript( dest );
+
+	// IE6-10 improperly clones children of object elements using classid.
+	// IE10 throws NoModificationAllowedError if parent is null, #12132.
+	} else if ( nodeName === "object" ) {
+		if ( dest.parentNode ) {
+			dest.outerHTML = src.outerHTML;
+		}
+
+		// This path appears unavoidable for IE9. When cloning an object
+		// element in IE9, the outerHTML strategy above is not sufficient.
+		// If the src has innerHTML and the destination does not,
+		// copy the src.innerHTML into the dest.innerHTML. #10324
+		if ( support.html5Clone && ( src.innerHTML && !jQuery.trim(dest.innerHTML) ) ) {
+			dest.innerHTML = src.innerHTML;
+		}
+
+	} else if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
+		// IE6-8 fails to persist the checked state of a cloned checkbox
+		// or radio button. Worse, IE6-7 fail to give the cloned element
+		// a checked appearance if the defaultChecked value isn't also set
+
+		dest.defaultChecked = dest.checked = src.checked;
+
+		// IE6-7 get confused and end up setting the value of a cloned
+		// checkbox/radio button to an empty string instead of "on"
+		if ( dest.value !== src.value ) {
+			dest.value = src.value;
+		}
+
+	// IE6-8 fails to return the selected option to the default selected
+	// state when cloning options
+	} else if ( nodeName === "option" ) {
+		dest.defaultSelected = dest.selected = src.defaultSelected;
+
+	// IE6-8 fails to set the defaultValue to the correct value when
+	// cloning other types of input fields
+	} else if ( nodeName === "input" || nodeName === "textarea" ) {
+		dest.defaultValue = src.defaultValue;
+	}
+}
+
+jQuery.extend({
+	clone: function( elem, dataAndEvents, deepDataAndEvents ) {
+		var destElements, node, clone, i, srcElements,
+			inPage = jQuery.contains( elem.ownerDocument, elem );
+
+		if ( support.html5Clone || jQuery.isXMLDoc(elem) || !rnoshimcache.test( "<" + elem.nodeName + ">" ) ) {
+			clone = elem.cloneNode( true );
+
+		// IE<=8 does not properly clone detached, unknown element nodes
+		} else {
+			fragmentDiv.innerHTML = elem.outerHTML;
+			fragmentDiv.removeChild( clone = fragmentDiv.firstChild );
+		}
+
+		if ( (!support.noCloneEvent || !support.noCloneChecked) &&
+				(elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
+
+			// We eschew Sizzle here for performance reasons: http://jsperf.com/getall-vs-sizzle/2
+			destElements = getAll( clone );
+			srcElements = getAll( elem );
+
+			// Fix all IE cloning issues
+			for ( i = 0; (node = srcElements[i]) != null; ++i ) {
+				// Ensure that the destination node is not null; Fixes #9587
+				if ( destElements[i] ) {
+					fixCloneNodeIssues( node, destElements[i] );
+				}
+			}
+		}
+
+		// Copy the events from the original to the clone
+		if ( dataAndEvents ) {
+			if ( deepDataAndEvents ) {
+				srcElements = srcElements || getAll( elem );
+				destElements = destElements || getAll( clone );
+
+				for ( i = 0; (node = srcElements[i]) != null; i++ ) {
+					cloneCopyEvent( node, destElements[i] );
+				}
+			} else {
+				cloneCopyEvent( elem, clone );
+			}
+		}
+
+		// Preserve script evaluation history
+		destElements = getAll( clone, "script" );
+		if ( destElements.length > 0 ) {
+			setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
+		}
+
+		destElements = srcElements = node = null;
+
+		// Return the cloned set
+		return clone;
+	},
+
+	buildFragment: function( elems, context, scripts, selection ) {
+		var j, elem, contains,
+			tmp, tag, tbody, wrap,
+			l = elems.length,
+
+			// Ensure a safe fragment
+			safe = createSafeFragment( context ),
+
+			nodes = [],
+			i = 0;
+
+		for ( ; i < l; i++ ) {
+			elem = elems[ i ];
+
+			if ( elem || elem === 0 ) {
+
+				// Add nodes directly
+				if ( jQuery.type( elem ) === "object" ) {
+					jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
+
+				// Convert non-html into a text node
+				} else if ( !rhtml.test( elem ) ) {
+					nodes.push( context.createTextNode( elem ) );
+
+				// Convert html into DOM nodes
+				} else {
+					tmp = tmp || safe.appendChild( context.createElement("div") );
+
+					// Deserialize a standard representation
+					tag = (rtagName.exec( elem ) || [ "", "" ])[ 1 ].toLowerCase();
+					wrap = wrapMap[ tag ] || wrapMap._default;
+
+					tmp.innerHTML = wrap[1] + elem.replace( rxhtmlTag, "<$1></$2>" ) + wrap[2];
+
+					// Descend through wrappers to the right content
+					j = wrap[0];
+					while ( j-- ) {
+						tmp = tmp.lastChild;
+					}
+
+					// Manually add leading whitespace removed by IE
+					if ( !support.leadingWhitespace && rleadingWhitespace.test( elem ) ) {
+						nodes.push( context.createTextNode( rleadingWhitespace.exec( elem )[0] ) );
+					}
+
+					// Remove IE's autoinserted <tbody> from table fragments
+					if ( !support.tbody ) {
+
+						// String was a <table>, *may* have spurious <tbody>
+						elem = tag === "table" && !rtbody.test( elem ) ?
+							tmp.firstChild :
+
+							// String was a bare <thead> or <tfoot>
+							wrap[1] === "<table>" && !rtbody.test( elem ) ?
+								tmp :
+								0;
+
+						j = elem && elem.childNodes.length;
+						while ( j-- ) {
+							if ( jQuery.nodeName( (tbody = elem.childNodes[j]), "tbody" ) && !tbody.childNodes.length ) {
+								elem.removeChild( tbody );
+							}
+						}
+					}
+
+					jQuery.merge( nodes, tmp.childNodes );
+
+					// Fix #12392 for WebKit and IE > 9
+					tmp.textContent = "";
+
+					// Fix #12392 for oldIE
+					while ( tmp.firstChild ) {
+						tmp.removeChild( tmp.firstChild );
+					}
+
+					// Remember the top-level container for proper cleanup
+					tmp = safe.lastChild;
+				}
+			}
+		}
+
+		// Fix #11356: Clear elements from fragment
+		if ( tmp ) {
+			safe.removeChild( tmp );
+		}
+
+		// Reset defaultChecked for any radios and checkboxes
+		// about to be appended to the DOM in IE 6/7 (#8060)
+		if ( !support.appendChecked ) {
+			jQuery.grep( getAll( nodes, "input" ), fixDefaultChecked );
+		}
+
+		i = 0;
+		while ( (elem = nodes[ i++ ]) ) {
+
+			// #4087 - If origin and destination elements are the same, and this is
+			// that element, do not do anything
+			if ( selection && jQuery.inArray( elem, selection ) !== -1 ) {
+				continue;
+			}
+
+			contains = jQuery.contains( elem.ownerDocument, elem );
+
+			// Append to fragment
+			tmp = getAll( safe.appendChild( elem ), "script" );
+
+			// Preserve script evaluation history
+			if ( contains ) {
+				setGlobalEval( tmp );
+			}
+
+			// Capture executables
+			if ( scripts ) {
+				j = 0;
+				while ( (elem = tmp[ j++ ]) ) {
+					if ( rscriptType.test( elem.type || "" ) ) {
+						scripts.push( elem );
+					}
+				}
+			}
+		}
+
+		tmp = null;
+
+		return safe;
+	},
+
+	cleanData: function( elems, /* internal */ acceptData ) {
+		var elem, type, id, data,
+			i = 0,
+			internalKey = jQuery.expando,
+			cache = jQuery.cache,
+			deleteExpando = support.deleteExpando,
+			special = jQuery.event.special;
+
+		for ( ; (elem = elems[i]) != null; i++ ) {
+			if ( acceptData || jQuery.acceptData( elem ) ) {
+
+				id = elem[ internalKey ];
+				data = id && cache[ id ];
+
+				if ( data ) {
+					if ( data.events ) {
+						for ( type in data.events ) {
+							if ( special[ type ] ) {
+								jQuery.event.remove( elem, type );
+
+							// This is a shortcut to avoid jQuery.event.remove's overhead
+							} else {
+								jQuery.removeEvent( elem, type, data.handle );
+							}
+						}
+					}
+
+					// Remove cache only if it was not already removed by jQuery.event.remove
+					if ( cache[ id ] ) {
+
+						delete cache[ id ];
+
+						// IE does not allow us to delete expando properties from nodes,
+						// nor does it have a removeAttribute function on Document nodes;
+						// we must handle all of these cases
+						if ( deleteExpando ) {
+							delete elem[ internalKey ];
+
+						} else if ( typeof elem.removeAttribute !== strundefined ) {
+							elem.removeAttribute( internalKey );
+
+						} else {
+							elem[ internalKey ] = null;
+						}
+
+						deletedIds.push( id );
+					}
+				}
+			}
+		}
+	}
+});
+
+jQuery.fn.extend({
+	text: function( value ) {
+		return access( this, function( value ) {
+			return value === undefined ?
+				jQuery.text( this ) :
+				this.empty().append( ( this[0] && this[0].ownerDocument || document ).createTextNode( value ) );
+		}, null, value, arguments.length );
+	},
+
+	append: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.appendChild( elem );
+			}
+		});
+	},
+
+	prepend: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.insertBefore( elem, target.firstChild );
+			}
+		});
+	},
+
+	before: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this );
+			}
+		});
+	},
+
+	after: function() {
+		return this.domManip( arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this.nextSibling );
+			}
+		});
+	},
+
+	remove: function( selector, keepData /* Internal Use Only */ ) {
+		var elem,
+			elems = selector ? jQuery.filter( selector, this ) : this,
+			i = 0;
+
+		for ( ; (elem = elems[i]) != null; i++ ) {
+
+			if ( !keepData && elem.nodeType === 1 ) {
+				jQuery.cleanData( getAll( elem ) );
+			}
+
+			if ( elem.parentNode ) {
+				if ( keepData && jQuery.contains( elem.ownerDocument, elem ) ) {
+					setGlobalEval( getAll( elem, "script" ) );
+				}
+				elem.parentNode.removeChild( elem );
+			}
+		}
+
+		return this;
+	},
+
+	empty: function() {
+		var elem,
+			i = 0;
+
+		for ( ; (elem = this[i]) != null; i++ ) {
+			// Remove element nodes and prevent memory leaks
+			if ( elem.nodeType === 1 ) {
+				jQuery.cleanData( getAll( elem, false ) );
+			}
+
+			// Remove any remaining nodes
+			while ( elem.firstChild ) {
+				elem.removeChild( elem.firstChild );
+			}
+
+			// If this is a select, ensure that it displays empty (#12336)
+			// Support: IE<9
+			if ( elem.options && jQuery.nodeName( elem, "select" ) ) {
+				elem.options.length = 0;
+			}
+		}
+
+		return this;
+	},
+
+	clone: function( dataAndEvents, deepDataAndEvents ) {
+		dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
+		deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
+
+		return this.map(function() {
+			return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
+		});
+	},
+
+	html: function( value ) {
+		return access( this, function( value ) {
+			var elem = this[ 0 ] || {},
+				i = 0,
+				l = this.length;
+
+			if ( value === undefined ) {
+				return elem.nodeType === 1 ?
+					elem.innerHTML.replace( rinlinejQuery, "" ) :
+					undefined;
+			}
+
+			// See if we can take a shortcut and just use innerHTML
+			if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
+				( support.htmlSerialize || !rnoshimcache.test( value )  ) &&
+				( support.leadingWhitespace || !rleadingWhitespace.test( value ) ) &&
+				!wrapMap[ (rtagName.exec( value ) || [ "", "" ])[ 1 ].toLowerCase() ] ) {
+
+				value = value.replace( rxhtmlTag, "<$1></$2>" );
+
+				try {
+					for (; i < l; i++ ) {
+						// Remove element nodes and prevent memory leaks
+						elem = this[i] || {};
+						if ( elem.nodeType === 1 ) {
+							jQuery.cleanData( getAll( elem, false ) );
+							elem.innerHTML = value;
+						}
+					}
+
+					elem = 0;
+
+				// If using innerHTML throws an exception, use the fallback method
+				} catch(e) {}
+			}
+
+			if ( elem ) {
+				this.empty().append( value );
+			}
+		}, null, value, arguments.length );
+	},
+
+	replaceWith: function() {
+		var arg = arguments[ 0 ];
+
+		// Make the changes, replacing each context element with the new content
+		this.domManip( arguments, function( elem ) {
+			arg = this.parentNode;
+
+			jQuery.cleanData( getAll( this ) );
+
+			if ( arg ) {
+				arg.replaceChild( elem, this );
+			}
+		});
+
+		// Force removal if there was no new content (e.g., from empty arguments)
+		return arg && (arg.length || arg.nodeType) ? this : this.remove();
+	},
+
+	detach: function( selector ) {
+		return this.remove( selector, true );
+	},
+
+	domManip: function( args, callback ) {
+
+		// Flatten any nested arrays
+		args = concat.apply( [], args );
+
+		var first, node, hasScripts,
+			scripts, doc, fragment,
+			i = 0,
+			l = this.length,
+			set = this,
+			iNoClone = l - 1,
+			value = args[0],
+			isFunction = jQuery.isFunction( value );
+
+		// We can't cloneNode fragments that contain checked, in WebKit
+		if ( isFunction ||
+				( l > 1 && typeof value === "string" &&
+					!support.checkClone && rchecked.test( value ) ) ) {
+			return this.each(function( index ) {
+				var self = set.eq( index );
+				if ( isFunction ) {
+					args[0] = value.call( this, index, self.html() );
+				}
+				self.domManip( args, callback );
+			});
+		}
+
+		if ( l ) {
+			fragment = jQuery.buildFragment( args, this[ 0 ].ownerDocument, false, this );
+			first = fragment.firstChild;
+
+			if ( fragment.childNodes.length === 1 ) {
+				fragment = first;
+			}
+
+			if ( first ) {
+				scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
+				hasScripts = scripts.length;
+
+				// Use the original fragment for the last item instead of the first because it can end up
+				// being emptied incorrectly in certain situations (#8070).
+				for ( ; i < l; i++ ) {
+					node = fragment;
+
+					if ( i !== iNoClone ) {
+						node = jQuery.clone( node, true, true );
+
+						// Keep references to cloned scripts for later restoration
+						if ( hasScripts ) {
+							jQuery.merge( scripts, getAll( node, "script" ) );
+						}
+					}
+
+					callback.call( this[i], node, i );
+				}
+
+				if ( hasScripts ) {
+					doc = scripts[ scripts.length - 1 ].ownerDocument;
+
+					// Reenable scripts
+					jQuery.map( scripts, restoreScript );
+
+					// Evaluate executable scripts on first document insertion
+					for ( i = 0; i < hasScripts; i++ ) {
+						node = scripts[ i ];
+						if ( rscriptType.test( node.type || "" ) &&
+							!jQuery._data( node, "globalEval" ) && jQuery.contains( doc, node ) ) {
+
+							if ( node.src ) {
+								// Optional AJAX dependency, but won't run scripts if not present
+								if ( jQuery._evalUrl ) {
+									jQuery._evalUrl( node.src );
+								}
+							} else {
+								jQuery.globalEval( ( node.text || node.textContent || node.innerHTML || "" ).replace( rcleanScript, "" ) );
+							}
+						}
+					}
+				}
+
+				// Fix #11809: Avoid leaking memory
+				fragment = first = null;
+			}
+		}
+
+		return this;
+	}
+});
+
+jQuery.each({
+	appendTo: "append",
+	prependTo: "prepend",
+	insertBefore: "before",
+	insertAfter: "after",
+	replaceAll: "replaceWith"
+}, function( name, original ) {
+	jQuery.fn[ name ] = function( selector ) {
+		var elems,
+			i = 0,
+			ret = [],
+			insert = jQuery( selector ),
+			last = insert.length - 1;
+
+		for ( ; i <= last; i++ ) {
+			elems = i === last ? this : this.clone(true);
+			jQuery( insert[i] )[ original ]( elems );
+
+			// Modern browsers can apply jQuery collections as arrays, but oldIE needs a .get()
+			push.apply( ret, elems.get() );
+		}
+
+		return this.pushStack( ret );
+	};
+});
+
+
+var iframe,
+	elemdisplay = {};
+
+/**
+ * Retrieve the actual display of a element
+ * @param {String} name nodeName of the element
+ * @param {Object} doc Document object
+ */
+// Called only from within defaultDisplay
+function actualDisplay( name, doc ) {
+	var style,
+		elem = jQuery( doc.createElement( name ) ).appendTo( doc.body ),
+
+		// getDefaultComputedStyle might be reliably used only on attached element
+		display = window.getDefaultComputedStyle && ( style = window.getDefaultComputedStyle( elem[ 0 ] ) ) ?
+
+			// Use of this method is a temporary fix (more like optmization) until something better comes along,
+			// since it was removed from specification and supported only in FF
+			style.display : jQuery.css( elem[ 0 ], "display" );
+
+	// We don't have any data stored on the element,
+	// so use "detach" method as fast way to get rid of the element
+	elem.detach();
+
+	return display;
+}
+
+/**
+ * Try to determine the default display value of an element
+ * @param {String} nodeName
+ */
+function defaultDisplay( nodeName ) {
+	var doc = document,
+		display = elemdisplay[ nodeName ];
+
+	if ( !display ) {
+		display = actualDisplay( nodeName, doc );
+
+		// If the simple way fails, read from inside an iframe
+		if ( display === "none" || !display ) {
+
+			// Use the already-created iframe if possible
+			iframe = (iframe || jQuery( "<iframe frameborder='0' width='0' height='0'/>" )).appendTo( doc.documentElement );
+
+			// Always write a new HTML skeleton so Webkit and Firefox don't choke on reuse
+			doc = ( iframe[ 0 ].contentWindow || iframe[ 0 ].contentDocument ).document;
+
+			// Support: IE
+			doc.write();
+			doc.close();
+
+			display = actualDisplay( nodeName, doc );
+			iframe.detach();
+		}
+
+		// Store the correct default display
+		elemdisplay[ nodeName ] = display;
+	}
+
+	return display;
+}
+
+
+(function() {
+	var shrinkWrapBlocksVal;
+
+	support.shrinkWrapBlocks = function() {
+		if ( shrinkWrapBlocksVal != null ) {
+			return shrinkWrapBlocksVal;
+		}
+
+		// Will be changed later if needed.
+		shrinkWrapBlocksVal = false;
+
+		// Minified: var b,c,d
+		var div, body, container;
+
+		body = document.getElementsByTagName( "body" )[ 0 ];
+		if ( !body || !body.style ) {
+			// Test fired too early or in an unsupported environment, exit.
+			return;
+		}
+
+		// Setup
+		div = document.createElement( "div" );
+		container = document.createElement( "div" );
+		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+		body.appendChild( container ).appendChild( div );
+
+		// Support: IE6
+		// Check if elements with layout shrink-wrap their children
+		if ( typeof div.style.zoom !== strundefined ) {
+			// Reset CSS: box-sizing; display; margin; border
+			div.style.cssText =
+				// Support: Firefox<29, Android 2.3
+				// Vendor-prefix box-sizing
+				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
+				"box-sizing:content-box;display:block;margin:0;border:0;" +
+				"padding:1px;width:1px;zoom:1";
+			div.appendChild( document.createElement( "div" ) ).style.width = "5px";
+			shrinkWrapBlocksVal = div.offsetWidth !== 3;
+		}
+
+		body.removeChild( container );
+
+		return shrinkWrapBlocksVal;
+	};
+
+})();
+var rmargin = (/^margin/);
+
+var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
+
+
+
+var getStyles, curCSS,
+	rposition = /^(top|right|bottom|left)$/;
+
+if ( window.getComputedStyle ) {
+	getStyles = function( elem ) {
+		// Support: IE<=11+, Firefox<=30+ (#15098, #14150)
+		// IE throws on elements created in popups
+		// FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
+		if ( elem.ownerDocument.defaultView.opener ) {
+			return elem.ownerDocument.defaultView.getComputedStyle( elem, null );
+		}
+
+		return window.getComputedStyle( elem, null );
+	};
+
+	curCSS = function( elem, name, computed ) {
+		var width, minWidth, maxWidth, ret,
+			style = elem.style;
+
+		computed = computed || getStyles( elem );
+
+		// getPropertyValue is only needed for .css('filter') in IE9, see #12537
+		ret = computed ? computed.getPropertyValue( name ) || computed[ name ] : undefined;
+
+		if ( computed ) {
+
+			if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
+				ret = jQuery.style( elem, name );
+			}
+
+			// A tribute to the "awesome hack by Dean Edwards"
+			// Chrome < 17 and Safari 5.0 uses "computed value" instead of "used value" for margin-right
+			// Safari 5.1.7 (at least) returns percentage for a larger set of values, but width seems to be reliably pixels
+			// this is against the CSSOM draft spec: http://dev.w3.org/csswg/cssom/#resolved-values
+			if ( rnumnonpx.test( ret ) && rmargin.test( name ) ) {
+
+				// Remember the original values
+				width = style.width;
+				minWidth = style.minWidth;
+				maxWidth = style.maxWidth;
+
+				// Put in the new values to get a computed value out
+				style.minWidth = style.maxWidth = style.width = ret;
+				ret = computed.width;
+
+				// Revert the changed values
+				style.width = width;
+				style.minWidth = minWidth;
+				style.maxWidth = maxWidth;
+			}
+		}
+
+		// Support: IE
+		// IE returns zIndex value as an integer.
+		return ret === undefined ?
+			ret :
+			ret + "";
+	};
+} else if ( document.documentElement.currentStyle ) {
+	getStyles = function( elem ) {
+		return elem.currentStyle;
+	};
+
+	curCSS = function( elem, name, computed ) {
+		var left, rs, rsLeft, ret,
+			style = elem.style;
+
+		computed = computed || getStyles( elem );
+		ret = computed ? computed[ name ] : undefined;
+
+		// Avoid setting ret to empty string here
+		// so we don't default to auto
+		if ( ret == null && style && style[ name ] ) {
+			ret = style[ name ];
+		}
+
+		// From the awesome hack by Dean Edwards
+		// http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
+
+		// If we're not dealing with a regular pixel number
+		// but a number that has a weird ending, we need to convert it to pixels
+		// but not position css attributes, as those are proportional to the parent element instead
+		// and we can't measure the parent instead because it might trigger a "stacking dolls" problem
+		if ( rnumnonpx.test( ret ) && !rposition.test( name ) ) {
+
+			// Remember the original values
+			left = style.left;
+			rs = elem.runtimeStyle;
+			rsLeft = rs && rs.left;
+
+			// Put in the new values to get a computed value out
+			if ( rsLeft ) {
+				rs.left = elem.currentStyle.left;
+			}
+			style.left = name === "fontSize" ? "1em" : ret;
+			ret = style.pixelLeft + "px";
+
+			// Revert the changed values
+			style.left = left;
+			if ( rsLeft ) {
+				rs.left = rsLeft;
+			}
+		}
+
+		// Support: IE
+		// IE returns zIndex value as an integer.
+		return ret === undefined ?
+			ret :
+			ret + "" || "auto";
+	};
+}
+
+
+
+
+function addGetHookIf( conditionFn, hookFn ) {
+	// Define the hook, we'll check on the first run if it's really needed.
+	return {
+		get: function() {
+			var condition = conditionFn();
+
+			if ( condition == null ) {
+				// The test was not ready at this point; screw the hook this time
+				// but check again when needed next time.
+				return;
+			}
+
+			if ( condition ) {
+				// Hook not needed (or it's not possible to use it due to missing dependency),
+				// remove it.
+				// Since there are no other hooks for marginRight, remove the whole object.
+				delete this.get;
+				return;
+			}
+
+			// Hook needed; redefine it so that the support test is not executed again.
+
+			return (this.get = hookFn).apply( this, arguments );
+		}
+	};
+}
+
+
+(function() {
+	// Minified: var b,c,d,e,f,g, h,i
+	var div, style, a, pixelPositionVal, boxSizingReliableVal,
+		reliableHiddenOffsetsVal, reliableMarginRightVal;
+
+	// Setup
+	div = document.createElement( "div" );
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+	a = div.getElementsByTagName( "a" )[ 0 ];
+	style = a && a.style;
+
+	// Finish early in limited (non-browser) environments
+	if ( !style ) {
+		return;
+	}
+
+	style.cssText = "float:left;opacity:.5";
+
+	// Support: IE<9
+	// Make sure that element opacity exists (as opposed to filter)
+	support.opacity = style.opacity === "0.5";
+
+	// Verify style float existence
+	// (IE uses styleFloat instead of cssFloat)
+	support.cssFloat = !!style.cssFloat;
+
+	div.style.backgroundClip = "content-box";
+	div.cloneNode( true ).style.backgroundClip = "";
+	support.clearCloneStyle = div.style.backgroundClip === "content-box";
+
+	// Support: Firefox<29, Android 2.3
+	// Vendor-prefix box-sizing
+	support.boxSizing = style.boxSizing === "" || style.MozBoxSizing === "" ||
+		style.WebkitBoxSizing === "";
+
+	jQuery.extend(support, {
+		reliableHiddenOffsets: function() {
+			if ( reliableHiddenOffsetsVal == null ) {
+				computeStyleTests();
+			}
+			return reliableHiddenOffsetsVal;
+		},
+
+		boxSizingReliable: function() {
+			if ( boxSizingReliableVal == null ) {
+				computeStyleTests();
+			}
+			return boxSizingReliableVal;
+		},
+
+		pixelPosition: function() {
+			if ( pixelPositionVal == null ) {
+				computeStyleTests();
+			}
+			return pixelPositionVal;
+		},
+
+		// Support: Android 2.3
+		reliableMarginRight: function() {
+			if ( reliableMarginRightVal == null ) {
+				computeStyleTests();
+			}
+			return reliableMarginRightVal;
+		}
+	});
+
+	function computeStyleTests() {
+		// Minified: var b,c,d,j
+		var div, body, container, contents;
+
+		body = document.getElementsByTagName( "body" )[ 0 ];
+		if ( !body || !body.style ) {
+			// Test fired too early or in an unsupported environment, exit.
+			return;
+		}
+
+		// Setup
+		div = document.createElement( "div" );
+		container = document.createElement( "div" );
+		container.style.cssText = "position:absolute;border:0;width:0;height:0;top:0;left:-9999px";
+		body.appendChild( container ).appendChild( div );
+
+		div.style.cssText =
+			// Support: Firefox<29, Android 2.3
+			// Vendor-prefix box-sizing
+			"-webkit-box-sizing:border-box;-moz-box-sizing:border-box;" +
+			"box-sizing:border-box;display:block;margin-top:1%;top:1%;" +
+			"border:1px;padding:1px;width:4px;position:absolute";
+
+		// Support: IE<9
+		// Assume reasonable values in the absence of getComputedStyle
+		pixelPositionVal = boxSizingReliableVal = false;
+		reliableMarginRightVal = true;
+
+		// Check for getComputedStyle so that this code is not run in IE<9.
+		if ( window.getComputedStyle ) {
+			pixelPositionVal = ( window.getComputedStyle( div, null ) || {} ).top !== "1%";
+			boxSizingReliableVal =
+				( window.getComputedStyle( div, null ) || { width: "4px" } ).width === "4px";
+
+			// Support: Android 2.3
+			// Div with explicit width and no margin-right incorrectly
+			// gets computed margin-right based on width of container (#3333)
+			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+			contents = div.appendChild( document.createElement( "div" ) );
+
+			// Reset CSS: box-sizing; display; margin; border; padding
+			contents.style.cssText = div.style.cssText =
+				// Support: Firefox<29, Android 2.3
+				// Vendor-prefix box-sizing
+				"-webkit-box-sizing:content-box;-moz-box-sizing:content-box;" +
+				"box-sizing:content-box;display:block;margin:0;border:0;padding:0";
+			contents.style.marginRight = contents.style.width = "0";
+			div.style.width = "1px";
+
+			reliableMarginRightVal =
+				!parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight );
+
+			div.removeChild( contents );
+		}
+
+		// Support: IE8
+		// Check if table cells still have offsetWidth/Height when they are set
+		// to display:none and there are still other visible table cells in a
+		// table row; if so, offsetWidth/Height are not reliable for use when
+		// determining if an element has been hidden directly using
+		// display:none (it is still safe to use offsets if a parent element is
+		// hidden; don safety goggles and see bug #4512 for more information).
+		div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
+		contents = div.getElementsByTagName( "td" );
+		contents[ 0 ].style.cssText = "margin:0;border:0;padding:0;display:none";
+		reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
+		if ( reliableHiddenOffsetsVal ) {
+			contents[ 0 ].style.display = "";
+			contents[ 1 ].style.display = "none";
+			reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
+		}
+
+		body.removeChild( container );
+	}
+
+})();
+
+
+// A method for quickly swapping in/out CSS properties to get correct calculations.
+jQuery.swap = function( elem, options, callback, args ) {
+	var ret, name,
+		old = {};
+
+	// Remember the old values, and insert the new ones
+	for ( name in options ) {
+		old[ name ] = elem.style[ name ];
+		elem.style[ name ] = options[ name ];
+	}
+
+	ret = callback.apply( elem, args || [] );
+
+	// Revert the old values
+	for ( name in options ) {
+		elem.style[ name ] = old[ name ];
+	}
+
+	return ret;
+};
+
+
+var
+		ralpha = /alpha\([^)]*\)/i,
+	ropacity = /opacity\s*=\s*([^)]*)/,
+
+	// swappable if display is none or starts with table except "table", "table-cell", or "table-caption"
+	// see here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
+	rdisplayswap = /^(none|table(?!-c[ea]).+)/,
+	rnumsplit = new RegExp( "^(" + pnum + ")(.*)$", "i" ),
+	rrelNum = new RegExp( "^([+-])=(" + pnum + ")", "i" ),
+
+	cssShow = { position: "absolute", visibility: "hidden", display: "block" },
+	cssNormalTransform = {
+		letterSpacing: "0",
+		fontWeight: "400"
+	},
+
+	cssPrefixes = [ "Webkit", "O", "Moz", "ms" ];
+
+
+// return a css property mapped to a potentially vendor prefixed property
+function vendorPropName( style, name ) {
+
+	// shortcut for names that are not vendor prefixed
+	if ( name in style ) {
+		return name;
+	}
+
+	// check for vendor prefixed names
+	var capName = name.charAt(0).toUpperCase() + name.slice(1),
+		origName = name,
+		i = cssPrefixes.length;
+
+	while ( i-- ) {
+		name = cssPrefixes[ i ] + capName;
+		if ( name in style ) {
+			return name;
+		}
+	}
+
+	return origName;
+}
+
+function showHide( elements, show ) {
+	var display, elem, hidden,
+		values = [],
+		index = 0,
+		length = elements.length;
+
+	for ( ; index < length; index++ ) {
+		elem = elements[ index ];
+		if ( !elem.style ) {
+			continue;
+		}
+
+		values[ index ] = jQuery._data( elem, "olddisplay" );
+		display = elem.style.display;
+		if ( show ) {
+			// Reset the inline display of this element to learn if it is
+			// being hidden by cascaded rules or not
+			if ( !values[ index ] && display === "none" ) {
+				elem.style.display = "";
+			}
+
+			// Set elements which have been overridden with display: none
+			// in a stylesheet to whatever the default browser style is
+			// for such an element
+			if ( elem.style.display === "" && isHidden( elem ) ) {
+				values[ index ] = jQuery._data( elem, "olddisplay", defaultDisplay(elem.nodeName) );
+			}
+		} else {
+			hidden = isHidden( elem );
+
+			if ( display && display !== "none" || !hidden ) {
+				jQuery._data( elem, "olddisplay", hidden ? display : jQuery.css( elem, "display" ) );
+			}
+		}
+	}
+
+	// Set the display of most of the elements in a second loop
+	// to avoid the constant reflow
+	for ( index = 0; index < length; index++ ) {
+		elem = elements[ index ];
+		if ( !elem.style ) {
+			continue;
+		}
+		if ( !show || elem.style.display === "none" || elem.style.display === "" ) {
+			elem.style.display = show ? values[ index ] || "" : "none";
+		}
+	}
+
+	return elements;
+}
+
+function setPositiveNumber( elem, value, subtract ) {
+	var matches = rnumsplit.exec( value );
+	return matches ?
+		// Guard against undefined "subtract", e.g., when used as in cssHooks
+		Math.max( 0, matches[ 1 ] - ( subtract || 0 ) ) + ( matches[ 2 ] || "px" ) :
+		value;
+}
+
+function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
+	var i = extra === ( isBorderBox ? "border" : "content" ) ?
+		// If we already have the right measurement, avoid augmentation
+		4 :
+		// Otherwise initialize for horizontal or vertical properties
+		name === "width" ? 1 : 0,
+
+		val = 0;
+
+	for ( ; i < 4; i += 2 ) {
+		// both box models exclude margin, so add it if we want it
+		if ( extra === "margin" ) {
+			val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
+		}
+
+		if ( isBorderBox ) {
+			// border-box includes padding, so remove it if we want content
+			if ( extra === "content" ) {
+				val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+			}
+
+			// at this point, extra isn't border nor margin, so remove border
+			if ( extra !== "margin" ) {
+				val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			}
+		} else {
+			// at this point, extra isn't content, so add padding
+			val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+
+			// at this point, extra isn't content nor padding, so add border
+			if ( extra !== "padding" ) {
+				val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			}
+		}
+	}
+
+	return val;
+}
+
+function getWidthOrHeight( elem, name, extra ) {
+
+	// Start with offset property, which is equivalent to the border-box value
+	var valueIsBorderBox = true,
+		val = name === "width" ? elem.offsetWidth : elem.offsetHeight,
+		styles = getStyles( elem ),
+		isBorderBox = support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
+
+	// some non-html elements return undefined for offsetWidth, so check for null/undefined
+	// svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285
+	// MathML - https://bugzilla.mozilla.org/show_bug.cgi?id=491668
+	if ( val <= 0 || val == null ) {
+		// Fall back to computed then uncomputed css if necessary
+		val = curCSS( elem, name, styles );
+		if ( val < 0 || val == null ) {
+			val = elem.style[ name ];
+		}
+
+		// Computed unit is not pixels. Stop here and return.
+		if ( rnumnonpx.test(val) ) {
+			return val;
+		}
+
+		// we need the check for style in case a browser which returns unreliable values
+		// for getComputedStyle silently falls back to the reliable elem.style
+		valueIsBorderBox = isBorderBox && ( support.boxSizingReliable() || val === elem.style[ name ] );
+
+		// Normalize "", auto, and prepare for extra
+		val = parseFloat( val ) || 0;
+	}
+
+	// use the active box-sizing model to add/subtract irrelevant styles
+	return ( val +
+		augmentWidthOrHeight(
+			elem,
+			name,
+			extra || ( isBorderBox ? "border" : "content" ),
+			valueIsBorderBox,
+			styles
+		)
+	) + "px";
+}
+
+jQuery.extend({
+	// Add in style property hooks for overriding the default
+	// behavior of getting and setting a style property
+	cssHooks: {
+		opacity: {
+			get: function( elem, computed ) {
+				if ( computed ) {
+					// We should always get a number back from opacity
+					var ret = curCSS( elem, "opacity" );
+					return ret === "" ? "1" : ret;
+				}
+			}
+		}
+	},
+
+	// Don't automatically add "px" to these possibly-unitless properties
+	cssNumber: {
+		"columnCount": true,
+		"fillOpacity": true,
+		"flexGrow": true,
+		"flexShrink": true,
+		"fontWeight": true,
+		"lineHeight": true,
+		"opacity": true,
+		"order": true,
+		"orphans": true,
+		"widows": true,
+		"zIndex": true,
+		"zoom": true
+	},
+
+	// Add in properties whose names you wish to fix before
+	// setting or getting the value
+	cssProps: {
+		// normalize float css property
+		"float": support.cssFloat ? "cssFloat" : "styleFloat"
+	},
+
+	// Get and set the style property on a DOM Node
+	style: function( elem, name, value, extra ) {
+		// Don't set styles on text and comment nodes
+		if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
+			return;
+		}
+
+		// Make sure that we're working with the right name
+		var ret, type, hooks,
+			origName = jQuery.camelCase( name ),
+			style = elem.style;
+
+		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( style, origName ) );
+
+		// gets hook for the prefixed version
+		// followed by the unprefixed version
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// Check if we're setting a value
+		if ( value !== undefined ) {
+			type = typeof value;
+
+			// convert relative number strings (+= or -=) to relative numbers. #7345
+			if ( type === "string" && (ret = rrelNum.exec( value )) ) {
+				value = ( ret[1] + 1 ) * ret[2] + parseFloat( jQuery.css( elem, name ) );
+				// Fixes bug #9237
+				type = "number";
+			}
+
+			// Make sure that null and NaN values aren't set. See: #7116
+			if ( value == null || value !== value ) {
+				return;
+			}
+
+			// If a number was passed in, add 'px' to the (except for certain CSS properties)
+			if ( type === "number" && !jQuery.cssNumber[ origName ] ) {
+				value += "px";
+			}
+
+			// Fixes #8908, it can be done more correctly by specifing setters in cssHooks,
+			// but it would mean to define eight (for every problematic property) identical functions
+			if ( !support.clearCloneStyle && value === "" && name.indexOf("background") === 0 ) {
+				style[ name ] = "inherit";
+			}
+
+			// If a hook was provided, use that value, otherwise just set the specified value
+			if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value, extra )) !== undefined ) {
+
+				// Support: IE
+				// Swallow errors from 'invalid' CSS values (#5509)
+				try {
+					style[ name ] = value;
+				} catch(e) {}
+			}
+
+		} else {
+			// If a hook was provided get the non-computed value from there
+			if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
+				return ret;
+			}
+
+			// Otherwise just get the value from the style object
+			return style[ name ];
+		}
+	},
+
+	css: function( elem, name, extra, styles ) {
+		var num, val, hooks,
+			origName = jQuery.camelCase( name );
+
+		// Make sure that we're working with the right name
+		name = jQuery.cssProps[ origName ] || ( jQuery.cssProps[ origName ] = vendorPropName( elem.style, origName ) );
+
+		// gets hook for the prefixed version
+		// followed by the unprefixed version
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// If a hook was provided get the computed value from there
+		if ( hooks && "get" in hooks ) {
+			val = hooks.get( elem, true, extra );
+		}
+
+		// Otherwise, if a way to get the computed value exists, use that
+		if ( val === undefined ) {
+			val = curCSS( elem, name, styles );
+		}
+
+		//convert "normal" to computed value
+		if ( val === "normal" && name in cssNormalTransform ) {
+			val = cssNormalTransform[ name ];
+		}
+
+		// Return, converting to number if forced or a qualifier was provided and val looks numeric
+		if ( extra === "" || extra ) {
+			num = parseFloat( val );
+			return extra === true || jQuery.isNumeric( num ) ? num || 0 : val;
+		}
+		return val;
+	}
+});
+
+jQuery.each([ "height", "width" ], function( i, name ) {
+	jQuery.cssHooks[ name ] = {
+		get: function( elem, computed, extra ) {
+			if ( computed ) {
+				// certain elements can have dimension info if we invisibly show them
+				// however, it must have a current display style that would benefit from this
+				return rdisplayswap.test( jQuery.css( elem, "display" ) ) && elem.offsetWidth === 0 ?
+					jQuery.swap( elem, cssShow, function() {
+						return getWidthOrHeight( elem, name, extra );
+					}) :
+					getWidthOrHeight( elem, name, extra );
+			}
+		},
+
+		set: function( elem, value, extra ) {
+			var styles = extra && getStyles( elem );
+			return setPositiveNumber( elem, value, extra ?
+				augmentWidthOrHeight(
+					elem,
+					name,
+					extra,
+					support.boxSizing && jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+					styles
+				) : 0
+			);
+		}
+	};
+});
+
+if ( !support.opacity ) {
+	jQuery.cssHooks.opacity = {
+		get: function( elem, computed ) {
+			// IE uses filters for opacity
+			return ropacity.test( (computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "" ) ?
+				( 0.01 * parseFloat( RegExp.$1 ) ) + "" :
+				computed ? "1" : "";
+		},
+
+		set: function( elem, value ) {
+			var style = elem.style,
+				currentStyle = elem.currentStyle,
+				opacity = jQuery.isNumeric( value ) ? "alpha(opacity=" + value * 100 + ")" : "",
+				filter = currentStyle && currentStyle.filter || style.filter || "";
+
+			// IE has trouble with opacity if it does not have layout
+			// Force it by setting the zoom level
+			style.zoom = 1;
+
+			// if setting opacity to 1, and no other filters exist - attempt to remove filter attribute #6652
+			// if value === "", then remove inline opacity #12685
+			if ( ( value >= 1 || value === "" ) &&
+					jQuery.trim( filter.replace( ralpha, "" ) ) === "" &&
+					style.removeAttribute ) {
+
+				// Setting style.filter to null, "" & " " still leave "filter:" in the cssText
+				// if "filter:" is present at all, clearType is disabled, we want to avoid this
+				// style.removeAttribute is IE Only, but so apparently is this code path...
+				style.removeAttribute( "filter" );
+
+				// if there is no filter style applied in a css rule or unset inline opacity, we are done
+				if ( value === "" || currentStyle && !currentStyle.filter ) {
+					return;
+				}
+			}
+
+			// otherwise, set new filter values
+			style.filter = ralpha.test( filter ) ?
+				filter.replace( ralpha, opacity ) :
+				filter + " " + opacity;
+		}
+	};
+}
+
+jQuery.cssHooks.marginRight = addGetHookIf( support.reliableMarginRight,
+	function( elem, computed ) {
+		if ( computed ) {
+			// WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right
+			// Work around by temporarily setting element display to inline-block
+			return jQuery.swap( elem, { "display": "inline-block" },
+				curCSS, [ elem, "marginRight" ] );
+		}
+	}
+);
+
+// These hooks are used by animate to expand properties
+jQuery.each({
+	margin: "",
+	padding: "",
+	border: "Width"
+}, function( prefix, suffix ) {
+	jQuery.cssHooks[ prefix + suffix ] = {
+		expand: function( value ) {
+			var i = 0,
+				expanded = {},
+
+				// assumes a single number if not a string
+				parts = typeof value === "string" ? value.split(" ") : [ value ];
+
+			for ( ; i < 4; i++ ) {
+				expanded[ prefix + cssExpand[ i ] + suffix ] =
+					parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
+			}
+
+			return expanded;
+		}
+	};
+
+	if ( !rmargin.test( prefix ) ) {
+		jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
+	}
+});
+
+jQuery.fn.extend({
+	css: function( name, value ) {
+		return access( this, function( elem, name, value ) {
+			var styles, len,
+				map = {},
+				i = 0;
+
+			if ( jQuery.isArray( name ) ) {
+				styles = getStyles( elem );
+				len = name.length;
+
+				for ( ; i < len; i++ ) {
+					map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
+				}
+
+				return map;
+			}
+
+			return value !== undefined ?
+				jQuery.style( elem, name, value ) :
+				jQuery.css( elem, name );
+		}, name, value, arguments.length > 1 );
+	},
+	show: function() {
+		return showHide( this, true );
+	},
+	hide: function() {
+		return showHide( this );
+	},
+	toggle: function( state ) {
+		if ( typeof state === "boolean" ) {
+			return state ? this.show() : this.hide();
+		}
+
+		return this.each(function() {
+			if ( isHidden( this ) ) {
+				jQuery( this ).show();
+			} else {
+				jQuery( this ).hide();
+			}
+		});
+	}
+});
+
+
+function Tween( elem, options, prop, end, easing ) {
+	return new Tween.prototype.init( elem, options, prop, end, easing );
+}
+jQuery.Tween = Tween;
+
+Tween.prototype = {
+	constructor: Tween,
+	init: function( elem, options, prop, end, easing, unit ) {
+		this.elem = elem;
+		this.prop = prop;
+		this.easing = easing || "swing";
+		this.options = options;
+		this.start = this.now = this.cur();
+		this.end = end;
+		this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
+	},
+	cur: function() {
+		var hooks = Tween.propHooks[ this.prop ];
+
+		return hooks && hooks.get ?
+			hooks.get( this ) :
+			Tween.propHooks._default.get( this );
+	},
+	run: function( percent ) {
+		var eased,
+			hooks = Tween.propHooks[ this.prop ];
+
+		if ( this.options.duration ) {
+			this.pos = eased = jQuery.easing[ this.easing ](
+				percent, this.options.duration * percent, 0, 1, this.options.duration
+			);
+		} else {
+			this.pos = eased = percent;
+		}
+		this.now = ( this.end - this.start ) * eased + this.start;
+
+		if ( this.options.step ) {
+			this.options.step.call( this.elem, this.now, this );
+		}
+
+		if ( hooks && hooks.set ) {
+			hooks.set( this );
+		} else {
+			Tween.propHooks._default.set( this );
+		}
+		return this;
+	}
+};
+
+Tween.prototype.init.prototype = Tween.prototype;
+
+Tween.propHooks = {
+	_default: {
+		get: function( tween ) {
+			var result;
+
+			if ( tween.elem[ tween.prop ] != null &&
+				(!tween.elem.style || tween.elem.style[ tween.prop ] == null) ) {
+				return tween.elem[ tween.prop ];
+			}
+
+			// passing an empty string as a 3rd parameter to .css will automatically
+			// attempt a parseFloat and fallback to a string if the parse fails
+			// so, simple values such as "10px" are parsed to Float.
+			// complex values such as "rotate(1rad)" are returned as is.
+			result = jQuery.css( tween.elem, tween.prop, "" );
+			// Empty strings, null, undefined and "auto" are converted to 0.
+			return !result || result === "auto" ? 0 : result;
+		},
+		set: function( tween ) {
+			// use step hook for back compat - use cssHook if its there - use .style if its
+			// available and use plain properties where available
+			if ( jQuery.fx.step[ tween.prop ] ) {
+				jQuery.fx.step[ tween.prop ]( tween );
+			} else if ( tween.elem.style && ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null || jQuery.cssHooks[ tween.prop ] ) ) {
+				jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
+			} else {
+				tween.elem[ tween.prop ] = tween.now;
+			}
+		}
+	}
+};
+
+// Support: IE <=9
+// Panic based approach to setting things on disconnected nodes
+
+Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
+	set: function( tween ) {
+		if ( tween.elem.nodeType && tween.elem.parentNode ) {
+			tween.elem[ tween.prop ] = tween.now;
+		}
+	}
+};
+
+jQuery.easing = {
+	linear: function( p ) {
+		return p;
+	},
+	swing: function( p ) {
+		return 0.5 - Math.cos( p * Math.PI ) / 2;
+	}
+};
+
+jQuery.fx = Tween.prototype.init;
+
+// Back Compat <1.8 extension point
+jQuery.fx.step = {};
+
+
+
+
+var
+	fxNow, timerId,
+	rfxtypes = /^(?:toggle|show|hide)$/,
+	rfxnum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ),
+	rrun = /queueHooks$/,
+	animationPrefilters = [ defaultPrefilter ],
+	tweeners = {
+		"*": [ function( prop, value ) {
+			var tween = this.createTween( prop, value ),
+				target = tween.cur(),
+				parts = rfxnum.exec( value ),
+				unit = parts && parts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
+
+				// Starting value computation is required for potential unit mismatches
+				start = ( jQuery.cssNumber[ prop ] || unit !== "px" && +target ) &&
+					rfxnum.exec( jQuery.css( tween.elem, prop ) ),
+				scale = 1,
+				maxIterations = 20;
+
+			if ( start && start[ 3 ] !== unit ) {
+				// Trust units reported by jQuery.css
+				unit = unit || start[ 3 ];
+
+				// Make sure we update the tween properties later on
+				parts = parts || [];
+
+				// Iteratively approximate from a nonzero starting point
+				start = +target || 1;
+
+				do {
+					// If previous iteration zeroed out, double until we get *something*
+					// Use a string for doubling factor so we don't accidentally see scale as unchanged below
+					scale = scale || ".5";
+
+					// Adjust and apply
+					start = start / scale;
+					jQuery.style( tween.elem, prop, start + unit );
+
+				// Update scale, tolerating zero or NaN from tween.cur()
+				// And breaking the loop if scale is unchanged or perfect, or if we've just had enough
+				} while ( scale !== (scale = tween.cur() / target) && scale !== 1 && --maxIterations );
+			}
+
+			// Update tween properties
+			if ( parts ) {
+				start = tween.start = +start || +target || 0;
+				tween.unit = unit;
+				// If a +=/-= token was provided, we're doing a relative animation
+				tween.end = parts[ 1 ] ?
+					start + ( parts[ 1 ] + 1 ) * parts[ 2 ] :
+					+parts[ 2 ];
+			}
+
+			return tween;
+		} ]
+	};
+
+// Animations created synchronously will run synchronously
+function createFxNow() {
+	setTimeout(function() {
+		fxNow = undefined;
+	});
+	return ( fxNow = jQuery.now() );
+}
+
+// Generate parameters to create a standard animation
+function genFx( type, includeWidth ) {
+	var which,
+		attrs = { height: type },
+		i = 0;
+
+	// if we include width, step value is 1 to do all cssExpand values,
+	// if we don't include width, step value is 2 to skip over Left and Right
+	includeWidth = includeWidth ? 1 : 0;
+	for ( ; i < 4 ; i += 2 - includeWidth ) {
+		which = cssExpand[ i ];
+		attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
+	}
+
+	if ( includeWidth ) {
+		attrs.opacity = attrs.width = type;
+	}
+
+	return attrs;
+}
+
+function createTween( value, prop, animation ) {
+	var tween,
+		collection = ( tweeners[ prop ] || [] ).concat( tweeners[ "*" ] ),
+		index = 0,
+		length = collection.length;
+	for ( ; index < length; index++ ) {
+		if ( (tween = collection[ index ].call( animation, prop, value )) ) {
+
+			// we're done with this property
+			return tween;
+		}
+	}
+}
+
+function defaultPrefilter( elem, props, opts ) {
+	/* jshint validthis: true */
+	var prop, value, toggle, tween, hooks, oldfire, display, checkDisplay,
+		anim = this,
+		orig = {},
+		style = elem.style,
+		hidden = elem.nodeType && isHidden( elem ),
+		dataShow = jQuery._data( elem, "fxshow" );
+
+	// handle queue: false promises
+	if ( !opts.queue ) {
+		hooks = jQuery._queueHooks( elem, "fx" );
+		if ( hooks.unqueued == null ) {
+			hooks.unqueued = 0;
+			oldfire = hooks.empty.fire;
+			hooks.empty.fire = function() {
+				if ( !hooks.unqueued ) {
+					oldfire();
+				}
+			};
+		}
+		hooks.unqueued++;
+
+		anim.always(function() {
+			// doing this makes sure that the complete handler will be called
+			// before this completes
+			anim.always(function() {
+				hooks.unqueued--;
+				if ( !jQuery.queue( elem, "fx" ).length ) {
+					hooks.empty.fire();
+				}
+			});
+		});
+	}
+
+	// height/width overflow pass
+	if ( elem.nodeType === 1 && ( "height" in props || "width" in props ) ) {
+		// Make sure that nothing sneaks out
+		// Record all 3 overflow attributes because IE does not
+		// change the overflow attribute when overflowX and
+		// overflowY are set to the same value
+		opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
+
+		// Set display property to inline-block for height/width
+		// animations on inline elements that are having width/height animated
+		display = jQuery.css( elem, "display" );
+
+		// Test default display if display is currently "none"
+		checkDisplay = display === "none" ?
+			jQuery._data( elem, "olddisplay" ) || defaultDisplay( elem.nodeName ) : display;
+
+		if ( checkDisplay === "inline" && jQuery.css( elem, "float" ) === "none" ) {
+
+			// inline-level elements accept inline-block;
+			// block-level elements need to be inline with layout
+			if ( !support.inlineBlockNeedsLayout || defaultDisplay( elem.nodeName ) === "inline" ) {
+				style.display = "inline-block";
+			} else {
+				style.zoom = 1;
+			}
+		}
+	}
+
+	if ( opts.overflow ) {
+		style.overflow = "hidden";
+		if ( !support.shrinkWrapBlocks() ) {
+			anim.always(function() {
+				style.overflow = opts.overflow[ 0 ];
+				style.overflowX = opts.overflow[ 1 ];
+				style.overflowY = opts.overflow[ 2 ];
+			});
+		}
+	}
+
+	// show/hide pass
+	for ( prop in props ) {
+		value = props[ prop ];
+		if ( rfxtypes.exec( value ) ) {
+			delete props[ prop ];
+			toggle = toggle || value === "toggle";
+			if ( value === ( hidden ? "hide" : "show" ) ) {
+
+				// If there is dataShow left over from a stopped hide or show and we are going to proceed with show, we should pretend to be hidden
+				if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
+					hidden = true;
+				} else {
+					continue;
+				}
+			}
+			orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
+
+		// Any non-fx value stops us from restoring the original display value
+		} else {
+			display = undefined;
+		}
+	}
+
+	if ( !jQuery.isEmptyObject( orig ) ) {
+		if ( dataShow ) {
+			if ( "hidden" in dataShow ) {
+				hidden = dataShow.hidden;
+			}
+		} else {
+			dataShow = jQuery._data( elem, "fxshow", {} );
+		}
+
+		// store state if its toggle - enables .stop().toggle() to "reverse"
+		if ( toggle ) {
+			dataShow.hidden = !hidden;
+		}
+		if ( hidden ) {
+			jQuery( elem ).show();
+		} else {
+			anim.done(function() {
+				jQuery( elem ).hide();
+			});
+		}
+		anim.done(function() {
+			var prop;
+			jQuery._removeData( elem, "fxshow" );
+			for ( prop in orig ) {
+				jQuery.style( elem, prop, orig[ prop ] );
+			}
+		});
+		for ( prop in orig ) {
+			tween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
+
+			if ( !( prop in dataShow ) ) {
+				dataShow[ prop ] = tween.start;
+				if ( hidden ) {
+					tween.end = tween.start;
+					tween.start = prop === "width" || prop === "height" ? 1 : 0;
+				}
+			}
+		}
+
+	// If this is a noop like .hide().hide(), restore an overwritten display value
+	} else if ( (display === "none" ? defaultDisplay( elem.nodeName ) : display) === "inline" ) {
+		style.display = display;
+	}
+}
+
+function propFilter( props, specialEasing ) {
+	var index, name, easing, value, hooks;
+
+	// camelCase, specialEasing and expand cssHook pass
+	for ( index in props ) {
+		name = jQuery.camelCase( index );
+		easing = specialEasing[ name ];
+		value = props[ index ];
+		if ( jQuery.isArray( value ) ) {
+			easing = value[ 1 ];
+			value = props[ index ] = value[ 0 ];
+		}
+
+		if ( index !== name ) {
+			props[ name ] = value;
+			delete props[ index ];
+		}
+
+		hooks = jQuery.cssHooks[ name ];
+		if ( hooks && "expand" in hooks ) {
+			value = hooks.expand( value );
+			delete props[ name ];
+
+			// not quite $.extend, this wont overwrite keys already present.
+			// also - reusing 'index' from above because we have the correct "name"
+			for ( index in value ) {
+				if ( !( index in props ) ) {
+					props[ index ] = value[ index ];
+					specialEasing[ index ] = easing;
+				}
+			}
+		} else {
+			specialEasing[ name ] = easing;
+		}
+	}
+}
+
+function Animation( elem, properties, options ) {
+	var result,
+		stopped,
+		index = 0,
+		length = animationPrefilters.length,
+		deferred = jQuery.Deferred().always( function() {
+			// don't match elem in the :animated selector
+			delete tick.elem;
+		}),
+		tick = function() {
+			if ( stopped ) {
+				return false;
+			}
+			var currentTime = fxNow || createFxNow(),
+				remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
+				// archaic crash bug won't allow us to use 1 - ( 0.5 || 0 ) (#12497)
+				temp = remaining / animation.duration || 0,
+				percent = 1 - temp,
+				index = 0,
+				length = animation.tweens.length;
+
+			for ( ; index < length ; index++ ) {
+				animation.tweens[ index ].run( percent );
+			}
+
+			deferred.notifyWith( elem, [ animation, percent, remaining ]);
+
+			if ( percent < 1 && length ) {
+				return remaining;
+			} else {
+				deferred.resolveWith( elem, [ animation ] );
+				return false;
+			}
+		},
+		animation = deferred.promise({
+			elem: elem,
+			props: jQuery.extend( {}, properties ),
+			opts: jQuery.extend( true, { specialEasing: {} }, options ),
+			originalProperties: properties,
+			originalOptions: options,
+			startTime: fxNow || createFxNow(),
+			duration: options.duration,
+			tweens: [],
+			createTween: function( prop, end ) {
+				var tween = jQuery.Tween( elem, animation.opts, prop, end,
+						animation.opts.specialEasing[ prop ] || animation.opts.easing );
+				animation.tweens.push( tween );
+				return tween;
+			},
+			stop: function( gotoEnd ) {
+				var index = 0,
+					// if we are going to the end, we want to run all the tweens
+					// otherwise we skip this part
+					length = gotoEnd ? animation.tweens.length : 0;
+				if ( stopped ) {
+					return this;
+				}
+				stopped = true;
+				for ( ; index < length ; index++ ) {
+					animation.tweens[ index ].run( 1 );
+				}
+
+				// resolve when we played the last frame
+				// otherwise, reject
+				if ( gotoEnd ) {
+					deferred.resolveWith( elem, [ animation, gotoEnd ] );
+				} else {
+					deferred.rejectWith( elem, [ animation, gotoEnd ] );
+				}
+				return this;
+			}
+		}),
+		props = animation.props;
+
+	propFilter( props, animation.opts.specialEasing );
+
+	for ( ; index < length ; index++ ) {
+		result = animationPrefilters[ index ].call( animation, elem, props, animation.opts );
+		if ( result ) {
+			return result;
+		}
+	}
+
+	jQuery.map( props, createTween, animation );
+
+	if ( jQuery.isFunction( animation.opts.start ) ) {
+		animation.opts.start.call( elem, animation );
+	}
+
+	jQuery.fx.timer(
+		jQuery.extend( tick, {
+			elem: elem,
+			anim: animation,
+			queue: animation.opts.queue
+		})
+	);
+
+	// attach callbacks from options
+	return animation.progress( animation.opts.progress )
+		.done( animation.opts.done, animation.opts.complete )
+		.fail( animation.opts.fail )
+		.always( animation.opts.always );
+}
+
+jQuery.Animation = jQuery.extend( Animation, {
+	tweener: function( props, callback ) {
+		if ( jQuery.isFunction( props ) ) {
+			callback = props;
+			props = [ "*" ];
+		} else {
+			props = props.split(" ");
+		}
+
+		var prop,
+			index = 0,
+			length = props.length;
+
+		for ( ; index < length ; index++ ) {
+			prop = props[ index ];
+			tweeners[ prop ] = tweeners[ prop ] || [];
+			tweeners[ prop ].unshift( callback );
+		}
+	},
+
+	prefilter: function( callback, prepend ) {
+		if ( prepend ) {
+			animationPrefilters.unshift( callback );
+		} else {
+			animationPrefilters.push( callback );
+		}
+	}
+});
+
+jQuery.speed = function( speed, easing, fn ) {
+	var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
+		complete: fn || !fn && easing ||
+			jQuery.isFunction( speed ) && speed,
+		duration: speed,
+		easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
+	};
+
+	opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
+		opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[ opt.duration ] : jQuery.fx.speeds._default;
+
+	// normalize opt.queue - true/undefined/null -> "fx"
+	if ( opt.queue == null || opt.queue === true ) {
+		opt.queue = "fx";
+	}
+
+	// Queueing
+	opt.old = opt.complete;
+
+	opt.complete = function() {
+		if ( jQuery.isFunction( opt.old ) ) {
+			opt.old.call( this );
+		}
+
+		if ( opt.queue ) {
+			jQuery.dequeue( this, opt.queue );
+		}
+	};
+
+	return opt;
+};
+
+jQuery.fn.extend({
+	fadeTo: function( speed, to, easing, callback ) {
+
+		// show any hidden elements after setting opacity to 0
+		return this.filter( isHidden ).css( "opacity", 0 ).show()
+
+			// animate to the value specified
+			.end().animate({ opacity: to }, speed, easing, callback );
+	},
+	animate: function( prop, speed, easing, callback ) {
+		var empty = jQuery.isEmptyObject( prop ),
+			optall = jQuery.speed( speed, easing, callback ),
+			doAnimation = function() {
+				// Operate on a copy of prop so per-property easing won't be lost
+				var anim = Animation( this, jQuery.extend( {}, prop ), optall );
+
+				// Empty animations, or finishing resolves immediately
+				if ( empty || jQuery._data( this, "finish" ) ) {
+					anim.stop( true );
+				}
+			};
+			doAnimation.finish = doAnimation;
+
+		return empty || optall.queue === false ?
+			this.each( doAnimation ) :
+			this.queue( optall.queue, doAnimation );
+	},
+	stop: function( type, clearQueue, gotoEnd ) {
+		var stopQueue = function( hooks ) {
+			var stop = hooks.stop;
+			delete hooks.stop;
+			stop( gotoEnd );
+		};
+
+		if ( typeof type !== "string" ) {
+			gotoEnd = clearQueue;
+			clearQueue = type;
+			type = undefined;
+		}
+		if ( clearQueue && type !== false ) {
+			this.queue( type || "fx", [] );
+		}
+
+		return this.each(function() {
+			var dequeue = true,
+				index = type != null && type + "queueHooks",
+				timers = jQuery.timers,
+				data = jQuery._data( this );
+
+			if ( index ) {
+				if ( data[ index ] && data[ index ].stop ) {
+					stopQueue( data[ index ] );
+				}
+			} else {
+				for ( index in data ) {
+					if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
+						stopQueue( data[ index ] );
+					}
+				}
+			}
+
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this && (type == null || timers[ index ].queue === type) ) {
+					timers[ index ].anim.stop( gotoEnd );
+					dequeue = false;
+					timers.splice( index, 1 );
+				}
+			}
+
+			// start the next in the queue if the last step wasn't forced
+			// timers currently will call their complete callbacks, which will dequeue
+			// but only if they were gotoEnd
+			if ( dequeue || !gotoEnd ) {
+				jQuery.dequeue( this, type );
+			}
+		});
+	},
+	finish: function( type ) {
+		if ( type !== false ) {
+			type = type || "fx";
+		}
+		return this.each(function() {
+			var index,
+				data = jQuery._data( this ),
+				queue = data[ type + "queue" ],
+				hooks = data[ type + "queueHooks" ],
+				timers = jQuery.timers,
+				length = queue ? queue.length : 0;
+
+			// enable finishing flag on private data
+			data.finish = true;
+
+			// empty the queue first
+			jQuery.queue( this, type, [] );
+
+			if ( hooks && hooks.stop ) {
+				hooks.stop.call( this, true );
+			}
+
+			// look for any active animations, and finish them
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
+					timers[ index ].anim.stop( true );
+					timers.splice( index, 1 );
+				}
+			}
+
+			// look for any animations in the old queue and finish them
+			for ( index = 0; index < length; index++ ) {
+				if ( queue[ index ] && queue[ index ].finish ) {
+					queue[ index ].finish.call( this );
+				}
+			}
+
+			// turn off finishing flag
+			delete data.finish;
+		});
+	}
+});
+
+jQuery.each([ "toggle", "show", "hide" ], function( i, name ) {
+	var cssFn = jQuery.fn[ name ];
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return speed == null || typeof speed === "boolean" ?
+			cssFn.apply( this, arguments ) :
+			this.animate( genFx( name, true ), speed, easing, callback );
+	};
+});
+
+// Generate shortcuts for custom animations
+jQuery.each({
+	slideDown: genFx("show"),
+	slideUp: genFx("hide"),
+	slideToggle: genFx("toggle"),
+	fadeIn: { opacity: "show" },
+	fadeOut: { opacity: "hide" },
+	fadeToggle: { opacity: "toggle" }
+}, function( name, props ) {
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return this.animate( props, speed, easing, callback );
+	};
+});
+
+jQuery.timers = [];
+jQuery.fx.tick = function() {
+	var timer,
+		timers = jQuery.timers,
+		i = 0;
+
+	fxNow = jQuery.now();
+
+	for ( ; i < timers.length; i++ ) {
+		timer = timers[ i ];
+		// Checks the timer has not already been removed
+		if ( !timer() && timers[ i ] === timer ) {
+			timers.splice( i--, 1 );
+		}
+	}
+
+	if ( !timers.length ) {
+		jQuery.fx.stop();
+	}
+	fxNow = undefined;
+};
+
+jQuery.fx.timer = function( timer ) {
+	jQuery.timers.push( timer );
+	if ( timer() ) {
+		jQuery.fx.start();
+	} else {
+		jQuery.timers.pop();
+	}
+};
+
+jQuery.fx.interval = 13;
+
+jQuery.fx.start = function() {
+	if ( !timerId ) {
+		timerId = setInterval( jQuery.fx.tick, jQuery.fx.interval );
+	}
+};
+
+jQuery.fx.stop = function() {
+	clearInterval( timerId );
+	timerId = null;
+};
+
+jQuery.fx.speeds = {
+	slow: 600,
+	fast: 200,
+	// Default speed
+	_default: 400
+};
+
+
+// Based off of the plugin by Clint Helfers, with permission.
+// http://blindsignals.com/index.php/2009/07/jquery-delay/
+jQuery.fn.delay = function( time, type ) {
+	time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
+	type = type || "fx";
+
+	return this.queue( type, function( next, hooks ) {
+		var timeout = setTimeout( next, time );
+		hooks.stop = function() {
+			clearTimeout( timeout );
+		};
+	});
+};
+
+
+(function() {
+	// Minified: var a,b,c,d,e
+	var input, div, select, a, opt;
+
+	// Setup
+	div = document.createElement( "div" );
+	div.setAttribute( "className", "t" );
+	div.innerHTML = "  <link/><table></table><a href='/a'>a</a><input type='checkbox'/>";
+	a = div.getElementsByTagName("a")[ 0 ];
+
+	// First batch of tests.
+	select = document.createElement("select");
+	opt = select.appendChild( document.createElement("option") );
+	input = div.getElementsByTagName("input")[ 0 ];
+
+	a.style.cssText = "top:1px";
+
+	// Test setAttribute on camelCase class. If it works, we need attrFixes when doing get/setAttribute (ie6/7)
+	support.getSetAttribute = div.className !== "t";
+
+	// Get the style information from getAttribute
+	// (IE uses .cssText instead)
+	support.style = /top/.test( a.getAttribute("style") );
+
+	// Make sure that URLs aren't manipulated
+	// (IE normalizes it by default)
+	support.hrefNormalized = a.getAttribute("href") === "/a";
+
+	// Check the default checkbox/radio value ("" on WebKit; "on" elsewhere)
+	support.checkOn = !!input.value;
+
+	// Make sure that a selected-by-default option has a working selected property.
+	// (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
+	support.optSelected = opt.selected;
+
+	// Tests for enctype support on a form (#6743)
+	support.enctype = !!document.createElement("form").enctype;
+
+	// Make sure that the options inside disabled selects aren't marked as disabled
+	// (WebKit marks them as disabled)
+	select.disabled = true;
+	support.optDisabled = !opt.disabled;
+
+	// Support: IE8 only
+	// Check if we can trust getAttribute("value")
+	input = document.createElement( "input" );
+	input.setAttribute( "value", "" );
+	support.input = input.getAttribute( "value" ) === "";
+
+	// Check if an input maintains its value after becoming a radio
+	input.value = "t";
+	input.setAttribute( "type", "radio" );
+	support.radioValue = input.value === "t";
+})();
+
+
+var rreturn = /\r/g;
+
+jQuery.fn.extend({
+	val: function( value ) {
+		var hooks, ret, isFunction,
+			elem = this[0];
+
+		if ( !arguments.length ) {
+			if ( elem ) {
+				hooks = jQuery.valHooks[ elem.type ] || jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+
+				if ( hooks && "get" in hooks && (ret = hooks.get( elem, "value" )) !== undefined ) {
+					return ret;
+				}
+
+				ret = elem.value;
+
+				return typeof ret === "string" ?
+					// handle most common string cases
+					ret.replace(rreturn, "") :
+					// handle cases where value is null/undef or number
+					ret == null ? "" : ret;
+			}
+
+			return;
+		}
+
+		isFunction = jQuery.isFunction( value );
+
+		return this.each(function( i ) {
+			var val;
+
+			if ( this.nodeType !== 1 ) {
+				return;
+			}
+
+			if ( isFunction ) {
+				val = value.call( this, i, jQuery( this ).val() );
+			} else {
+				val = value;
+			}
+
+			// Treat null/undefined as ""; convert numbers to string
+			if ( val == null ) {
+				val = "";
+			} else if ( typeof val === "number" ) {
+				val += "";
+			} else if ( jQuery.isArray( val ) ) {
+				val = jQuery.map( val, function( value ) {
+					return value == null ? "" : value + "";
+				});
+			}
+
+			hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
+
+			// If set returns undefined, fall back to normal setting
+			if ( !hooks || !("set" in hooks) || hooks.set( this, val, "value" ) === undefined ) {
+				this.value = val;
+			}
+		});
+	}
+});
+
+jQuery.extend({
+	valHooks: {
+		option: {
+			get: function( elem ) {
+				var val = jQuery.find.attr( elem, "value" );
+				return val != null ?
+					val :
+					// Support: IE10-11+
+					// option.text throws exceptions (#14686, #14858)
+					jQuery.trim( jQuery.text( elem ) );
+			}
+		},
+		select: {
+			get: function( elem ) {
+				var value, option,
+					options = elem.options,
+					index = elem.selectedIndex,
+					one = elem.type === "select-one" || index < 0,
+					values = one ? null : [],
+					max = one ? index + 1 : options.length,
+					i = index < 0 ?
+						max :
+						one ? index : 0;
+
+				// Loop through all the selected options
+				for ( ; i < max; i++ ) {
+					option = options[ i ];
+
+					// oldIE doesn't update selected after form reset (#2551)
+					if ( ( option.selected || i === index ) &&
+							// Don't return options that are disabled or in a disabled optgroup
+							( support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null ) &&
+							( !option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" ) ) ) {
+
+						// Get the specific value for the option
+						value = jQuery( option ).val();
+
+						// We don't need an array for one selects
+						if ( one ) {
+							return value;
+						}
+
+						// Multi-Selects return an array
+						values.push( value );
+					}
+				}
+
+				return values;
+			},
+
+			set: function( elem, value ) {
+				var optionSet, option,
+					options = elem.options,
+					values = jQuery.makeArray( value ),
+					i = options.length;
+
+				while ( i-- ) {
+					option = options[ i ];
+
+					if ( jQuery.inArray( jQuery.valHooks.option.get( option ), values ) >= 0 ) {
+
+						// Support: IE6
+						// When new option element is added to select box we need to
+						// force reflow of newly added node in order to workaround delay
+						// of initialization properties
+						try {
+							option.selected = optionSet = true;
+
+						} catch ( _ ) {
+
+							// Will be executed only in IE6
+							option.scrollHeight;
+						}
+
+					} else {
+						option.selected = false;
+					}
+				}
+
+				// Force browsers to behave consistently when non-matching value is set
+				if ( !optionSet ) {
+					elem.selectedIndex = -1;
+				}
+
+				return options;
+			}
+		}
+	}
+});
+
+// Radios and checkboxes getter/setter
+jQuery.each([ "radio", "checkbox" ], function() {
+	jQuery.valHooks[ this ] = {
+		set: function( elem, value ) {
+			if ( jQuery.isArray( value ) ) {
+				return ( elem.checked = jQuery.inArray( jQuery(elem).val(), value ) >= 0 );
+			}
+		}
+	};
+	if ( !support.checkOn ) {
+		jQuery.valHooks[ this ].get = function( elem ) {
+			// Support: Webkit
+			// "" is returned instead of "on" if a value isn't specified
+			return elem.getAttribute("value") === null ? "on" : elem.value;
+		};
+	}
+});
+
+
+
+
+var nodeHook, boolHook,
+	attrHandle = jQuery.expr.attrHandle,
+	ruseDefault = /^(?:checked|selected)$/i,
+	getSetAttribute = support.getSetAttribute,
+	getSetInput = support.input;
+
+jQuery.fn.extend({
+	attr: function( name, value ) {
+		return access( this, jQuery.attr, name, value, arguments.length > 1 );
+	},
+
+	removeAttr: function( name ) {
+		return this.each(function() {
+			jQuery.removeAttr( this, name );
+		});
+	}
+});
+
+jQuery.extend({
+	attr: function( elem, name, value ) {
+		var hooks, ret,
+			nType = elem.nodeType;
+
+		// don't get/set attributes on text, comment and attribute nodes
+		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
+
+		// Fallback to prop when attributes are not supported
+		if ( typeof elem.getAttribute === strundefined ) {
+			return jQuery.prop( elem, name, value );
+		}
+
+		// All attributes are lowercase
+		// Grab necessary hook if one is defined
+		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+			name = name.toLowerCase();
+			hooks = jQuery.attrHooks[ name ] ||
+				( jQuery.expr.match.bool.test( name ) ? boolHook : nodeHook );
+		}
+
+		if ( value !== undefined ) {
+
+			if ( value === null ) {
+				jQuery.removeAttr( elem, name );
+
+			} else if ( hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ) {
+				return ret;
+
+			} else {
+				elem.setAttribute( name, value + "" );
+				return value;
+			}
+
+		} else if ( hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ) {
+			return ret;
+
+		} else {
+			ret = jQuery.find.attr( elem, name );
+
+			// Non-existent attributes return null, we normalize to undefined
+			return ret == null ?
+				undefined :
+				ret;
+		}
+	},
+
+	removeAttr: function( elem, value ) {
+		var name, propName,
+			i = 0,
+			attrNames = value && value.match( rnotwhite );
+
+		if ( attrNames && elem.nodeType === 1 ) {
+			while ( (name = attrNames[i++]) ) {
+				propName = jQuery.propFix[ name ] || name;
+
+				// Boolean attributes get special treatment (#10870)
+				if ( jQuery.expr.match.bool.test( name ) ) {
+					// Set corresponding property to false
+					if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
+						elem[ propName ] = false;
+					// Support: IE<9
+					// Also clear defaultChecked/defaultSelected (if appropriate)
+					} else {
+						elem[ jQuery.camelCase( "default-" + name ) ] =
+							elem[ propName ] = false;
+					}
+
+				// See #9699 for explanation of this approach (setting first, then removal)
+				} else {
+					jQuery.attr( elem, name, "" );
+				}
+
+				elem.removeAttribute( getSetAttribute ? name : propName );
+			}
+		}
+	},
+
+	attrHooks: {
+		type: {
+			set: function( elem, value ) {
+				if ( !support.radioValue && value === "radio" && jQuery.nodeName(elem, "input") ) {
+					// Setting the type on a radio button after the value resets the value in IE6-9
+					// Reset value to default in case type is set after value during creation
+					var val = elem.value;
+					elem.setAttribute( "type", value );
+					if ( val ) {
+						elem.value = val;
+					}
+					return value;
+				}
+			}
+		}
+	}
+});
+
+// Hook for boolean attributes
+boolHook = {
+	set: function( elem, value, name ) {
+		if ( value === false ) {
+			// Remove boolean attributes when set to false
+			jQuery.removeAttr( elem, name );
+		} else if ( getSetInput && getSetAttribute || !ruseDefault.test( name ) ) {
+			// IE<8 needs the *property* name
+			elem.setAttribute( !getSetAttribute && jQuery.propFix[ name ] || name, name );
+
+		// Use defaultChecked and defaultSelected for oldIE
+		} else {
+			elem[ jQuery.camelCase( "default-" + name ) ] = elem[ name ] = true;
+		}
+
+		return name;
+	}
+};
+
+// Retrieve booleans specially
+jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
+
+	var getter = attrHandle[ name ] || jQuery.find.attr;
+
+	attrHandle[ name ] = getSetInput && getSetAttribute || !ruseDefault.test( name ) ?
+		function( elem, name, isXML ) {
+			var ret, handle;
+			if ( !isXML ) {
+				// Avoid an infinite loop by temporarily removing this function from the getter
+				handle = attrHandle[ name ];
+				attrHandle[ name ] = ret;
+				ret = getter( elem, name, isXML ) != null ?
+					name.toLowerCase() :
+					null;
+				attrHandle[ name ] = handle;
+			}
+			return ret;
+		} :
+		function( elem, name, isXML ) {
+			if ( !isXML ) {
+				return elem[ jQuery.camelCase( "default-" + name ) ] ?
+					name.toLowerCase() :
+					null;
+			}
+		};
+});
+
+// fix oldIE attroperties
+if ( !getSetInput || !getSetAttribute ) {
+	jQuery.attrHooks.value = {
+		set: function( elem, value, name ) {
+			if ( jQuery.nodeName( elem, "input" ) ) {
+				// Does not return so that setAttribute is also used
+				elem.defaultValue = value;
+			} else {
+				// Use nodeHook if defined (#1954); otherwise setAttribute is fine
+				return nodeHook && nodeHook.set( elem, value, name );
+			}
+		}
+	};
+}
+
+// IE6/7 do not support getting/setting some attributes with get/setAttribute
+if ( !getSetAttribute ) {
+
+	// Use this for any attribute in IE6/7
+	// This fixes almost every IE6/7 issue
+	nodeHook = {
+		set: function( elem, value, name ) {
+			// Set the existing or create a new attribute node
+			var ret = elem.getAttributeNode( name );
+			if ( !ret ) {
+				elem.setAttributeNode(
+					(ret = elem.ownerDocument.createAttribute( name ))
+				);
+			}
+
+			ret.value = value += "";
+
+			// Break association with cloned elements by also using setAttribute (#9646)
+			if ( name === "value" || value === elem.getAttribute( name ) ) {
+				return value;
+			}
+		}
+	};
+
+	// Some attributes are constructed with empty-string values when not defined
+	attrHandle.id = attrHandle.name = attrHandle.coords =
+		function( elem, name, isXML ) {
+			var ret;
+			if ( !isXML ) {
+				return (ret = elem.getAttributeNode( name )) && ret.value !== "" ?
+					ret.value :
+					null;
+			}
+		};
+
+	// Fixing value retrieval on a button requires this module
+	jQuery.valHooks.button = {
+		get: function( elem, name ) {
+			var ret = elem.getAttributeNode( name );
+			if ( ret && ret.specified ) {
+				return ret.value;
+			}
+		},
+		set: nodeHook.set
+	};
+
+	// Set contenteditable to false on removals(#10429)
+	// Setting to empty string throws an error as an invalid value
+	jQuery.attrHooks.contenteditable = {
+		set: function( elem, value, name ) {
+			nodeHook.set( elem, value === "" ? false : value, name );
+		}
+	};
+
+	// Set width and height to auto instead of 0 on empty string( Bug #8150 )
+	// This is for removals
+	jQuery.each([ "width", "height" ], function( i, name ) {
+		jQuery.attrHooks[ name ] = {
+			set: function( elem, value ) {
+				if ( value === "" ) {
+					elem.setAttribute( name, "auto" );
+					return value;
+				}
+			}
+		};
+	});
+}
+
+if ( !support.style ) {
+	jQuery.attrHooks.style = {
+		get: function( elem ) {
+			// Return undefined in the case of empty string
+			// Note: IE uppercases css property names, but if we were to .toLowerCase()
+			// .cssText, that would destroy case senstitivity in URL's, like in "background"
+			return elem.style.cssText || undefined;
+		},
+		set: function( elem, value ) {
+			return ( elem.style.cssText = value + "" );
+		}
+	};
+}
+
+
+
+
+var rfocusable = /^(?:input|select|textarea|button|object)$/i,
+	rclickable = /^(?:a|area)$/i;
+
+jQuery.fn.extend({
+	prop: function( name, value ) {
+		return access( this, jQuery.prop, name, value, arguments.length > 1 );
+	},
+
+	removeProp: function( name ) {
+		name = jQuery.propFix[ name ] || name;
+		return this.each(function() {
+			// try/catch handles cases where IE balks (such as removing a property on window)
+			try {
+				this[ name ] = undefined;
+				delete this[ name ];
+			} catch( e ) {}
+		});
+	}
+});
+
+jQuery.extend({
+	propFix: {
+		"for": "htmlFor",
+		"class": "className"
+	},
+
+	prop: function( elem, name, value ) {
+		var ret, hooks, notxml,
+			nType = elem.nodeType;
+
+		// don't get/set properties on text, comment and attribute nodes
+		if ( !elem || nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
+
+		notxml = nType !== 1 || !jQuery.isXMLDoc( elem );
+
+		if ( notxml ) {
+			// Fix name and attach hooks
+			name = jQuery.propFix[ name ] || name;
+			hooks = jQuery.propHooks[ name ];
+		}
+
+		if ( value !== undefined ) {
+			return hooks && "set" in hooks && (ret = hooks.set( elem, value, name )) !== undefined ?
+				ret :
+				( elem[ name ] = value );
+
+		} else {
+			return hooks && "get" in hooks && (ret = hooks.get( elem, name )) !== null ?
+				ret :
+				elem[ name ];
+		}
+	},
+
+	propHooks: {
+		tabIndex: {
+			get: function( elem ) {
+				// elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set
+				// http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
+				// Use proper attribute retrieval(#12072)
+				var tabindex = jQuery.find.attr( elem, "tabindex" );
+
+				return tabindex ?
+					parseInt( tabindex, 10 ) :
+					rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ?
+						0 :
+						-1;
+			}
+		}
+	}
+});
+
+// Some attributes require a special call on IE
+// http://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !support.hrefNormalized ) {
+	// href/src property should get the full normalized URL (#10299/#12915)
+	jQuery.each([ "href", "src" ], function( i, name ) {
+		jQuery.propHooks[ name ] = {
+			get: function( elem ) {
+				return elem.getAttribute( name, 4 );
+			}
+		};
+	});
+}
+
+// Support: Safari, IE9+
+// mis-reports the default selected property of an option
+// Accessing the parent's selectedIndex property fixes it
+if ( !support.optSelected ) {
+	jQuery.propHooks.selected = {
+		get: function( elem ) {
+			var parent = elem.parentNode;
+
+			if ( parent ) {
+				parent.selectedIndex;
+
+				// Make sure that it also works with optgroups, see #5701
+				if ( parent.parentNode ) {
+					parent.parentNode.selectedIndex;
+				}
+			}
+			return null;
+		}
+	};
+}
+
+jQuery.each([
+	"tabIndex",
+	"readOnly",
+	"maxLength",
+	"cellSpacing",
+	"cellPadding",
+	"rowSpan",
+	"colSpan",
+	"useMap",
+	"frameBorder",
+	"contentEditable"
+], function() {
+	jQuery.propFix[ this.toLowerCase() ] = this;
+});
+
+// IE6/7 call enctype encoding
+if ( !support.enctype ) {
+	jQuery.propFix.enctype = "encoding";
+}
+
+
+
+
+var rclass = /[\t\r\n\f]/g;
+
+jQuery.fn.extend({
+	addClass: function( value ) {
+		var classes, elem, cur, clazz, j, finalValue,
+			i = 0,
+			len = this.length,
+			proceed = typeof value === "string" && value;
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( j ) {
+				jQuery( this ).addClass( value.call( this, j, this.className ) );
+			});
+		}
+
+		if ( proceed ) {
+			// The disjunction here is for better compressibility (see removeClass)
+			classes = ( value || "" ).match( rnotwhite ) || [];
+
+			for ( ; i < len; i++ ) {
+				elem = this[ i ];
+				cur = elem.nodeType === 1 && ( elem.className ?
+					( " " + elem.className + " " ).replace( rclass, " " ) :
+					" "
+				);
+
+				if ( cur ) {
+					j = 0;
+					while ( (clazz = classes[j++]) ) {
+						if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
+							cur += clazz + " ";
+						}
+					}
+
+					// only assign if different to avoid unneeded rendering.
+					finalValue = jQuery.trim( cur );
+					if ( elem.className !== finalValue ) {
+						elem.className = finalValue;
+					}
+				}
+			}
+		}
+
+		return this;
+	},
+
+	removeClass: function( value ) {
+		var classes, elem, cur, clazz, j, finalValue,
+			i = 0,
+			len = this.length,
+			proceed = arguments.length === 0 || typeof value === "string" && value;
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( j ) {
+				jQuery( this ).removeClass( value.call( this, j, this.className ) );
+			});
+		}
+		if ( proceed ) {
+			classes = ( value || "" ).match( rnotwhite ) || [];
+
+			for ( ; i < len; i++ ) {
+				elem = this[ i ];
+				// This expression is here for better compressibility (see addClass)
+				cur = elem.nodeType === 1 && ( elem.className ?
+					( " " + elem.className + " " ).replace( rclass, " " ) :
+					""
+				);
+
+				if ( cur ) {
+					j = 0;
+					while ( (clazz = classes[j++]) ) {
+						// Remove *all* instances
+						while ( cur.indexOf( " " + clazz + " " ) >= 0 ) {
+							cur = cur.replace( " " + clazz + " ", " " );
+						}
+					}
+
+					// only assign if different to avoid unneeded rendering.
+					finalValue = value ? jQuery.trim( cur ) : "";
+					if ( elem.className !== finalValue ) {
+						elem.className = finalValue;
+					}
+				}
+			}
+		}
+
+		return this;
+	},
+
+	toggleClass: function( value, stateVal ) {
+		var type = typeof value;
+
+		if ( typeof stateVal === "boolean" && type === "string" ) {
+			return stateVal ? this.addClass( value ) : this.removeClass( value );
+		}
+
+		if ( jQuery.isFunction( value ) ) {
+			return this.each(function( i ) {
+				jQuery( this ).toggleClass( value.call(this, i, this.className, stateVal), stateVal );
+			});
+		}
+
+		return this.each(function() {
+			if ( type === "string" ) {
+				// toggle individual class names
+				var className,
+					i = 0,
+					self = jQuery( this ),
+					classNames = value.match( rnotwhite ) || [];
+
+				while ( (className = classNames[ i++ ]) ) {
+					// check each className given, space separated list
+					if ( self.hasClass( className ) ) {
+						self.removeClass( className );
+					} else {
+						self.addClass( className );
+					}
+				}
+
+			// Toggle whole class name
+			} else if ( type === strundefined || type === "boolean" ) {
+				if ( this.className ) {
+					// store className if set
+					jQuery._data( this, "__className__", this.className );
+				}
+
+				// If the element has a class name or if we're passed "false",
+				// then remove the whole classname (if there was one, the above saved it).
+				// Otherwise bring back whatever was previously saved (if anything),
+				// falling back to the empty string if nothing was stored.
+				this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
+			}
+		});
+	},
+
+	hasClass: function( selector ) {
+		var className = " " + selector + " ",
+			i = 0,
+			l = this.length;
+		for ( ; i < l; i++ ) {
+			if ( this[i].nodeType === 1 && (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) >= 0 ) {
+				return true;
+			}
+		}
+
+		return false;
+	}
+});
+
+
+
+
+// Return jQuery for attributes-only inclusion
+
+
+jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
+	"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
+	"change select submit keydown keypress keyup error contextmenu").split(" "), function( i, name ) {
+
+	// Handle event binding
+	jQuery.fn[ name ] = function( data, fn ) {
+		return arguments.length > 0 ?
+			this.on( name, null, data, fn ) :
+			this.trigger( name );
+	};
+});
+
+jQuery.fn.extend({
+	hover: function( fnOver, fnOut ) {
+		return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
+	},
+
+	bind: function( types, data, fn ) {
+		return this.on( types, null, data, fn );
+	},
+	unbind: function( types, fn ) {
+		return this.off( types, null, fn );
+	},
+
+	delegate: function( selector, types, data, fn ) {
+		return this.on( types, selector, data, fn );
+	},
+	undelegate: function( selector, types, fn ) {
+		// ( namespace ) or ( selector, types [, fn] )
+		return arguments.length === 1 ? this.off( selector, "**" ) : this.off( types, selector || "**", fn );
+	}
+});
+
+
+var nonce = jQuery.now();
+
+var rquery = (/\?/);
+
+
+
+var rvalidtokens = /(,)|(\[|{)|(}|])|"(?:[^"\\\r\n]|\\["\\\/bfnrt]|\\u[\da-fA-F]{4})*"\s*:?|true|false|null|-?(?!0\d)\d+(?:\.\d+|)(?:[eE][+-]?\d+|)/g;
+
+jQuery.parseJSON = function( data ) {
+	// Attempt to parse using the native JSON parser first
+	if ( window.JSON && window.JSON.parse ) {
+		// Support: Android 2.3
+		// Workaround failure to string-cast null input
+		return window.JSON.parse( data + "" );
+	}
+
+	var requireNonComma,
+		depth = null,
+		str = jQuery.trim( data + "" );
+
+	// Guard against invalid (and possibly dangerous) input by ensuring that nothing remains
+	// after removing valid tokens
+	return str && !jQuery.trim( str.replace( rvalidtokens, function( token, comma, open, close ) {
+
+		// Force termination if we see a misplaced comma
+		if ( requireNonComma && comma ) {
+			depth = 0;
+		}
+
+		// Perform no more replacements after returning to outermost depth
+		if ( depth === 0 ) {
+			return token;
+		}
+
+		// Commas must not follow "[", "{", or ","
+		requireNonComma = open || comma;
+
+		// Determine new depth
+		// array/object open ("[" or "{"): depth += true - false (increment)
+		// array/object close ("]" or "}"): depth += false - true (decrement)
+		// other cases ("," or primitive): depth += true - true (numeric cast)
+		depth += !close - !open;
+
+		// Remove this token
+		return "";
+	}) ) ?
+		( Function( "return " + str ) )() :
+		jQuery.error( "Invalid JSON: " + data );
+};
+
+
+// Cross-browser xml parsing
+jQuery.parseXML = function( data ) {
+	var xml, tmp;
+	if ( !data || typeof data !== "string" ) {
+		return null;
+	}
+	try {
+		if ( window.DOMParser ) { // Standard
+			tmp = new DOMParser();
+			xml = tmp.parseFromString( data, "text/xml" );
+		} else { // IE
+			xml = new ActiveXObject( "Microsoft.XMLDOM" );
+			xml.async = "false";
+			xml.loadXML( data );
+		}
+	} catch( e ) {
+		xml = undefined;
+	}
+	if ( !xml || !xml.documentElement || xml.getElementsByTagName( "parsererror" ).length ) {
+		jQuery.error( "Invalid XML: " + data );
+	}
+	return xml;
+};
+
+
+var
+	// Document location
+	ajaxLocParts,
+	ajaxLocation,
+
+	rhash = /#.*$/,
+	rts = /([?&])_=[^&]*/,
+	rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL
+	// #7653, #8125, #8152: local protocol detection
+	rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
+	rnoContent = /^(?:GET|HEAD)$/,
+	rprotocol = /^\/\//,
+	rurl = /^([\w.+-]+:)(?:\/\/(?:[^\/?#]*@|)([^\/?#:]*)(?::(\d+)|)|)/,
+
+	/* Prefilters
+	 * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
+	 * 2) These are called:
+	 *    - BEFORE asking for a transport
+	 *    - AFTER param serialization (s.data is a string if s.processData is true)
+	 * 3) key is the dataType
+	 * 4) the catchall symbol "*" can be used
+	 * 5) execution will start with transport dataType and THEN continue down to "*" if needed
+	 */
+	prefilters = {},
+
+	/* Transports bindings
+	 * 1) key is the dataType
+	 * 2) the catchall symbol "*" can be used
+	 * 3) selection will start with transport dataType and THEN go to "*" if needed
+	 */
+	transports = {},
+
+	// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
+	allTypes = "*/".concat("*");
+
+// #8138, IE may throw an exception when accessing
+// a field from window.location if document.domain has been set
+try {
+	ajaxLocation = location.href;
+} catch( e ) {
+	// Use the href attribute of an A element
+	// since IE will modify it given document.location
+	ajaxLocation = document.createElement( "a" );
+	ajaxLocation.href = "";
+	ajaxLocation = ajaxLocation.href;
+}
+
+// Segment location into parts
+ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || [];
+
+// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
+function addToPrefiltersOrTransports( structure ) {
+
+	// dataTypeExpression is optional and defaults to "*"
+	return function( dataTypeExpression, func ) {
+
+		if ( typeof dataTypeExpression !== "string" ) {
+			func = dataTypeExpression;
+			dataTypeExpression = "*";
+		}
+
+		var dataType,
+			i = 0,
+			dataTypes = dataTypeExpression.toLowerCase().match( rnotwhite ) || [];
+
+		if ( jQuery.isFunction( func ) ) {
+			// For each dataType in the dataTypeExpression
+			while ( (dataType = dataTypes[i++]) ) {
+				// Prepend if requested
+				if ( dataType.charAt( 0 ) === "+" ) {
+					dataType = dataType.slice( 1 ) || "*";
+					(structure[ dataType ] = structure[ dataType ] || []).unshift( func );
+
+				// Otherwise append
+				} else {
+					(structure[ dataType ] = structure[ dataType ] || []).push( func );
+				}
+			}
+		}
+	};
+}
+
+// Base inspection function for prefilters and transports
+function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
+
+	var inspected = {},
+		seekingTransport = ( structure === transports );
+
+	function inspect( dataType ) {
+		var selected;
+		inspected[ dataType ] = true;
+		jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
+			var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
+			if ( typeof dataTypeOrTransport === "string" && !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
+				options.dataTypes.unshift( dataTypeOrTransport );
+				inspect( dataTypeOrTransport );
+				return false;
+			} else if ( seekingTransport ) {
+				return !( selected = dataTypeOrTransport );
+			}
+		});
+		return selected;
+	}
+
+	return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
+}
+
+// A special extend for ajax options
+// that takes "flat" options (not to be deep extended)
+// Fixes #9887
+function ajaxExtend( target, src ) {
+	var deep, key,
+		flatOptions = jQuery.ajaxSettings.flatOptions || {};
+
+	for ( key in src ) {
+		if ( src[ key ] !== undefined ) {
+			( flatOptions[ key ] ? target : ( deep || (deep = {}) ) )[ key ] = src[ key ];
+		}
+	}
+	if ( deep ) {
+		jQuery.extend( true, target, deep );
+	}
+
+	return target;
+}
+
+/* Handles responses to an ajax request:
+ * - finds the right dataType (mediates between content-type and expected dataType)
+ * - returns the corresponding response
+ */
+function ajaxHandleResponses( s, jqXHR, responses ) {
+	var firstDataType, ct, finalDataType, type,
+		contents = s.contents,
+		dataTypes = s.dataTypes;
+
+	// Remove auto dataType and get content-type in the process
+	while ( dataTypes[ 0 ] === "*" ) {
+		dataTypes.shift();
+		if ( ct === undefined ) {
+			ct = s.mimeType || jqXHR.getResponseHeader("Content-Type");
+		}
+	}
+
+	// Check if we're dealing with a known content-type
+	if ( ct ) {
+		for ( type in contents ) {
+			if ( contents[ type ] && contents[ type ].test( ct ) ) {
+				dataTypes.unshift( type );
+				break;
+			}
+		}
+	}
+
+	// Check to see if we have a response for the expected dataType
+	if ( dataTypes[ 0 ] in responses ) {
+		finalDataType = dataTypes[ 0 ];
+	} else {
+		// Try convertible dataTypes
+		for ( type in responses ) {
+			if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
+				finalDataType = type;
+				break;
+			}
+			if ( !firstDataType ) {
+				firstDataType = type;
+			}
+		}
+		// Or just use first one
+		finalDataType = finalDataType || firstDataType;
+	}
+
+	// If we found a dataType
+	// We add the dataType to the list if needed
+	// and return the corresponding response
+	if ( finalDataType ) {
+		if ( finalDataType !== dataTypes[ 0 ] ) {
+			dataTypes.unshift( finalDataType );
+		}
+		return responses[ finalDataType ];
+	}
+}
+
+/* Chain conversions given the request and the original response
+ * Also sets the responseXXX fields on the jqXHR instance
+ */
+function ajaxConvert( s, response, jqXHR, isSuccess ) {
+	var conv2, current, conv, tmp, prev,
+		converters = {},
+		// Work with a copy of dataTypes in case we need to modify it for conversion
+		dataTypes = s.dataTypes.slice();
+
+	// Create converters map with lowercased keys
+	if ( dataTypes[ 1 ] ) {
+		for ( conv in s.converters ) {
+			converters[ conv.toLowerCase() ] = s.converters[ conv ];
+		}
+	}
+
+	current = dataTypes.shift();
+
+	// Convert to each sequential dataType
+	while ( current ) {
+
+		if ( s.responseFields[ current ] ) {
+			jqXHR[ s.responseFields[ current ] ] = response;
+		}
+
+		// Apply the dataFilter if provided
+		if ( !prev && isSuccess && s.dataFilter ) {
+			response = s.dataFilter( response, s.dataType );
+		}
+
+		prev = current;
+		current = dataTypes.shift();
+
+		if ( current ) {
+
+			// There's only work to do if current dataType is non-auto
+			if ( current === "*" ) {
+
+				current = prev;
+
+			// Convert response if prev dataType is non-auto and differs from current
+			} else if ( prev !== "*" && prev !== current ) {
+
+				// Seek a direct converter
+				conv = converters[ prev + " " + current ] || converters[ "* " + current ];
+
+				// If none found, seek a pair
+				if ( !conv ) {
+					for ( conv2 in converters ) {
+
+						// If conv2 outputs current
+						tmp = conv2.split( " " );
+						if ( tmp[ 1 ] === current ) {
+
+							// If prev can be converted to accepted input
+							conv = converters[ prev + " " + tmp[ 0 ] ] ||
+								converters[ "* " + tmp[ 0 ] ];
+							if ( conv ) {
+								// Condense equivalence converters
+								if ( conv === true ) {
+									conv = converters[ conv2 ];
+
+								// Otherwise, insert the intermediate dataType
+								} else if ( converters[ conv2 ] !== true ) {
+									current = tmp[ 0 ];
+									dataTypes.unshift( tmp[ 1 ] );
+								}
+								break;
+							}
+						}
+					}
+				}
+
+				// Apply converter (if not an equivalence)
+				if ( conv !== true ) {
+
+					// Unless errors are allowed to bubble, catch and return them
+					if ( conv && s[ "throws" ] ) {
+						response = conv( response );
+					} else {
+						try {
+							response = conv( response );
+						} catch ( e ) {
+							return { state: "parsererror", error: conv ? e : "No conversion from " + prev + " to " + current };
+						}
+					}
+				}
+			}
+		}
+	}
+
+	return { state: "success", data: response };
+}
+
+jQuery.extend({
+
+	// Counter for holding the number of active queries
+	active: 0,
+
+	// Last-Modified header cache for next request
+	lastModified: {},
+	etag: {},
+
+	ajaxSettings: {
+		url: ajaxLocation,
+		type: "GET",
+		isLocal: rlocalProtocol.test( ajaxLocParts[ 1 ] ),
+		global: true,
+		processData: true,
+		async: true,
+		contentType: "application/x-www-form-urlencoded; charset=UTF-8",
+		/*
+		timeout: 0,
+		data: null,
+		dataType: null,
+		username: null,
+		password: null,
+		cache: null,
+		throws: false,
+		traditional: false,
+		headers: {},
+		*/
+
+		accepts: {
+			"*": allTypes,
+			text: "text/plain",
+			html: "text/html",
+			xml: "application/xml, text/xml",
+			json: "application/json, text/javascript"
+		},
+
+		contents: {
+			xml: /xml/,
+			html: /html/,
+			json: /json/
+		},
+
+		responseFields: {
+			xml: "responseXML",
+			text: "responseText",
+			json: "responseJSON"
+		},
+
+		// Data converters
+		// Keys separate source (or catchall "*") and destination types with a single space
+		converters: {
+
+			// Convert anything to text
+			"* text": String,
+
+			// Text to html (true = no transformation)
+			"text html": true,
+
+			// Evaluate text as a json expression
+			"text json": jQuery.parseJSON,
+
+			// Parse text as xml
+			"text xml": jQuery.parseXML
+		},
+
+		// For options that shouldn't be deep extended:
+		// you can add your own custom options here if
+		// and when you create one that shouldn't be
+		// deep extended (see ajaxExtend)
+		flatOptions: {
+			url: true,
+			context: true
+		}
+	},
+
+	// Creates a full fledged settings object into target
+	// with both ajaxSettings and settings fields.
+	// If target is omitted, writes into ajaxSettings.
+	ajaxSetup: function( target, settings ) {
+		return settings ?
+
+			// Building a settings object
+			ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
+
+			// Extending ajaxSettings
+			ajaxExtend( jQuery.ajaxSettings, target );
+	},
+
+	ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
+	ajaxTransport: addToPrefiltersOrTransports( transports ),
+
+	// Main method
+	ajax: function( url, options ) {
+
+		// If url is an object, simulate pre-1.5 signature
+		if ( typeof url === "object" ) {
+			options = url;
+			url = undefined;
+		}
+
+		// Force options to be an object
+		options = options || {};
+
+		var // Cross-domain detection vars
+			parts,
+			// Loop variable
+			i,
+			// URL without anti-cache param
+			cacheURL,
+			// Response headers as string
+			responseHeadersString,
+			// timeout handle
+			timeoutTimer,
+
+			// To know if global events are to be dispatched
+			fireGlobals,
+
+			transport,
+			// Response headers
+			responseHeaders,
+			// Create the final options object
+			s = jQuery.ajaxSetup( {}, options ),
+			// Callbacks context
+			callbackContext = s.context || s,
+			// Context for global events is callbackContext if it is a DOM node or jQuery collection
+			globalEventContext = s.context && ( callbackContext.nodeType || callbackContext.jquery ) ?
+				jQuery( callbackContext ) :
+				jQuery.event,
+			// Deferreds
+			deferred = jQuery.Deferred(),
+			completeDeferred = jQuery.Callbacks("once memory"),
+			// Status-dependent callbacks
+			statusCode = s.statusCode || {},
+			// Headers (they are sent all at once)
+			requestHeaders = {},
+			requestHeadersNames = {},
+			// The jqXHR state
+			state = 0,
+			// Default abort message
+			strAbort = "canceled",
+			// Fake xhr
+			jqXHR = {
+				readyState: 0,
+
+				// Builds headers hashtable if needed
+				getResponseHeader: function( key ) {
+					var match;
+					if ( state === 2 ) {
+						if ( !responseHeaders ) {
+							responseHeaders = {};
+							while ( (match = rheaders.exec( responseHeadersString )) ) {
+								responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
+							}
+						}
+						match = responseHeaders[ key.toLowerCase() ];
+					}
+					return match == null ? null : match;
+				},
+
+				// Raw string
+				getAllResponseHeaders: function() {
+					return state === 2 ? responseHeadersString : null;
+				},
+
+				// Caches the header
+				setRequestHeader: function( name, value ) {
+					var lname = name.toLowerCase();
+					if ( !state ) {
+						name = requestHeadersNames[ lname ] = requestHeadersNames[ lname ] || name;
+						requestHeaders[ name ] = value;
+					}
+					return this;
+				},
+
+				// Overrides response content-type header
+				overrideMimeType: function( type ) {
+					if ( !state ) {
+						s.mimeType = type;
+					}
+					return this;
+				},
+
+				// Status-dependent callbacks
+				statusCode: function( map ) {
+					var code;
+					if ( map ) {
+						if ( state < 2 ) {
+							for ( code in map ) {
+								// Lazy-add the new callback in a way that preserves old ones
+								statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
+							}
+						} else {
+							// Execute the appropriate callbacks
+							jqXHR.always( map[ jqXHR.status ] );
+						}
+					}
+					return this;
+				},
+
+				// Cancel the request
+				abort: function( statusText ) {
+					var finalText = statusText || strAbort;
+					if ( transport ) {
+						transport.abort( finalText );
+					}
+					done( 0, finalText );
+					return this;
+				}
+			};
+
+		// Attach deferreds
+		deferred.promise( jqXHR ).complete = completeDeferred.add;
+		jqXHR.success = jqXHR.done;
+		jqXHR.error = jqXHR.fail;
+
+		// Remove hash character (#7531: and string promotion)
+		// Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
+		// Handle falsy url in the settings object (#10093: consistency with old signature)
+		// We also use the url parameter if available
+		s.url = ( ( url || s.url || ajaxLocation ) + "" ).replace( rhash, "" ).replace( rprotocol, ajaxLocParts[ 1 ] + "//" );
+
+		// Alias method option to type as per ticket #12004
+		s.type = options.method || options.type || s.method || s.type;
+
+		// Extract dataTypes list
+		s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().match( rnotwhite ) || [ "" ];
+
+		// A cross-domain request is in order when we have a protocol:host:port mismatch
+		if ( s.crossDomain == null ) {
+			parts = rurl.exec( s.url.toLowerCase() );
+			s.crossDomain = !!( parts &&
+				( parts[ 1 ] !== ajaxLocParts[ 1 ] || parts[ 2 ] !== ajaxLocParts[ 2 ] ||
+					( parts[ 3 ] || ( parts[ 1 ] === "http:" ? "80" : "443" ) ) !==
+						( ajaxLocParts[ 3 ] || ( ajaxLocParts[ 1 ] === "http:" ? "80" : "443" ) ) )
+			);
+		}
+
+		// Convert data if not already a string
+		if ( s.data && s.processData && typeof s.data !== "string" ) {
+			s.data = jQuery.param( s.data, s.traditional );
+		}
+
+		// Apply prefilters
+		inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
+
+		// If request was aborted inside a prefilter, stop there
+		if ( state === 2 ) {
+			return jqXHR;
+		}
+
+		// We can fire global events as of now if asked to
+		// Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
+		fireGlobals = jQuery.event && s.global;
+
+		// Watch for a new set of requests
+		if ( fireGlobals && jQuery.active++ === 0 ) {
+			jQuery.event.trigger("ajaxStart");
+		}
+
+		// Uppercase the type
+		s.type = s.type.toUpperCase();
+
+		// Determine if request has content
+		s.hasContent = !rnoContent.test( s.type );
+
+		// Save the URL in case we're toying with the If-Modified-Since
+		// and/or If-None-Match header later on
+		cacheURL = s.url;
+
+		// More options handling for requests with no content
+		if ( !s.hasContent ) {
+
+			// If data is available, append data to url
+			if ( s.data ) {
+				cacheURL = ( s.url += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data );
+				// #9682: remove data so that it's not used in an eventual retry
+				delete s.data;
+			}
+
+			// Add anti-cache in url if needed
+			if ( s.cache === false ) {
+				s.url = rts.test( cacheURL ) ?
+
+					// If there is already a '_' parameter, set its value
+					cacheURL.replace( rts, "$1_=" + nonce++ ) :
+
+					// Otherwise add one to the end
+					cacheURL + ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + nonce++;
+			}
+		}
+
+		// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+		if ( s.ifModified ) {
+			if ( jQuery.lastModified[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
+			}
+			if ( jQuery.etag[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
+			}
+		}
+
+		// Set the correct header, if data is being sent
+		if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
+			jqXHR.setRequestHeader( "Content-Type", s.contentType );
+		}
+
+		// Set the Accepts header for the server, depending on the dataType
+		jqXHR.setRequestHeader(
+			"Accept",
+			s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
+				s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
+				s.accepts[ "*" ]
+		);
+
+		// Check for headers option
+		for ( i in s.headers ) {
+			jqXHR.setRequestHeader( i, s.headers[ i ] );
+		}
+
+		// Allow custom headers/mimetypes and early abort
+		if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || state === 2 ) ) {
+			// Abort if not done already and return
+			return jqXHR.abort();
+		}
+
+		// aborting is no longer a cancellation
+		strAbort = "abort";
+
+		// Install callbacks on deferreds
+		for ( i in { success: 1, error: 1, complete: 1 } ) {
+			jqXHR[ i ]( s[ i ] );
+		}
+
+		// Get transport
+		transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
+
+		// If no transport, we auto-abort
+		if ( !transport ) {
+			done( -1, "No Transport" );
+		} else {
+			jqXHR.readyState = 1;
+
+			// Send global event
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
+			}
+			// Timeout
+			if ( s.async && s.timeout > 0 ) {
+				timeoutTimer = setTimeout(function() {
+					jqXHR.abort("timeout");
+				}, s.timeout );
+			}
+
+			try {
+				state = 1;
+				transport.send( requestHeaders, done );
+			} catch ( e ) {
+				// Propagate exception as error if not done
+				if ( state < 2 ) {
+					done( -1, e );
+				// Simply rethrow otherwise
+				} else {
+					throw e;
+				}
+			}
+		}
+
+		// Callback for when everything is done
+		function done( status, nativeStatusText, responses, headers ) {
+			var isSuccess, success, error, response, modified,
+				statusText = nativeStatusText;
+
+			// Called once
+			if ( state === 2 ) {
+				return;
+			}
+
+			// State is "done" now
+			state = 2;
+
+			// Clear timeout if it exists
+			if ( timeoutTimer ) {
+				clearTimeout( timeoutTimer );
+			}
+
+			// Dereference transport for early garbage collection
+			// (no matter how long the jqXHR object will be used)
+			transport = undefined;
+
+			// Cache response headers
+			responseHeadersString = headers || "";
+
+			// Set readyState
+			jqXHR.readyState = status > 0 ? 4 : 0;
+
+			// Determine if successful
+			isSuccess = status >= 200 && status < 300 || status === 304;
+
+			// Get response data
+			if ( responses ) {
+				response = ajaxHandleResponses( s, jqXHR, responses );
+			}
+
+			// Convert no matter what (that way responseXXX fields are always set)
+			response = ajaxConvert( s, response, jqXHR, isSuccess );
+
+			// If successful, handle type chaining
+			if ( isSuccess ) {
+
+				// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+				if ( s.ifModified ) {
+					modified = jqXHR.getResponseHeader("Last-Modified");
+					if ( modified ) {
+						jQuery.lastModified[ cacheURL ] = modified;
+					}
+					modified = jqXHR.getResponseHeader("etag");
+					if ( modified ) {
+						jQuery.etag[ cacheURL ] = modified;
+					}
+				}
+
+				// if no content
+				if ( status === 204 || s.type === "HEAD" ) {
+					statusText = "nocontent";
+
+				// if not modified
+				} else if ( status === 304 ) {
+					statusText = "notmodified";
+
+				// If we have data, let's convert it
+				} else {
+					statusText = response.state;
+					success = response.data;
+					error = response.error;
+					isSuccess = !error;
+				}
+			} else {
+				// We extract error from statusText
+				// then normalize statusText and status for non-aborts
+				error = statusText;
+				if ( status || !statusText ) {
+					statusText = "error";
+					if ( status < 0 ) {
+						status = 0;
+					}
+				}
+			}
+
+			// Set data for the fake xhr object
+			jqXHR.status = status;
+			jqXHR.statusText = ( nativeStatusText || statusText ) + "";
+
+			// Success/Error
+			if ( isSuccess ) {
+				deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
+			} else {
+				deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
+			}
+
+			// Status-dependent callbacks
+			jqXHR.statusCode( statusCode );
+			statusCode = undefined;
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
+					[ jqXHR, s, isSuccess ? success : error ] );
+			}
+
+			// Complete
+			completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
+				// Handle the global AJAX counter
+				if ( !( --jQuery.active ) ) {
+					jQuery.event.trigger("ajaxStop");
+				}
+			}
+		}
+
+		return jqXHR;
+	},
+
+	getJSON: function( url, data, callback ) {
+		return jQuery.get( url, data, callback, "json" );
+	},
+
+	getScript: function( url, callback ) {
+		return jQuery.get( url, undefined, callback, "script" );
+	}
+});
+
+jQuery.each( [ "get", "post" ], function( i, method ) {
+	jQuery[ method ] = function( url, data, callback, type ) {
+		// shift arguments if data argument was omitted
+		if ( jQuery.isFunction( data ) ) {
+			type = type || callback;
+			callback = data;
+			data = undefined;
+		}
+
+		return jQuery.ajax({
+			url: url,
+			type: method,
+			dataType: type,
+			data: data,
+			success: callback
+		});
+	};
+});
+
+
+jQuery._evalUrl = function( url ) {
+	return jQuery.ajax({
+		url: url,
+		type: "GET",
+		dataType: "script",
+		async: false,
+		global: false,
+		"throws": true
+	});
+};
+
+
+jQuery.fn.extend({
+	wrapAll: function( html ) {
+		if ( jQuery.isFunction( html ) ) {
+			return this.each(function(i) {
+				jQuery(this).wrapAll( html.call(this, i) );
+			});
+		}
+
+		if ( this[0] ) {
+			// The elements to wrap the target around
+			var wrap = jQuery( html, this[0].ownerDocument ).eq(0).clone(true);
+
+			if ( this[0].parentNode ) {
+				wrap.insertBefore( this[0] );
+			}
+
+			wrap.map(function() {
+				var elem = this;
+
+				while ( elem.firstChild && elem.firstChild.nodeType === 1 ) {
+					elem = elem.firstChild;
+				}
+
+				return elem;
+			}).append( this );
+		}
+
+		return this;
+	},
+
+	wrapInner: function( html ) {
+		if ( jQuery.isFunction( html ) ) {
+			return this.each(function(i) {
+				jQuery(this).wrapInner( html.call(this, i) );
+			});
+		}
+
+		return this.each(function() {
+			var self = jQuery( this ),
+				contents = self.contents();
+
+			if ( contents.length ) {
+				contents.wrapAll( html );
+
+			} else {
+				self.append( html );
+			}
+		});
+	},
+
+	wrap: function( html ) {
+		var isFunction = jQuery.isFunction( html );
+
+		return this.each(function(i) {
+			jQuery( this ).wrapAll( isFunction ? html.call(this, i) : html );
+		});
+	},
+
+	unwrap: function() {
+		return this.parent().each(function() {
+			if ( !jQuery.nodeName( this, "body" ) ) {
+				jQuery( this ).replaceWith( this.childNodes );
+			}
+		}).end();
+	}
+});
+
+
+jQuery.expr.filters.hidden = function( elem ) {
+	// Support: Opera <= 12.12
+	// Opera reports offsetWidths and offsetHeights less than zero on some elements
+	return elem.offsetWidth <= 0 && elem.offsetHeight <= 0 ||
+		(!support.reliableHiddenOffsets() &&
+			((elem.style && elem.style.display) || jQuery.css( elem, "display" )) === "none");
+};
+
+jQuery.expr.filters.visible = function( elem ) {
+	return !jQuery.expr.filters.hidden( elem );
+};
+
+
+
+
+var r20 = /%20/g,
+	rbracket = /\[\]$/,
+	rCRLF = /\r?\n/g,
+	rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
+	rsubmittable = /^(?:input|select|textarea|keygen)/i;
+
+function buildParams( prefix, obj, traditional, add ) {
+	var name;
+
+	if ( jQuery.isArray( obj ) ) {
+		// Serialize array item.
+		jQuery.each( obj, function( i, v ) {
+			if ( traditional || rbracket.test( prefix ) ) {
+				// Treat each array item as a scalar.
+				add( prefix, v );
+
+			} else {
+				// Item is non-scalar (array or object), encode its numeric index.
+				buildParams( prefix + "[" + ( typeof v === "object" ? i : "" ) + "]", v, traditional, add );
+			}
+		});
+
+	} else if ( !traditional && jQuery.type( obj ) === "object" ) {
+		// Serialize object item.
+		for ( name in obj ) {
+			buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+		}
+
+	} else {
+		// Serialize scalar item.
+		add( prefix, obj );
+	}
+}
+
+// Serialize an array of form elements or a set of
+// key/values into a query string
+jQuery.param = function( a, traditional ) {
+	var prefix,
+		s = [],
+		add = function( key, value ) {
+			// If value is a function, invoke it and return its value
+			value = jQuery.isFunction( value ) ? value() : ( value == null ? "" : value );
+			s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
+		};
+
+	// Set traditional to true for jQuery <= 1.3.2 behavior.
+	if ( traditional === undefined ) {
+		traditional = jQuery.ajaxSettings && jQuery.ajaxSettings.traditional;
+	}
+
+	// If an array was passed in, assume that it is an array of form elements.
+	if ( jQuery.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
+		// Serialize the form elements
+		jQuery.each( a, function() {
+			add( this.name, this.value );
+		});
+
+	} else {
+		// If traditional, encode the "old" way (the way 1.3.2 or older
+		// did it), otherwise encode params recursively.
+		for ( prefix in a ) {
+			buildParams( prefix, a[ prefix ], traditional, add );
+		}
+	}
+
+	// Return the resulting serialization
+	return s.join( "&" ).replace( r20, "+" );
+};
+
+jQuery.fn.extend({
+	serialize: function() {
+		return jQuery.param( this.serializeArray() );
+	},
+	serializeArray: function() {
+		return this.map(function() {
+			// Can add propHook for "elements" to filter or add form elements
+			var elements = jQuery.prop( this, "elements" );
+			return elements ? jQuery.makeArray( elements ) : this;
+		})
+		.filter(function() {
+			var type = this.type;
+			// Use .is(":disabled") so that fieldset[disabled] works
+			return this.name && !jQuery( this ).is( ":disabled" ) &&
+				rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
+				( this.checked || !rcheckableType.test( type ) );
+		})
+		.map(function( i, elem ) {
+			var val = jQuery( this ).val();
+
+			return val == null ?
+				null :
+				jQuery.isArray( val ) ?
+					jQuery.map( val, function( val ) {
+						return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+					}) :
+					{ name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+		}).get();
+	}
+});
+
+
+// Create the request object
+// (This is still attached to ajaxSettings for backward compatibility)
+jQuery.ajaxSettings.xhr = window.ActiveXObject !== undefined ?
+	// Support: IE6+
+	function() {
+
+		// XHR cannot access local files, always use ActiveX for that case
+		return !this.isLocal &&
+
+			// Support: IE7-8
+			// oldIE XHR does not support non-RFC2616 methods (#13240)
+			// See http://msdn.microsoft.com/en-us/library/ie/ms536648(v=vs.85).aspx
+			// and http://www.w3.org/Protocols/rfc2616/rfc2616-sec9.html#sec9
+			// Although this check for six methods instead of eight
+			// since IE also does not support "trace" and "connect"
+			/^(get|post|head|put|delete|options)$/i.test( this.type ) &&
+
+			createStandardXHR() || createActiveXHR();
+	} :
+	// For all other browsers, use the standard XMLHttpRequest object
+	createStandardXHR;
+
+var xhrId = 0,
+	xhrCallbacks = {},
+	xhrSupported = jQuery.ajaxSettings.xhr();
+
+// Support: IE<10
+// Open requests must be manually aborted on unload (#5280)
+// See https://support.microsoft.com/kb/2856746 for more info
+if ( window.attachEvent ) {
+	window.attachEvent( "onunload", function() {
+		for ( var key in xhrCallbacks ) {
+			xhrCallbacks[ key ]( undefined, true );
+		}
+	});
+}
+
+// Determine support properties
+support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
+xhrSupported = support.ajax = !!xhrSupported;
+
+// Create transport if the browser can provide an xhr
+if ( xhrSupported ) {
+
+	jQuery.ajaxTransport(function( options ) {
+		// Cross domain only allowed if supported through XMLHttpRequest
+		if ( !options.crossDomain || support.cors ) {
+
+			var callback;
+
+			return {
+				send: function( headers, complete ) {
+					var i,
+						xhr = options.xhr(),
+						id = ++xhrId;
+
+					// Open the socket
+					xhr.open( options.type, options.url, options.async, options.username, options.password );
+
+					// Apply custom fields if provided
+					if ( options.xhrFields ) {
+						for ( i in options.xhrFields ) {
+							xhr[ i ] = options.xhrFields[ i ];
+						}
+					}
+
+					// Override mime type if needed
+					if ( options.mimeType && xhr.overrideMimeType ) {
+						xhr.overrideMimeType( options.mimeType );
+					}
+
+					// X-Requested-With header
+					// For cross-domain requests, seeing as conditions for a preflight are
+					// akin to a jigsaw puzzle, we simply never set it to be sure.
+					// (it can always be set on a per-request basis or even using ajaxSetup)
+					// For same-domain requests, won't change header if already provided.
+					if ( !options.crossDomain && !headers["X-Requested-With"] ) {
+						headers["X-Requested-With"] = "XMLHttpRequest";
+					}
+
+					// Set headers
+					for ( i in headers ) {
+						// Support: IE<9
+						// IE's ActiveXObject throws a 'Type Mismatch' exception when setting
+						// request header to a null-value.
+						//
+						// To keep consistent with other XHR implementations, cast the value
+						// to string and ignore `undefined`.
+						if ( headers[ i ] !== undefined ) {
+							xhr.setRequestHeader( i, headers[ i ] + "" );
+						}
+					}
+
+					// Do send the request
+					// This may raise an exception which is actually
+					// handled in jQuery.ajax (so no try/catch here)
+					xhr.send( ( options.hasContent && options.data ) || null );
+
+					// Listener
+					callback = function( _, isAbort ) {
+						var status, statusText, responses;
+
+						// Was never called and is aborted or complete
+						if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
+							// Clean up
+							delete xhrCallbacks[ id ];
+							callback = undefined;
+							xhr.onreadystatechange = jQuery.noop;
+
+							// Abort manually if needed
+							if ( isAbort ) {
+								if ( xhr.readyState !== 4 ) {
+									xhr.abort();
+								}
+							} else {
+								responses = {};
+								status = xhr.status;
+
+								// Support: IE<10
+								// Accessing binary-data responseText throws an exception
+								// (#11426)
+								if ( typeof xhr.responseText === "string" ) {
+									responses.text = xhr.responseText;
+								}
+
+								// Firefox throws an exception when accessing
+								// statusText for faulty cross-domain requests
+								try {
+									statusText = xhr.statusText;
+								} catch( e ) {
+									// We normalize with Webkit giving an empty statusText
+									statusText = "";
+								}
+
+								// Filter status for non standard behaviors
+
+								// If the request is local and we have data: assume a success
+								// (success with no data won't get notified, that's the best we
+								// can do given current implementations)
+								if ( !status && options.isLocal && !options.crossDomain ) {
+									status = responses.text ? 200 : 404;
+								// IE - #1450: sometimes returns 1223 when it should be 204
+								} else if ( status === 1223 ) {
+									status = 204;
+								}
+							}
+						}
+
+						// Call complete if needed
+						if ( responses ) {
+							complete( status, statusText, responses, xhr.getAllResponseHeaders() );
+						}
+					};
+
+					if ( !options.async ) {
+						// if we're in sync mode we fire the callback
+						callback();
+					} else if ( xhr.readyState === 4 ) {
+						// (IE6 & IE7) if it's in cache and has been
+						// retrieved directly we need to fire the callback
+						setTimeout( callback );
+					} else {
+						// Add to the list of active xhr callbacks
+						xhr.onreadystatechange = xhrCallbacks[ id ] = callback;
+					}
+				},
+
+				abort: function() {
+					if ( callback ) {
+						callback( undefined, true );
+					}
+				}
+			};
+		}
+	});
+}
+
+// Functions to create xhrs
+function createStandardXHR() {
+	try {
+		return new window.XMLHttpRequest();
+	} catch( e ) {}
+}
+
+function createActiveXHR() {
+	try {
+		return new window.ActiveXObject( "Microsoft.XMLHTTP" );
+	} catch( e ) {}
+}
+
+
+
+
+// Install script dataType
+jQuery.ajaxSetup({
+	accepts: {
+		script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
+	},
+	contents: {
+		script: /(?:java|ecma)script/
+	},
+	converters: {
+		"text script": function( text ) {
+			jQuery.globalEval( text );
+			return text;
+		}
+	}
+});
+
+// Handle cache's special case and global
+jQuery.ajaxPrefilter( "script", function( s ) {
+	if ( s.cache === undefined ) {
+		s.cache = false;
+	}
+	if ( s.crossDomain ) {
+		s.type = "GET";
+		s.global = false;
+	}
+});
+
+// Bind script tag hack transport
+jQuery.ajaxTransport( "script", function(s) {
+
+	// This transport only deals with cross domain requests
+	if ( s.crossDomain ) {
+
+		var script,
+			head = document.head || jQuery("head")[0] || document.documentElement;
+
+		return {
+
+			send: function( _, callback ) {
+
+				script = document.createElement("script");
+
+				script.async = true;
+
+				if ( s.scriptCharset ) {
+					script.charset = s.scriptCharset;
+				}
+
+				script.src = s.url;
+
+				// Attach handlers for all browsers
+				script.onload = script.onreadystatechange = function( _, isAbort ) {
+
+					if ( isAbort || !script.readyState || /loaded|complete/.test( script.readyState ) ) {
+
+						// Handle memory leak in IE
+						script.onload = script.onreadystatechange = null;
+
+						// Remove the script
+						if ( script.parentNode ) {
+							script.parentNode.removeChild( script );
+						}
+
+						// Dereference the script
+						script = null;
+
+						// Callback if not abort
+						if ( !isAbort ) {
+							callback( 200, "success" );
+						}
+					}
+				};
+
+				// Circumvent IE6 bugs with base elements (#2709 and #4378) by prepending
+				// Use native DOM manipulation to avoid our domManip AJAX trickery
+				head.insertBefore( script, head.firstChild );
+			},
+
+			abort: function() {
+				if ( script ) {
+					script.onload( undefined, true );
+				}
+			}
+		};
+	}
+});
+
+
+
+
+var oldCallbacks = [],
+	rjsonp = /(=)\?(?=&|$)|\?\?/;
+
+// Default jsonp settings
+jQuery.ajaxSetup({
+	jsonp: "callback",
+	jsonpCallback: function() {
+		var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
+		this[ callback ] = true;
+		return callback;
+	}
+});
+
+// Detect, normalize options and install callbacks for jsonp requests
+jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
+
+	var callbackName, overwritten, responseContainer,
+		jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
+			"url" :
+			typeof s.data === "string" && !( s.contentType || "" ).indexOf("application/x-www-form-urlencoded") && rjsonp.test( s.data ) && "data"
+		);
+
+	// Handle iff the expected data type is "jsonp" or we have a parameter to set
+	if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
+
+		// Get callback name, remembering preexisting value associated with it
+		callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ?
+			s.jsonpCallback() :
+			s.jsonpCallback;
+
+		// Insert callback into url or form data
+		if ( jsonProp ) {
+			s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
+		} else if ( s.jsonp !== false ) {
+			s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
+		}
+
+		// Use data converter to retrieve json after script execution
+		s.converters["script json"] = function() {
+			if ( !responseContainer ) {
+				jQuery.error( callbackName + " was not called" );
+			}
+			return responseContainer[ 0 ];
+		};
+
+		// force json dataType
+		s.dataTypes[ 0 ] = "json";
+
+		// Install callback
+		overwritten = window[ callbackName ];
+		window[ callbackName ] = function() {
+			responseContainer = arguments;
+		};
+
+		// Clean-up function (fires after converters)
+		jqXHR.always(function() {
+			// Restore preexisting value
+			window[ callbackName ] = overwritten;
+
+			// Save back as free
+			if ( s[ callbackName ] ) {
+				// make sure that re-using the options doesn't screw things around
+				s.jsonpCallback = originalSettings.jsonpCallback;
+
+				// save the callback name for future use
+				oldCallbacks.push( callbackName );
+			}
+
+			// Call if it was a function and we have a response
+			if ( responseContainer && jQuery.isFunction( overwritten ) ) {
+				overwritten( responseContainer[ 0 ] );
+			}
+
+			responseContainer = overwritten = undefined;
+		});
+
+		// Delegate to script
+		return "script";
+	}
+});
+
+
+
+
+// data: string of html
+// context (optional): If specified, the fragment will be created in this context, defaults to document
+// keepScripts (optional): If true, will include scripts passed in the html string
+jQuery.parseHTML = function( data, context, keepScripts ) {
+	if ( !data || typeof data !== "string" ) {
+		return null;
+	}
+	if ( typeof context === "boolean" ) {
+		keepScripts = context;
+		context = false;
+	}
+	context = context || document;
+
+	var parsed = rsingleTag.exec( data ),
+		scripts = !keepScripts && [];
+
+	// Single tag
+	if ( parsed ) {
+		return [ context.createElement( parsed[1] ) ];
+	}
+
+	parsed = jQuery.buildFragment( [ data ], context, scripts );
+
+	if ( scripts && scripts.length ) {
+		jQuery( scripts ).remove();
+	}
+
+	return jQuery.merge( [], parsed.childNodes );
+};
+
+
+// Keep a copy of the old load method
+var _load = jQuery.fn.load;
+
+/**
+ * Load a url into a page
+ */
+jQuery.fn.load = function( url, params, callback ) {
+	if ( typeof url !== "string" && _load ) {
+		return _load.apply( this, arguments );
+	}
+
+	var selector, response, type,
+		self = this,
+		off = url.indexOf(" ");
+
+	if ( off >= 0 ) {
+		selector = jQuery.trim( url.slice( off, url.length ) );
+		url = url.slice( 0, off );
+	}
+
+	// If it's a function
+	if ( jQuery.isFunction( params ) ) {
+
+		// We assume that it's the callback
+		callback = params;
+		params = undefined;
+
+	// Otherwise, build a param string
+	} else if ( params && typeof params === "object" ) {
+		type = "POST";
+	}
+
+	// If we have elements to modify, make the request
+	if ( self.length > 0 ) {
+		jQuery.ajax({
+			url: url,
+
+			// if "type" variable is undefined, then "GET" method will be used
+			type: type,
+			dataType: "html",
+			data: params
+		}).done(function( responseText ) {
+
+			// Save response for use in complete callback
+			response = arguments;
+
+			self.html( selector ?
+
+				// If a selector was specified, locate the right elements in a dummy div
+				// Exclude scripts to avoid IE 'Permission Denied' errors
+				jQuery("<div>").append( jQuery.parseHTML( responseText ) ).find( selector ) :
+
+				// Otherwise use the full result
+				responseText );
+
+		}).complete( callback && function( jqXHR, status ) {
+			self.each( callback, response || [ jqXHR.responseText, status, jqXHR ] );
+		});
+	}
+
+	return this;
+};
+
+
+
+
+// Attach a bunch of functions for handling common AJAX events
+jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) {
+	jQuery.fn[ type ] = function( fn ) {
+		return this.on( type, fn );
+	};
+});
+
+
+
+
+jQuery.expr.filters.animated = function( elem ) {
+	return jQuery.grep(jQuery.timers, function( fn ) {
+		return elem === fn.elem;
+	}).length;
+};
+
+
+
+
+
+var docElem = window.document.documentElement;
+
+/**
+ * Gets a window from an element
+ */
+function getWindow( elem ) {
+	return jQuery.isWindow( elem ) ?
+		elem :
+		elem.nodeType === 9 ?
+			elem.defaultView || elem.parentWindow :
+			false;
+}
+
+jQuery.offset = {
+	setOffset: function( elem, options, i ) {
+		var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition,
+			position = jQuery.css( elem, "position" ),
+			curElem = jQuery( elem ),
+			props = {};
+
+		// set position first, in-case top/left are set even on static elem
+		if ( position === "static" ) {
+			elem.style.position = "relative";
+		}
+
+		curOffset = curElem.offset();
+		curCSSTop = jQuery.css( elem, "top" );
+		curCSSLeft = jQuery.css( elem, "left" );
+		calculatePosition = ( position === "absolute" || position === "fixed" ) &&
+			jQuery.inArray("auto", [ curCSSTop, curCSSLeft ] ) > -1;
+
+		// need to be able to calculate position if either top or left is auto and position is either absolute or fixed
+		if ( calculatePosition ) {
+			curPosition = curElem.position();
+			curTop = curPosition.top;
+			curLeft = curPosition.left;
+		} else {
+			curTop = parseFloat( curCSSTop ) || 0;
+			curLeft = parseFloat( curCSSLeft ) || 0;
+		}
+
+		if ( jQuery.isFunction( options ) ) {
+			options = options.call( elem, i, curOffset );
+		}
+
+		if ( options.top != null ) {
+			props.top = ( options.top - curOffset.top ) + curTop;
+		}
+		if ( options.left != null ) {
+			props.left = ( options.left - curOffset.left ) + curLeft;
+		}
+
+		if ( "using" in options ) {
+			options.using.call( elem, props );
+		} else {
+			curElem.css( props );
+		}
+	}
+};
+
+jQuery.fn.extend({
+	offset: function( options ) {
+		if ( arguments.length ) {
+			return options === undefined ?
+				this :
+				this.each(function( i ) {
+					jQuery.offset.setOffset( this, options, i );
+				});
+		}
+
+		var docElem, win,
+			box = { top: 0, left: 0 },
+			elem = this[ 0 ],
+			doc = elem && elem.ownerDocument;
+
+		if ( !doc ) {
+			return;
+		}
+
+		docElem = doc.documentElement;
+
+		// Make sure it's not a disconnected DOM node
+		if ( !jQuery.contains( docElem, elem ) ) {
+			return box;
+		}
+
+		// If we don't have gBCR, just use 0,0 rather than error
+		// BlackBerry 5, iOS 3 (original iPhone)
+		if ( typeof elem.getBoundingClientRect !== strundefined ) {
+			box = elem.getBoundingClientRect();
+		}
+		win = getWindow( doc );
+		return {
+			top: box.top  + ( win.pageYOffset || docElem.scrollTop )  - ( docElem.clientTop  || 0 ),
+			left: box.left + ( win.pageXOffset || docElem.scrollLeft ) - ( docElem.clientLeft || 0 )
+		};
+	},
+
+	position: function() {
+		if ( !this[ 0 ] ) {
+			return;
+		}
+
+		var offsetParent, offset,
+			parentOffset = { top: 0, left: 0 },
+			elem = this[ 0 ];
+
+		// fixed elements are offset from window (parentOffset = {top:0, left: 0}, because it is its only offset parent
+		if ( jQuery.css( elem, "position" ) === "fixed" ) {
+			// we assume that getBoundingClientRect is available when computed position is fixed
+			offset = elem.getBoundingClientRect();
+		} else {
+			// Get *real* offsetParent
+			offsetParent = this.offsetParent();
+
+			// Get correct offsets
+			offset = this.offset();
+			if ( !jQuery.nodeName( offsetParent[ 0 ], "html" ) ) {
+				parentOffset = offsetParent.offset();
+			}
+
+			// Add offsetParent borders
+			parentOffset.top  += jQuery.css( offsetParent[ 0 ], "borderTopWidth", true );
+			parentOffset.left += jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true );
+		}
+
+		// Subtract parent offsets and element margins
+		// note: when an element has margin: auto the offsetLeft and marginLeft
+		// are the same in Safari causing offset.left to incorrectly be 0
+		return {
+			top:  offset.top  - parentOffset.top - jQuery.css( elem, "marginTop", true ),
+			left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true)
+		};
+	},
+
+	offsetParent: function() {
+		return this.map(function() {
+			var offsetParent = this.offsetParent || docElem;
+
+			while ( offsetParent && ( !jQuery.nodeName( offsetParent, "html" ) && jQuery.css( offsetParent, "position" ) === "static" ) ) {
+				offsetParent = offsetParent.offsetParent;
+			}
+			return offsetParent || docElem;
+		});
+	}
+});
+
+// Create scrollLeft and scrollTop methods
+jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
+	var top = /Y/.test( prop );
+
+	jQuery.fn[ method ] = function( val ) {
+		return access( this, function( elem, method, val ) {
+			var win = getWindow( elem );
+
+			if ( val === undefined ) {
+				return win ? (prop in win) ? win[ prop ] :
+					win.document.documentElement[ method ] :
+					elem[ method ];
+			}
+
+			if ( win ) {
+				win.scrollTo(
+					!top ? val : jQuery( win ).scrollLeft(),
+					top ? val : jQuery( win ).scrollTop()
+				);
+
+			} else {
+				elem[ method ] = val;
+			}
+		}, method, val, arguments.length, null );
+	};
+});
+
+// Add the top/left cssHooks using jQuery.fn.position
+// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
+// getComputedStyle returns percent when specified for top/left/bottom/right
+// rather than make the css module depend on the offset module, we just check for it here
+jQuery.each( [ "top", "left" ], function( i, prop ) {
+	jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
+		function( elem, computed ) {
+			if ( computed ) {
+				computed = curCSS( elem, prop );
+				// if curCSS returns percentage, fallback to offset
+				return rnumnonpx.test( computed ) ?
+					jQuery( elem ).position()[ prop ] + "px" :
+					computed;
+			}
+		}
+	);
+});
+
+
+// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
+jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
+	jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {
+		// margin is only for outerHeight, outerWidth
+		jQuery.fn[ funcName ] = function( margin, value ) {
+			var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
+				extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
+
+			return access( this, function( elem, type, value ) {
+				var doc;
+
+				if ( jQuery.isWindow( elem ) ) {
+					// As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there
+					// isn't a whole lot we can do. See pull request at this URL for discussion:
+					// https://github.com/jquery/jquery/pull/764
+					return elem.document.documentElement[ "client" + name ];
+				}
+
+				// Get document width or height
+				if ( elem.nodeType === 9 ) {
+					doc = elem.documentElement;
+
+					// Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest
+					// unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it.
+					return Math.max(
+						elem.body[ "scroll" + name ], doc[ "scroll" + name ],
+						elem.body[ "offset" + name ], doc[ "offset" + name ],
+						doc[ "client" + name ]
+					);
+				}
+
+				return value === undefined ?
+					// Get width or height on the element, requesting but not forcing parseFloat
+					jQuery.css( elem, type, extra ) :
+
+					// Set width or height on the element
+					jQuery.style( elem, type, value, extra );
+			}, type, chainable ? margin : undefined, chainable, null );
+		};
+	});
+});
+
+
+// The number of elements contained in the matched element set
+jQuery.fn.size = function() {
+	return this.length;
+};
+
+jQuery.fn.andSelf = jQuery.fn.addBack;
+
+
+
+
+// Register as a named AMD module, since jQuery can be concatenated with other
+// files that may use define, but not via a proper concatenation script that
+// understands anonymous AMD modules. A named AMD is safest and most robust
+// way to register. Lowercase jquery is used because AMD module names are
+// derived from file names, and jQuery is normally delivered in a lowercase
+// file name. Do this after creating the global so that if an AMD module wants
+// to call noConflict to hide this version of jQuery, it will work.
+
+// Note that for maximum portability, libraries that are not jQuery should
+// declare themselves as anonymous modules, and avoid setting a global if an
+// AMD loader is present. jQuery is a special case. For more information, see
+// https://github.com/jrburke/requirejs/wiki/Updating-existing-libraries#wiki-anon
+
+if ( typeof define === "function" && define.amd ) {
+	define( "jquery", [], function() {
+		return jQuery;
+	});
+}
+
+
+
+
+var
+	// Map over jQuery in case of overwrite
+	_jQuery = window.jQuery,
+
+	// Map over the $ in case of overwrite
+	_$ = window.$;
+
+jQuery.noConflict = function( deep ) {
+	if ( window.$ === jQuery ) {
+		window.$ = _$;
+	}
+
+	if ( deep && window.jQuery === jQuery ) {
+		window.jQuery = _jQuery;
+	}
+
+	return jQuery;
+};
+
+// Expose jQuery and $ identifiers, even in
+// AMD (#7102#comment:10, https://github.com/jquery/jquery/pull/557)
+// and CommonJS for browser emulators (#13566)
+if ( typeof noGlobal === strundefined ) {
+	window.jQuery = window.$ = jQuery;
+}
+
+
+
+
+return jQuery;
+
+
+}));
diff --git a/doc/html/_static/searchtools.js b/doc/html/_static/searchtools.js
index 066857ce21b1b4b055f9a9308eb351237260fcca..cb7446728a2f4217a74dea81a69bbb10c12c6621 100644
--- a/doc/html/_static/searchtools.js
+++ b/doc/html/_static/searchtools.js
@@ -2,7 +2,7 @@
  * searchtools.js_t
  * ~~~~~~~~~~~~~~~~
  *
- * Sphinx JavaScript utilities for the full-text search.
+ * Sphinx JavaScript utilties for the full-text search.
  *
  * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
@@ -623,7 +623,7 @@ var Search = {
    * helper function to return a node containing the
    * search summary for a given text. keywords is a list
    * of stemmed words, hlwords is the list of normal, unstemmed
-   * words. the first one is used to find the occurrence, the
+   * words. the first one is used to find the occurance, the
    * latter for highlighting it.
    */
   makeSearchSummary : function(text, keywords, hlwords) {
diff --git a/doc/html/_static/underscore-1.3.1.js b/doc/html/_static/underscore-1.3.1.js
deleted file mode 100644
index 208d4cd890c3183d946092ebe982738ade565061..0000000000000000000000000000000000000000
--- a/doc/html/_static/underscore-1.3.1.js
+++ /dev/null
@@ -1,999 +0,0 @@
-//     Underscore.js 1.3.1
-//     (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-//     Underscore is freely distributable under the MIT license.
-//     Portions of Underscore are inspired or borrowed from Prototype,
-//     Oliver Steele's Functional, and John Resig's Micro-Templating.
-//     For all details and documentation:
-//     http://documentcloud.github.com/underscore
-
-(function() {
-
-  // Baseline setup
-  // --------------
-
-  // Establish the root object, `window` in the browser, or `global` on the server.
-  var root = this;
-
-  // Save the previous value of the `_` variable.
-  var previousUnderscore = root._;
-
-  // Establish the object that gets returned to break out of a loop iteration.
-  var breaker = {};
-
-  // Save bytes in the minified (but not gzipped) version:
-  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
-
-  // Create quick reference variables for speed access to core prototypes.
-  var slice            = ArrayProto.slice,
-      unshift          = ArrayProto.unshift,
-      toString         = ObjProto.toString,
-      hasOwnProperty   = ObjProto.hasOwnProperty;
-
-  // All **ECMAScript 5** native function implementations that we hope to use
-  // are declared here.
-  var
-    nativeForEach      = ArrayProto.forEach,
-    nativeMap          = ArrayProto.map,
-    nativeReduce       = ArrayProto.reduce,
-    nativeReduceRight  = ArrayProto.reduceRight,
-    nativeFilter       = ArrayProto.filter,
-    nativeEvery        = ArrayProto.every,
-    nativeSome         = ArrayProto.some,
-    nativeIndexOf      = ArrayProto.indexOf,
-    nativeLastIndexOf  = ArrayProto.lastIndexOf,
-    nativeIsArray      = Array.isArray,
-    nativeKeys         = Object.keys,
-    nativeBind         = FuncProto.bind;
-
-  // Create a safe reference to the Underscore object for use below.
-  var _ = function(obj) { return new wrapper(obj); };
-
-  // Export the Underscore object for **Node.js**, with
-  // backwards-compatibility for the old `require()` API. If we're in
-  // the browser, add `_` as a global object via a string identifier,
-  // for Closure Compiler "advanced" mode.
-  if (typeof exports !== 'undefined') {
-    if (typeof module !== 'undefined' && module.exports) {
-      exports = module.exports = _;
-    }
-    exports._ = _;
-  } else {
-    root['_'] = _;
-  }
-
-  // Current version.
-  _.VERSION = '1.3.1';
-
-  // Collection Functions
-  // --------------------
-
-  // The cornerstone, an `each` implementation, aka `forEach`.
-  // Handles objects with the built-in `forEach`, arrays, and raw objects.
-  // Delegates to **ECMAScript 5**'s native `forEach` if available.
-  var each = _.each = _.forEach = function(obj, iterator, context) {
-    if (obj == null) return;
-    if (nativeForEach && obj.forEach === nativeForEach) {
-      obj.forEach(iterator, context);
-    } else if (obj.length === +obj.length) {
-      for (var i = 0, l = obj.length; i < l; i++) {
-        if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
-      }
-    } else {
-      for (var key in obj) {
-        if (_.has(obj, key)) {
-          if (iterator.call(context, obj[key], key, obj) === breaker) return;
-        }
-      }
-    }
-  };
-
-  // Return the results of applying the iterator to each element.
-  // Delegates to **ECMAScript 5**'s native `map` if available.
-  _.map = _.collect = function(obj, iterator, context) {
-    var results = [];
-    if (obj == null) return results;
-    if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
-    each(obj, function(value, index, list) {
-      results[results.length] = iterator.call(context, value, index, list);
-    });
-    if (obj.length === +obj.length) results.length = obj.length;
-    return results;
-  };
-
-  // **Reduce** builds up a single result from a list of values, aka `inject`,
-  // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
-  _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
-    var initial = arguments.length > 2;
-    if (obj == null) obj = [];
-    if (nativeReduce && obj.reduce === nativeReduce) {
-      if (context) iterator = _.bind(iterator, context);
-      return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
-    }
-    each(obj, function(value, index, list) {
-      if (!initial) {
-        memo = value;
-        initial = true;
-      } else {
-        memo = iterator.call(context, memo, value, index, list);
-      }
-    });
-    if (!initial) throw new TypeError('Reduce of empty array with no initial value');
-    return memo;
-  };
-
-  // The right-associative version of reduce, also known as `foldr`.
-  // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
-  _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
-    var initial = arguments.length > 2;
-    if (obj == null) obj = [];
-    if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
-      if (context) iterator = _.bind(iterator, context);
-      return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
-    }
-    var reversed = _.toArray(obj).reverse();
-    if (context && !initial) iterator = _.bind(iterator, context);
-    return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
-  };
-
-  // Return the first value which passes a truth test. Aliased as `detect`.
-  _.find = _.detect = function(obj, iterator, context) {
-    var result;
-    any(obj, function(value, index, list) {
-      if (iterator.call(context, value, index, list)) {
-        result = value;
-        return true;
-      }
-    });
-    return result;
-  };
-
-  // Return all the elements that pass a truth test.
-  // Delegates to **ECMAScript 5**'s native `filter` if available.
-  // Aliased as `select`.
-  _.filter = _.select = function(obj, iterator, context) {
-    var results = [];
-    if (obj == null) return results;
-    if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
-    each(obj, function(value, index, list) {
-      if (iterator.call(context, value, index, list)) results[results.length] = value;
-    });
-    return results;
-  };
-
-  // Return all the elements for which a truth test fails.
-  _.reject = function(obj, iterator, context) {
-    var results = [];
-    if (obj == null) return results;
-    each(obj, function(value, index, list) {
-      if (!iterator.call(context, value, index, list)) results[results.length] = value;
-    });
-    return results;
-  };
-
-  // Determine whether all of the elements match a truth test.
-  // Delegates to **ECMAScript 5**'s native `every` if available.
-  // Aliased as `all`.
-  _.every = _.all = function(obj, iterator, context) {
-    var result = true;
-    if (obj == null) return result;
-    if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
-    each(obj, function(value, index, list) {
-      if (!(result = result && iterator.call(context, value, index, list))) return breaker;
-    });
-    return result;
-  };
-
-  // Determine if at least one element in the object matches a truth test.
-  // Delegates to **ECMAScript 5**'s native `some` if available.
-  // Aliased as `any`.
-  var any = _.some = _.any = function(obj, iterator, context) {
-    iterator || (iterator = _.identity);
-    var result = false;
-    if (obj == null) return result;
-    if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
-    each(obj, function(value, index, list) {
-      if (result || (result = iterator.call(context, value, index, list))) return breaker;
-    });
-    return !!result;
-  };
-
-  // Determine if a given value is included in the array or object using `===`.
-  // Aliased as `contains`.
-  _.include = _.contains = function(obj, target) {
-    var found = false;
-    if (obj == null) return found;
-    if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
-    found = any(obj, function(value) {
-      return value === target;
-    });
-    return found;
-  };
-
-  // Invoke a method (with arguments) on every item in a collection.
-  _.invoke = function(obj, method) {
-    var args = slice.call(arguments, 2);
-    return _.map(obj, function(value) {
-      return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
-    });
-  };
-
-  // Convenience version of a common use case of `map`: fetching a property.
-  _.pluck = function(obj, key) {
-    return _.map(obj, function(value){ return value[key]; });
-  };
-
-  // Return the maximum element or (element-based computation).
-  _.max = function(obj, iterator, context) {
-    if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
-    if (!iterator && _.isEmpty(obj)) return -Infinity;
-    var result = {computed : -Infinity};
-    each(obj, function(value, index, list) {
-      var computed = iterator ? iterator.call(context, value, index, list) : value;
-      computed >= result.computed && (result = {value : value, computed : computed});
-    });
-    return result.value;
-  };
-
-  // Return the minimum element (or element-based computation).
-  _.min = function(obj, iterator, context) {
-    if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
-    if (!iterator && _.isEmpty(obj)) return Infinity;
-    var result = {computed : Infinity};
-    each(obj, function(value, index, list) {
-      var computed = iterator ? iterator.call(context, value, index, list) : value;
-      computed < result.computed && (result = {value : value, computed : computed});
-    });
-    return result.value;
-  };
-
-  // Shuffle an array.
-  _.shuffle = function(obj) {
-    var shuffled = [], rand;
-    each(obj, function(value, index, list) {
-      if (index == 0) {
-        shuffled[0] = value;
-      } else {
-        rand = Math.floor(Math.random() * (index + 1));
-        shuffled[index] = shuffled[rand];
-        shuffled[rand] = value;
-      }
-    });
-    return shuffled;
-  };
-
-  // Sort the object's values by a criterion produced by an iterator.
-  _.sortBy = function(obj, iterator, context) {
-    return _.pluck(_.map(obj, function(value, index, list) {
-      return {
-        value : value,
-        criteria : iterator.call(context, value, index, list)
-      };
-    }).sort(function(left, right) {
-      var a = left.criteria, b = right.criteria;
-      return a < b ? -1 : a > b ? 1 : 0;
-    }), 'value');
-  };
-
-  // Groups the object's values by a criterion. Pass either a string attribute
-  // to group by, or a function that returns the criterion.
-  _.groupBy = function(obj, val) {
-    var result = {};
-    var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
-    each(obj, function(value, index) {
-      var key = iterator(value, index);
-      (result[key] || (result[key] = [])).push(value);
-    });
-    return result;
-  };
-
-  // Use a comparator function to figure out at what index an object should
-  // be inserted so as to maintain order. Uses binary search.
-  _.sortedIndex = function(array, obj, iterator) {
-    iterator || (iterator = _.identity);
-    var low = 0, high = array.length;
-    while (low < high) {
-      var mid = (low + high) >> 1;
-      iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
-    }
-    return low;
-  };
-
-  // Safely convert anything iterable into a real, live array.
-  _.toArray = function(iterable) {
-    if (!iterable)                return [];
-    if (iterable.toArray)         return iterable.toArray();
-    if (_.isArray(iterable))      return slice.call(iterable);
-    if (_.isArguments(iterable))  return slice.call(iterable);
-    return _.values(iterable);
-  };
-
-  // Return the number of elements in an object.
-  _.size = function(obj) {
-    return _.toArray(obj).length;
-  };
-
-  // Array Functions
-  // ---------------
-
-  // Get the first element of an array. Passing **n** will return the first N
-  // values in the array. Aliased as `head`. The **guard** check allows it to work
-  // with `_.map`.
-  _.first = _.head = function(array, n, guard) {
-    return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
-  };
-
-  // Returns everything but the last entry of the array. Especcialy useful on
-  // the arguments object. Passing **n** will return all the values in
-  // the array, excluding the last N. The **guard** check allows it to work with
-  // `_.map`.
-  _.initial = function(array, n, guard) {
-    return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
-  };
-
-  // Get the last element of an array. Passing **n** will return the last N
-  // values in the array. The **guard** check allows it to work with `_.map`.
-  _.last = function(array, n, guard) {
-    if ((n != null) && !guard) {
-      return slice.call(array, Math.max(array.length - n, 0));
-    } else {
-      return array[array.length - 1];
-    }
-  };
-
-  // Returns everything but the first entry of the array. Aliased as `tail`.
-  // Especially useful on the arguments object. Passing an **index** will return
-  // the rest of the values in the array from that index onward. The **guard**
-  // check allows it to work with `_.map`.
-  _.rest = _.tail = function(array, index, guard) {
-    return slice.call(array, (index == null) || guard ? 1 : index);
-  };
-
-  // Trim out all falsy values from an array.
-  _.compact = function(array) {
-    return _.filter(array, function(value){ return !!value; });
-  };
-
-  // Return a completely flattened version of an array.
-  _.flatten = function(array, shallow) {
-    return _.reduce(array, function(memo, value) {
-      if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
-      memo[memo.length] = value;
-      return memo;
-    }, []);
-  };
-
-  // Return a version of the array that does not contain the specified value(s).
-  _.without = function(array) {
-    return _.difference(array, slice.call(arguments, 1));
-  };
-
-  // Produce a duplicate-free version of the array. If the array has already
-  // been sorted, you have the option of using a faster algorithm.
-  // Aliased as `unique`.
-  _.uniq = _.unique = function(array, isSorted, iterator) {
-    var initial = iterator ? _.map(array, iterator) : array;
-    var result = [];
-    _.reduce(initial, function(memo, el, i) {
-      if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
-        memo[memo.length] = el;
-        result[result.length] = array[i];
-      }
-      return memo;
-    }, []);
-    return result;
-  };
-
-  // Produce an array that contains the union: each distinct element from all of
-  // the passed-in arrays.
-  _.union = function() {
-    return _.uniq(_.flatten(arguments, true));
-  };
-
-  // Produce an array that contains every item shared between all the
-  // passed-in arrays. (Aliased as "intersect" for back-compat.)
-  _.intersection = _.intersect = function(array) {
-    var rest = slice.call(arguments, 1);
-    return _.filter(_.uniq(array), function(item) {
-      return _.every(rest, function(other) {
-        return _.indexOf(other, item) >= 0;
-      });
-    });
-  };
-
-  // Take the difference between one array and a number of other arrays.
-  // Only the elements present in just the first array will remain.
-  _.difference = function(array) {
-    var rest = _.flatten(slice.call(arguments, 1));
-    return _.filter(array, function(value){ return !_.include(rest, value); });
-  };
-
-  // Zip together multiple lists into a single array -- elements that share
-  // an index go together.
-  _.zip = function() {
-    var args = slice.call(arguments);
-    var length = _.max(_.pluck(args, 'length'));
-    var results = new Array(length);
-    for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
-    return results;
-  };
-
-  // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
-  // we need this function. Return the position of the first occurrence of an
-  // item in an array, or -1 if the item is not included in the array.
-  // Delegates to **ECMAScript 5**'s native `indexOf` if available.
-  // If the array is large and already in sort order, pass `true`
-  // for **isSorted** to use binary search.
-  _.indexOf = function(array, item, isSorted) {
-    if (array == null) return -1;
-    var i, l;
-    if (isSorted) {
-      i = _.sortedIndex(array, item);
-      return array[i] === item ? i : -1;
-    }
-    if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
-    for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
-    return -1;
-  };
-
-  // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
-  _.lastIndexOf = function(array, item) {
-    if (array == null) return -1;
-    if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
-    var i = array.length;
-    while (i--) if (i in array && array[i] === item) return i;
-    return -1;
-  };
-
-  // Generate an integer Array containing an arithmetic progression. A port of
-  // the native Python `range()` function. See
-  // [the Python documentation](http://docs.python.org/library/functions.html#range).
-  _.range = function(start, stop, step) {
-    if (arguments.length <= 1) {
-      stop = start || 0;
-      start = 0;
-    }
-    step = arguments[2] || 1;
-
-    var len = Math.max(Math.ceil((stop - start) / step), 0);
-    var idx = 0;
-    var range = new Array(len);
-
-    while(idx < len) {
-      range[idx++] = start;
-      start += step;
-    }
-
-    return range;
-  };
-
-  // Function (ahem) Functions
-  // ------------------
-
-  // Reusable constructor function for prototype setting.
-  var ctor = function(){};
-
-  // Create a function bound to a given object (assigning `this`, and arguments,
-  // optionally). Binding with arguments is also known as `curry`.
-  // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
-  // We check for `func.bind` first, to fail fast when `func` is undefined.
-  _.bind = function bind(func, context) {
-    var bound, args;
-    if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
-    if (!_.isFunction(func)) throw new TypeError;
-    args = slice.call(arguments, 2);
-    return bound = function() {
-      if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
-      ctor.prototype = func.prototype;
-      var self = new ctor;
-      var result = func.apply(self, args.concat(slice.call(arguments)));
-      if (Object(result) === result) return result;
-      return self;
-    };
-  };
-
-  // Bind all of an object's methods to that object. Useful for ensuring that
-  // all callbacks defined on an object belong to it.
-  _.bindAll = function(obj) {
-    var funcs = slice.call(arguments, 1);
-    if (funcs.length == 0) funcs = _.functions(obj);
-    each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
-    return obj;
-  };
-
-  // Memoize an expensive function by storing its results.
-  _.memoize = function(func, hasher) {
-    var memo = {};
-    hasher || (hasher = _.identity);
-    return function() {
-      var key = hasher.apply(this, arguments);
-      return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
-    };
-  };
-
-  // Delays a function for the given number of milliseconds, and then calls
-  // it with the arguments supplied.
-  _.delay = function(func, wait) {
-    var args = slice.call(arguments, 2);
-    return setTimeout(function(){ return func.apply(func, args); }, wait);
-  };
-
-  // Defers a function, scheduling it to run after the current call stack has
-  // cleared.
-  _.defer = function(func) {
-    return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
-  };
-
-  // Returns a function, that, when invoked, will only be triggered at most once
-  // during a given window of time.
-  _.throttle = function(func, wait) {
-    var context, args, timeout, throttling, more;
-    var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
-    return function() {
-      context = this; args = arguments;
-      var later = function() {
-        timeout = null;
-        if (more) func.apply(context, args);
-        whenDone();
-      };
-      if (!timeout) timeout = setTimeout(later, wait);
-      if (throttling) {
-        more = true;
-      } else {
-        func.apply(context, args);
-      }
-      whenDone();
-      throttling = true;
-    };
-  };
-
-  // Returns a function, that, as long as it continues to be invoked, will not
-  // be triggered. The function will be called after it stops being called for
-  // N milliseconds.
-  _.debounce = function(func, wait) {
-    var timeout;
-    return function() {
-      var context = this, args = arguments;
-      var later = function() {
-        timeout = null;
-        func.apply(context, args);
-      };
-      clearTimeout(timeout);
-      timeout = setTimeout(later, wait);
-    };
-  };
-
-  // Returns a function that will be executed at most one time, no matter how
-  // often you call it. Useful for lazy initialization.
-  _.once = function(func) {
-    var ran = false, memo;
-    return function() {
-      if (ran) return memo;
-      ran = true;
-      return memo = func.apply(this, arguments);
-    };
-  };
-
-  // Returns the first function passed as an argument to the second,
-  // allowing you to adjust arguments, run code before and after, and
-  // conditionally execute the original function.
-  _.wrap = function(func, wrapper) {
-    return function() {
-      var args = [func].concat(slice.call(arguments, 0));
-      return wrapper.apply(this, args);
-    };
-  };
-
-  // Returns a function that is the composition of a list of functions, each
-  // consuming the return value of the function that follows.
-  _.compose = function() {
-    var funcs = arguments;
-    return function() {
-      var args = arguments;
-      for (var i = funcs.length - 1; i >= 0; i--) {
-        args = [funcs[i].apply(this, args)];
-      }
-      return args[0];
-    };
-  };
-
-  // Returns a function that will only be executed after being called N times.
-  _.after = function(times, func) {
-    if (times <= 0) return func();
-    return function() {
-      if (--times < 1) { return func.apply(this, arguments); }
-    };
-  };
-
-  // Object Functions
-  // ----------------
-
-  // Retrieve the names of an object's properties.
-  // Delegates to **ECMAScript 5**'s native `Object.keys`
-  _.keys = nativeKeys || function(obj) {
-    if (obj !== Object(obj)) throw new TypeError('Invalid object');
-    var keys = [];
-    for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
-    return keys;
-  };
-
-  // Retrieve the values of an object's properties.
-  _.values = function(obj) {
-    return _.map(obj, _.identity);
-  };
-
-  // Return a sorted list of the function names available on the object.
-  // Aliased as `methods`
-  _.functions = _.methods = function(obj) {
-    var names = [];
-    for (var key in obj) {
-      if (_.isFunction(obj[key])) names.push(key);
-    }
-    return names.sort();
-  };
-
-  // Extend a given object with all the properties in passed-in object(s).
-  _.extend = function(obj) {
-    each(slice.call(arguments, 1), function(source) {
-      for (var prop in source) {
-        obj[prop] = source[prop];
-      }
-    });
-    return obj;
-  };
-
-  // Fill in a given object with default properties.
-  _.defaults = function(obj) {
-    each(slice.call(arguments, 1), function(source) {
-      for (var prop in source) {
-        if (obj[prop] == null) obj[prop] = source[prop];
-      }
-    });
-    return obj;
-  };
-
-  // Create a (shallow-cloned) duplicate of an object.
-  _.clone = function(obj) {
-    if (!_.isObject(obj)) return obj;
-    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
-  };
-
-  // Invokes interceptor with the obj, and then returns obj.
-  // The primary purpose of this method is to "tap into" a method chain, in
-  // order to perform operations on intermediate results within the chain.
-  _.tap = function(obj, interceptor) {
-    interceptor(obj);
-    return obj;
-  };
-
-  // Internal recursive comparison function.
-  function eq(a, b, stack) {
-    // Identical objects are equal. `0 === -0`, but they aren't identical.
-    // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
-    if (a === b) return a !== 0 || 1 / a == 1 / b;
-    // A strict comparison is necessary because `null == undefined`.
-    if (a == null || b == null) return a === b;
-    // Unwrap any wrapped objects.
-    if (a._chain) a = a._wrapped;
-    if (b._chain) b = b._wrapped;
-    // Invoke a custom `isEqual` method if one is provided.
-    if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
-    if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
-    // Compare `[[Class]]` names.
-    var className = toString.call(a);
-    if (className != toString.call(b)) return false;
-    switch (className) {
-      // Strings, numbers, dates, and booleans are compared by value.
-      case '[object String]':
-        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
-        // equivalent to `new String("5")`.
-        return a == String(b);
-      case '[object Number]':
-        // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
-        // other numeric values.
-        return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
-      case '[object Date]':
-      case '[object Boolean]':
-        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
-        // millisecond representations. Note that invalid dates with millisecond representations
-        // of `NaN` are not equivalent.
-        return +a == +b;
-      // RegExps are compared by their source patterns and flags.
-      case '[object RegExp]':
-        return a.source == b.source &&
-               a.global == b.global &&
-               a.multiline == b.multiline &&
-               a.ignoreCase == b.ignoreCase;
-    }
-    if (typeof a != 'object' || typeof b != 'object') return false;
-    // Assume equality for cyclic structures. The algorithm for detecting cyclic
-    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
-    var length = stack.length;
-    while (length--) {
-      // Linear search. Performance is inversely proportional to the number of
-      // unique nested structures.
-      if (stack[length] == a) return true;
-    }
-    // Add the first object to the stack of traversed objects.
-    stack.push(a);
-    var size = 0, result = true;
-    // Recursively compare objects and arrays.
-    if (className == '[object Array]') {
-      // Compare array lengths to determine if a deep comparison is necessary.
-      size = a.length;
-      result = size == b.length;
-      if (result) {
-        // Deep compare the contents, ignoring non-numeric properties.
-        while (size--) {
-          // Ensure commutative equality for sparse arrays.
-          if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
-        }
-      }
-    } else {
-      // Objects with different constructors are not equivalent.
-      if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
-      // Deep compare objects.
-      for (var key in a) {
-        if (_.has(a, key)) {
-          // Count the expected number of properties.
-          size++;
-          // Deep compare each member.
-          if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
-        }
-      }
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-        }
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-      }
-    }
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-    stack.pop();
-    return result;
-  }
-
-  // Perform a deep comparison to check if two objects are equal.
-  _.isEqual = function(a, b) {
-    return eq(a, b, []);
-  };
-
-  // Is a given array, string, or object empty?
-  // An "empty" object has no enumerable own-properties.
-  _.isEmpty = function(obj) {
-    if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
-    for (var key in obj) if (_.has(obj, key)) return false;
-    return true;
-  };
-
-  // Is a given value a DOM element?
-  _.isElement = function(obj) {
-    return !!(obj && obj.nodeType == 1);
-  };
-
-  // Is a given value an array?
-  // Delegates to ECMA5's native Array.isArray
-  _.isArray = nativeIsArray || function(obj) {
-    return toString.call(obj) == '[object Array]';
-  };
-
-  // Is a given variable an object?
-  _.isObject = function(obj) {
-    return obj === Object(obj);
-  };
-
-  // Is a given variable an arguments object?
-  _.isArguments = function(obj) {
-    return toString.call(obj) == '[object Arguments]';
-  };
-  if (!_.isArguments(arguments)) {
-    _.isArguments = function(obj) {
-      return !!(obj && _.has(obj, 'callee'));
-    };
-  }
-
-  // Is a given value a function?
-  _.isFunction = function(obj) {
-    return toString.call(obj) == '[object Function]';
-  };
-
-  // Is a given value a string?
-  _.isString = function(obj) {
-    return toString.call(obj) == '[object String]';
-  };
-
-  // Is a given value a number?
-  _.isNumber = function(obj) {
-    return toString.call(obj) == '[object Number]';
-  };
-
-  // Is the given value `NaN`?
-  _.isNaN = function(obj) {
-    // `NaN` is the only value for which `===` is not reflexive.
-    return obj !== obj;
-  };
-
-  // Is a given value a boolean?
-  _.isBoolean = function(obj) {
-    return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
-  };
-
-  // Is a given value a date?
-  _.isDate = function(obj) {
-    return toString.call(obj) == '[object Date]';
-  };
-
-  // Is the given value a regular expression?
-  _.isRegExp = function(obj) {
-    return toString.call(obj) == '[object RegExp]';
-  };
-
-  // Is a given value equal to null?
-  _.isNull = function(obj) {
-    return obj === null;
-  };
-
-  // Is a given variable undefined?
-  _.isUndefined = function(obj) {
-    return obj === void 0;
-  };
-
-  // Has own property?
-  _.has = function(obj, key) {
-    return hasOwnProperty.call(obj, key);
-  };
-
-  // Utility Functions
-  // -----------------
-
-  // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
-  // previous owner. Returns a reference to the Underscore object.
-  _.noConflict = function() {
-    root._ = previousUnderscore;
-    return this;
-  };
-
-  // Keep the identity function around for default iterators.
-  _.identity = function(value) {
-    return value;
-  };
-
-  // Run a function **n** times.
-  _.times = function (n, iterator, context) {
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-  };
-
-  // Escape a string for HTML interpolation.
-  _.escape = function(string) {
-    return (''+string).replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;').replace(/"/g, '&quot;').replace(/'/g, '&#x27;').replace(/\//g,'&#x2F;');
-  };
-
-  // Add your own custom functions to the Underscore object, ensuring that
-  // they're correctly added to the OOP wrapper as well.
-  _.mixin = function(obj) {
-    each(_.functions(obj), function(name){
-      addToWrapper(name, _[name] = obj[name]);
-    });
-  };
-
-  // Generate a unique integer id (unique within the entire client session).
-  // Useful for temporary DOM ids.
-  var idCounter = 0;
-  _.uniqueId = function(prefix) {
-    var id = idCounter++;
-    return prefix ? prefix + id : id;
-  };
-
-  // By default, Underscore uses ERB-style template delimiters, change the
-  // following template settings to use alternative delimiters.
-  _.templateSettings = {
-    evaluate    : /<%([\s\S]+?)%>/g,
-    interpolate : /<%=([\s\S]+?)%>/g,
-    escape      : /<%-([\s\S]+?)%>/g
-  };
-
-  // When customizing `templateSettings`, if you don't want to define an
-  // interpolation, evaluation or escaping regex, we need one that is
-  // guaranteed not to match.
-  var noMatch = /.^/;
-
-  // Within an interpolation, evaluation, or escaping, remove HTML escaping
-  // that had been previously added.
-  var unescape = function(code) {
-    return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
-  };
-
-  // JavaScript micro-templating, similar to John Resig's implementation.
-  // Underscore templating handles arbitrary delimiters, preserves whitespace,
-  // and correctly escapes quotes within interpolated code.
-  _.template = function(str, data) {
-    var c  = _.templateSettings;
-    var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
-      'with(obj||{}){__p.push(\'' +
-      str.replace(/\\/g, '\\\\')
-         .replace(/'/g, "\\'")
-         .replace(c.escape || noMatch, function(match, code) {
-           return "',_.escape(" + unescape(code) + "),'";
-         })
-         .replace(c.interpolate || noMatch, function(match, code) {
-           return "'," + unescape(code) + ",'";
-         })
-         .replace(c.evaluate || noMatch, function(match, code) {
-           return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
-         })
-         .replace(/\r/g, '\\r')
-         .replace(/\n/g, '\\n')
-         .replace(/\t/g, '\\t')
-         + "');}return __p.join('');";
-    var func = new Function('obj', '_', tmpl);
-    if (data) return func(data, _);
-    return function(data) {
-      return func.call(this, data, _);
-    };
-  };
-
-  // Add a "chain" function, which will delegate to the wrapper.
-  _.chain = function(obj) {
-    return _(obj).chain();
-  };
-
-  // The OOP Wrapper
-  // ---------------
-
-  // If Underscore is called as a function, it returns a wrapped object that
-  // can be used OO-style. This wrapper holds altered versions of all the
-  // underscore functions. Wrapped objects may be chained.
-  var wrapper = function(obj) { this._wrapped = obj; };
-
-  // Expose `wrapper.prototype` as `_.prototype`
-  _.prototype = wrapper.prototype;
-
-  // Helper function to continue chaining intermediate results.
-  var result = function(obj, chain) {
-    return chain ? _(obj).chain() : obj;
-  };
-
-  // A method to easily add functions to the OOP wrapper.
-  var addToWrapper = function(name, func) {
-    wrapper.prototype[name] = function() {
-      var args = slice.call(arguments);
-      unshift.call(args, this._wrapped);
-      return result(func.apply(_, args), this._chain);
-    };
-  };
-
-  // Add all of the Underscore functions to the wrapper object.
-  _.mixin(_);
-
-  // Add all mutator Array functions to the wrapper.
-  each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
-    var method = ArrayProto[name];
-    wrapper.prototype[name] = function() {
-      var wrapped = this._wrapped;
-      method.apply(wrapped, arguments);
-      var length = wrapped.length;
-      if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
-      return result(wrapped, this._chain);
-    };
-  });
-
-  // Add all accessor Array functions to the wrapper.
-  each(['concat', 'join', 'slice'], function(name) {
-    var method = ArrayProto[name];
-    wrapper.prototype[name] = function() {
-      return result(method.apply(this._wrapped, arguments), this._chain);
-    };
-  });
-
-  // Start chaining a wrapped Underscore object.
-  wrapper.prototype.chain = function() {
-    this._chain = true;
-    return this;
-  };
-
-  // Extracts the result from a wrapped and chained object.
-  wrapper.prototype.value = function() {
-    return this._wrapped;
-  };
-
-}).call(this);
diff --git a/doc/html/_static/underscore.js b/doc/html/_static/underscore.js
index 5b55f32beaca186f84cca115514f02cddbd1bbd5..b4f49a0204cae8f267d9ae0f3009d9a485c1ba46 100644
--- a/doc/html/_static/underscore.js
+++ b/doc/html/_static/underscore.js
@@ -1,31 +1,1415 @@
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+//     Underscore.js 1.7.0
+//     http://underscorejs.org
+//     (c) 2009-2014 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
+//     Underscore may be freely distributed under the MIT license.
+
+(function() {
+
+  // Baseline setup
+  // --------------
+
+  // Establish the root object, `window` in the browser, or `exports` on the server.
+  var root = this;
+
+  // Save the previous value of the `_` variable.
+  var previousUnderscore = root._;
+
+  // Save bytes in the minified (but not gzipped) version:
+  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
+
+  // Create quick reference variables for speed access to core prototypes.
+  var
+    push             = ArrayProto.push,
+    slice            = ArrayProto.slice,
+    concat           = ArrayProto.concat,
+    toString         = ObjProto.toString,
+    hasOwnProperty   = ObjProto.hasOwnProperty;
+
+  // All **ECMAScript 5** native function implementations that we hope to use
+  // are declared here.
+  var
+    nativeIsArray      = Array.isArray,
+    nativeKeys         = Object.keys,
+    nativeBind         = FuncProto.bind;
+
+  // Create a safe reference to the Underscore object for use below.
+  var _ = function(obj) {
+    if (obj instanceof _) return obj;
+    if (!(this instanceof _)) return new _(obj);
+    this._wrapped = obj;
+  };
+
+  // Export the Underscore object for **Node.js**, with
+  // backwards-compatibility for the old `require()` API. If we're in
+  // the browser, add `_` as a global object.
+  if (typeof exports !== 'undefined') {
+    if (typeof module !== 'undefined' && module.exports) {
+      exports = module.exports = _;
+    }
+    exports._ = _;
+  } else {
+    root._ = _;
+  }
+
+  // Current version.
+  _.VERSION = '1.7.0';
+
+  // Internal function that returns an efficient (for current engines) version
+  // of the passed-in callback, to be repeatedly applied in other Underscore
+  // functions.
+  var createCallback = function(func, context, argCount) {
+    if (context === void 0) return func;
+    switch (argCount == null ? 3 : argCount) {
+      case 1: return function(value) {
+        return func.call(context, value);
+      };
+      case 2: return function(value, other) {
+        return func.call(context, value, other);
+      };
+      case 3: return function(value, index, collection) {
+        return func.call(context, value, index, collection);
+      };
+      case 4: return function(accumulator, value, index, collection) {
+        return func.call(context, accumulator, value, index, collection);
+      };
+    }
+    return function() {
+      return func.apply(context, arguments);
+    };
+  };
+
+  // A mostly-internal function to generate callbacks that can be applied
+  // to each element in a collection, returning the desired result — either
+  // identity, an arbitrary callback, a property matcher, or a property accessor.
+  _.iteratee = function(value, context, argCount) {
+    if (value == null) return _.identity;
+    if (_.isFunction(value)) return createCallback(value, context, argCount);
+    if (_.isObject(value)) return _.matches(value);
+    return _.property(value);
+  };
+
+  // Collection Functions
+  // --------------------
+
+  // The cornerstone, an `each` implementation, aka `forEach`.
+  // Handles raw objects in addition to array-likes. Treats all
+  // sparse array-likes as if they were dense.
+  _.each = _.forEach = function(obj, iteratee, context) {
+    if (obj == null) return obj;
+    iteratee = createCallback(iteratee, context);
+    var i, length = obj.length;
+    if (length === +length) {
+      for (i = 0; i < length; i++) {
+        iteratee(obj[i], i, obj);
+      }
+    } else {
+      var keys = _.keys(obj);
+      for (i = 0, length = keys.length; i < length; i++) {
+        iteratee(obj[keys[i]], keys[i], obj);
+      }
+    }
+    return obj;
+  };
+
+  // Return the results of applying the iteratee to each element.
+  _.map = _.collect = function(obj, iteratee, context) {
+    if (obj == null) return [];
+    iteratee = _.iteratee(iteratee, context);
+    var keys = obj.length !== +obj.length && _.keys(obj),
+        length = (keys || obj).length,
+        results = Array(length),
+        currentKey;
+    for (var index = 0; index < length; index++) {
+      currentKey = keys ? keys[index] : index;
+      results[index] = iteratee(obj[currentKey], currentKey, obj);
+    }
+    return results;
+  };
+
+  var reduceError = 'Reduce of empty array with no initial value';
+
+  // **Reduce** builds up a single result from a list of values, aka `inject`,
+  // or `foldl`.
+  _.reduce = _.foldl = _.inject = function(obj, iteratee, memo, context) {
+    if (obj == null) obj = [];
+    iteratee = createCallback(iteratee, context, 4);
+    var keys = obj.length !== +obj.length && _.keys(obj),
+        length = (keys || obj).length,
+        index = 0, currentKey;
+    if (arguments.length < 3) {
+      if (!length) throw new TypeError(reduceError);
+      memo = obj[keys ? keys[index++] : index++];
+    }
+    for (; index < length; index++) {
+      currentKey = keys ? keys[index] : index;
+      memo = iteratee(memo, obj[currentKey], currentKey, obj);
+    }
+    return memo;
+  };
+
+  // The right-associative version of reduce, also known as `foldr`.
+  _.reduceRight = _.foldr = function(obj, iteratee, memo, context) {
+    if (obj == null) obj = [];
+    iteratee = createCallback(iteratee, context, 4);
+    var keys = obj.length !== + obj.length && _.keys(obj),
+        index = (keys || obj).length,
+        currentKey;
+    if (arguments.length < 3) {
+      if (!index) throw new TypeError(reduceError);
+      memo = obj[keys ? keys[--index] : --index];
+    }
+    while (index--) {
+      currentKey = keys ? keys[index] : index;
+      memo = iteratee(memo, obj[currentKey], currentKey, obj);
+    }
+    return memo;
+  };
+
+  // Return the first value which passes a truth test. Aliased as `detect`.
+  _.find = _.detect = function(obj, predicate, context) {
+    var result;
+    predicate = _.iteratee(predicate, context);
+    _.some(obj, function(value, index, list) {
+      if (predicate(value, index, list)) {
+        result = value;
+        return true;
+      }
+    });
+    return result;
+  };
+
+  // Return all the elements that pass a truth test.
+  // Aliased as `select`.
+  _.filter = _.select = function(obj, predicate, context) {
+    var results = [];
+    if (obj == null) return results;
+    predicate = _.iteratee(predicate, context);
+    _.each(obj, function(value, index, list) {
+      if (predicate(value, index, list)) results.push(value);
+    });
+    return results;
+  };
+
+  // Return all the elements for which a truth test fails.
+  _.reject = function(obj, predicate, context) {
+    return _.filter(obj, _.negate(_.iteratee(predicate)), context);
+  };
+
+  // Determine whether all of the elements match a truth test.
+  // Aliased as `all`.
+  _.every = _.all = function(obj, predicate, context) {
+    if (obj == null) return true;
+    predicate = _.iteratee(predicate, context);
+    var keys = obj.length !== +obj.length && _.keys(obj),
+        length = (keys || obj).length,
+        index, currentKey;
+    for (index = 0; index < length; index++) {
+      currentKey = keys ? keys[index] : index;
+      if (!predicate(obj[currentKey], currentKey, obj)) return false;
+    }
+    return true;
+  };
+
+  // Determine if at least one element in the object matches a truth test.
+  // Aliased as `any`.
+  _.some = _.any = function(obj, predicate, context) {
+    if (obj == null) return false;
+    predicate = _.iteratee(predicate, context);
+    var keys = obj.length !== +obj.length && _.keys(obj),
+        length = (keys || obj).length,
+        index, currentKey;
+    for (index = 0; index < length; index++) {
+      currentKey = keys ? keys[index] : index;
+      if (predicate(obj[currentKey], currentKey, obj)) return true;
+    }
+    return false;
+  };
+
+  // Determine if the array or object contains a given value (using `===`).
+  // Aliased as `include`.
+  _.contains = _.include = function(obj, target) {
+    if (obj == null) return false;
+    if (obj.length !== +obj.length) obj = _.values(obj);
+    return _.indexOf(obj, target) >= 0;
+  };
+
+  // Invoke a method (with arguments) on every item in a collection.
+  _.invoke = function(obj, method) {
+    var args = slice.call(arguments, 2);
+    var isFunc = _.isFunction(method);
+    return _.map(obj, function(value) {
+      return (isFunc ? method : value[method]).apply(value, args);
+    });
+  };
+
+  // Convenience version of a common use case of `map`: fetching a property.
+  _.pluck = function(obj, key) {
+    return _.map(obj, _.property(key));
+  };
+
+  // Convenience version of a common use case of `filter`: selecting only objects
+  // containing specific `key:value` pairs.
+  _.where = function(obj, attrs) {
+    return _.filter(obj, _.matches(attrs));
+  };
+
+  // Convenience version of a common use case of `find`: getting the first object
+  // containing specific `key:value` pairs.
+  _.findWhere = function(obj, attrs) {
+    return _.find(obj, _.matches(attrs));
+  };
+
+  // Return the maximum element (or element-based computation).
+  _.max = function(obj, iteratee, context) {
+    var result = -Infinity, lastComputed = -Infinity,
+        value, computed;
+    if (iteratee == null && obj != null) {
+      obj = obj.length === +obj.length ? obj : _.values(obj);
+      for (var i = 0, length = obj.length; i < length; i++) {
+        value = obj[i];
+        if (value > result) {
+          result = value;
+        }
+      }
+    } else {
+      iteratee = _.iteratee(iteratee, context);
+      _.each(obj, function(value, index, list) {
+        computed = iteratee(value, index, list);
+        if (computed > lastComputed || computed === -Infinity && result === -Infinity) {
+          result = value;
+          lastComputed = computed;
+        }
+      });
+    }
+    return result;
+  };
+
+  // Return the minimum element (or element-based computation).
+  _.min = function(obj, iteratee, context) {
+    var result = Infinity, lastComputed = Infinity,
+        value, computed;
+    if (iteratee == null && obj != null) {
+      obj = obj.length === +obj.length ? obj : _.values(obj);
+      for (var i = 0, length = obj.length; i < length; i++) {
+        value = obj[i];
+        if (value < result) {
+          result = value;
+        }
+      }
+    } else {
+      iteratee = _.iteratee(iteratee, context);
+      _.each(obj, function(value, index, list) {
+        computed = iteratee(value, index, list);
+        if (computed < lastComputed || computed === Infinity && result === Infinity) {
+          result = value;
+          lastComputed = computed;
+        }
+      });
+    }
+    return result;
+  };
+
+  // Shuffle a collection, using the modern version of the
+  // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle).
+  _.shuffle = function(obj) {
+    var set = obj && obj.length === +obj.length ? obj : _.values(obj);
+    var length = set.length;
+    var shuffled = Array(length);
+    for (var index = 0, rand; index < length; index++) {
+      rand = _.random(0, index);
+      if (rand !== index) shuffled[index] = shuffled[rand];
+      shuffled[rand] = set[index];
+    }
+    return shuffled;
+  };
+
+  // Sample **n** random values from a collection.
+  // If **n** is not specified, returns a single random element.
+  // The internal `guard` argument allows it to work with `map`.
+  _.sample = function(obj, n, guard) {
+    if (n == null || guard) {
+      if (obj.length !== +obj.length) obj = _.values(obj);
+      return obj[_.random(obj.length - 1)];
+    }
+    return _.shuffle(obj).slice(0, Math.max(0, n));
+  };
+
+  // Sort the object's values by a criterion produced by an iteratee.
+  _.sortBy = function(obj, iteratee, context) {
+    iteratee = _.iteratee(iteratee, context);
+    return _.pluck(_.map(obj, function(value, index, list) {
+      return {
+        value: value,
+        index: index,
+        criteria: iteratee(value, index, list)
+      };
+    }).sort(function(left, right) {
+      var a = left.criteria;
+      var b = right.criteria;
+      if (a !== b) {
+        if (a > b || a === void 0) return 1;
+        if (a < b || b === void 0) return -1;
+      }
+      return left.index - right.index;
+    }), 'value');
+  };
+
+  // An internal function used for aggregate "group by" operations.
+  var group = function(behavior) {
+    return function(obj, iteratee, context) {
+      var result = {};
+      iteratee = _.iteratee(iteratee, context);
+      _.each(obj, function(value, index) {
+        var key = iteratee(value, index, obj);
+        behavior(result, value, key);
+      });
+      return result;
+    };
+  };
+
+  // Groups the object's values by a criterion. Pass either a string attribute
+  // to group by, or a function that returns the criterion.
+  _.groupBy = group(function(result, value, key) {
+    if (_.has(result, key)) result[key].push(value); else result[key] = [value];
+  });
+
+  // Indexes the object's values by a criterion, similar to `groupBy`, but for
+  // when you know that your index values will be unique.
+  _.indexBy = group(function(result, value, key) {
+    result[key] = value;
+  });
+
+  // Counts instances of an object that group by a certain criterion. Pass
+  // either a string attribute to count by, or a function that returns the
+  // criterion.
+  _.countBy = group(function(result, value, key) {
+    if (_.has(result, key)) result[key]++; else result[key] = 1;
+  });
+
+  // Use a comparator function to figure out the smallest index at which
+  // an object should be inserted so as to maintain order. Uses binary search.
+  _.sortedIndex = function(array, obj, iteratee, context) {
+    iteratee = _.iteratee(iteratee, context, 1);
+    var value = iteratee(obj);
+    var low = 0, high = array.length;
+    while (low < high) {
+      var mid = low + high >>> 1;
+      if (iteratee(array[mid]) < value) low = mid + 1; else high = mid;
+    }
+    return low;
+  };
+
+  // Safely create a real, live array from anything iterable.
+  _.toArray = function(obj) {
+    if (!obj) return [];
+    if (_.isArray(obj)) return slice.call(obj);
+    if (obj.length === +obj.length) return _.map(obj, _.identity);
+    return _.values(obj);
+  };
+
+  // Return the number of elements in an object.
+  _.size = function(obj) {
+    if (obj == null) return 0;
+    return obj.length === +obj.length ? obj.length : _.keys(obj).length;
+  };
+
+  // Split a collection into two arrays: one whose elements all satisfy the given
+  // predicate, and one whose elements all do not satisfy the predicate.
+  _.partition = function(obj, predicate, context) {
+    predicate = _.iteratee(predicate, context);
+    var pass = [], fail = [];
+    _.each(obj, function(value, key, obj) {
+      (predicate(value, key, obj) ? pass : fail).push(value);
+    });
+    return [pass, fail];
+  };
+
+  // Array Functions
+  // ---------------
+
+  // Get the first element of an array. Passing **n** will return the first N
+  // values in the array. Aliased as `head` and `take`. The **guard** check
+  // allows it to work with `_.map`.
+  _.first = _.head = _.take = function(array, n, guard) {
+    if (array == null) return void 0;
+    if (n == null || guard) return array[0];
+    if (n < 0) return [];
+    return slice.call(array, 0, n);
+  };
+
+  // Returns everything but the last entry of the array. Especially useful on
+  // the arguments object. Passing **n** will return all the values in
+  // the array, excluding the last N. The **guard** check allows it to work with
+  // `_.map`.
+  _.initial = function(array, n, guard) {
+    return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n)));
+  };
+
+  // Get the last element of an array. Passing **n** will return the last N
+  // values in the array. The **guard** check allows it to work with `_.map`.
+  _.last = function(array, n, guard) {
+    if (array == null) return void 0;
+    if (n == null || guard) return array[array.length - 1];
+    return slice.call(array, Math.max(array.length - n, 0));
+  };
+
+  // Returns everything but the first entry of the array. Aliased as `tail` and `drop`.
+  // Especially useful on the arguments object. Passing an **n** will return
+  // the rest N values in the array. The **guard**
+  // check allows it to work with `_.map`.
+  _.rest = _.tail = _.drop = function(array, n, guard) {
+    return slice.call(array, n == null || guard ? 1 : n);
+  };
+
+  // Trim out all falsy values from an array.
+  _.compact = function(array) {
+    return _.filter(array, _.identity);
+  };
+
+  // Internal implementation of a recursive `flatten` function.
+  var flatten = function(input, shallow, strict, output) {
+    if (shallow && _.every(input, _.isArray)) {
+      return concat.apply(output, input);
+    }
+    for (var i = 0, length = input.length; i < length; i++) {
+      var value = input[i];
+      if (!_.isArray(value) && !_.isArguments(value)) {
+        if (!strict) output.push(value);
+      } else if (shallow) {
+        push.apply(output, value);
+      } else {
+        flatten(value, shallow, strict, output);
+      }
+    }
+    return output;
+  };
+
+  // Flatten out an array, either recursively (by default), or just one level.
+  _.flatten = function(array, shallow) {
+    return flatten(array, shallow, false, []);
+  };
+
+  // Return a version of the array that does not contain the specified value(s).
+  _.without = function(array) {
+    return _.difference(array, slice.call(arguments, 1));
+  };
+
+  // Produce a duplicate-free version of the array. If the array has already
+  // been sorted, you have the option of using a faster algorithm.
+  // Aliased as `unique`.
+  _.uniq = _.unique = function(array, isSorted, iteratee, context) {
+    if (array == null) return [];
+    if (!_.isBoolean(isSorted)) {
+      context = iteratee;
+      iteratee = isSorted;
+      isSorted = false;
+    }
+    if (iteratee != null) iteratee = _.iteratee(iteratee, context);
+    var result = [];
+    var seen = [];
+    for (var i = 0, length = array.length; i < length; i++) {
+      var value = array[i];
+      if (isSorted) {
+        if (!i || seen !== value) result.push(value);
+        seen = value;
+      } else if (iteratee) {
+        var computed = iteratee(value, i, array);
+        if (_.indexOf(seen, computed) < 0) {
+          seen.push(computed);
+          result.push(value);
+        }
+      } else if (_.indexOf(result, value) < 0) {
+        result.push(value);
+      }
+    }
+    return result;
+  };
+
+  // Produce an array that contains the union: each distinct element from all of
+  // the passed-in arrays.
+  _.union = function() {
+    return _.uniq(flatten(arguments, true, true, []));
+  };
+
+  // Produce an array that contains every item shared between all the
+  // passed-in arrays.
+  _.intersection = function(array) {
+    if (array == null) return [];
+    var result = [];
+    var argsLength = arguments.length;
+    for (var i = 0, length = array.length; i < length; i++) {
+      var item = array[i];
+      if (_.contains(result, item)) continue;
+      for (var j = 1; j < argsLength; j++) {
+        if (!_.contains(arguments[j], item)) break;
+      }
+      if (j === argsLength) result.push(item);
+    }
+    return result;
+  };
+
+  // Take the difference between one array and a number of other arrays.
+  // Only the elements present in just the first array will remain.
+  _.difference = function(array) {
+    var rest = flatten(slice.call(arguments, 1), true, true, []);
+    return _.filter(array, function(value){
+      return !_.contains(rest, value);
+    });
+  };
+
+  // Zip together multiple lists into a single array -- elements that share
+  // an index go together.
+  _.zip = function(array) {
+    if (array == null) return [];
+    var length = _.max(arguments, 'length').length;
+    var results = Array(length);
+    for (var i = 0; i < length; i++) {
+      results[i] = _.pluck(arguments, i);
+    }
+    return results;
+  };
+
+  // Converts lists into objects. Pass either a single array of `[key, value]`
+  // pairs, or two parallel arrays of the same length -- one of keys, and one of
+  // the corresponding values.
+  _.object = function(list, values) {
+    if (list == null) return {};
+    var result = {};
+    for (var i = 0, length = list.length; i < length; i++) {
+      if (values) {
+        result[list[i]] = values[i];
+      } else {
+        result[list[i][0]] = list[i][1];
+      }
+    }
+    return result;
+  };
+
+  // Return the position of the first occurrence of an item in an array,
+  // or -1 if the item is not included in the array.
+  // If the array is large and already in sort order, pass `true`
+  // for **isSorted** to use binary search.
+  _.indexOf = function(array, item, isSorted) {
+    if (array == null) return -1;
+    var i = 0, length = array.length;
+    if (isSorted) {
+      if (typeof isSorted == 'number') {
+        i = isSorted < 0 ? Math.max(0, length + isSorted) : isSorted;
+      } else {
+        i = _.sortedIndex(array, item);
+        return array[i] === item ? i : -1;
+      }
+    }
+    for (; i < length; i++) if (array[i] === item) return i;
+    return -1;
+  };
+
+  _.lastIndexOf = function(array, item, from) {
+    if (array == null) return -1;
+    var idx = array.length;
+    if (typeof from == 'number') {
+      idx = from < 0 ? idx + from + 1 : Math.min(idx, from + 1);
+    }
+    while (--idx >= 0) if (array[idx] === item) return idx;
+    return -1;
+  };
+
+  // Generate an integer Array containing an arithmetic progression. A port of
+  // the native Python `range()` function. See
+  // [the Python documentation](http://docs.python.org/library/functions.html#range).
+  _.range = function(start, stop, step) {
+    if (arguments.length <= 1) {
+      stop = start || 0;
+      start = 0;
+    }
+    step = step || 1;
+
+    var length = Math.max(Math.ceil((stop - start) / step), 0);
+    var range = Array(length);
+
+    for (var idx = 0; idx < length; idx++, start += step) {
+      range[idx] = start;
+    }
+
+    return range;
+  };
+
+  // Function (ahem) Functions
+  // ------------------
+
+  // Reusable constructor function for prototype setting.
+  var Ctor = function(){};
+
+  // Create a function bound to a given object (assigning `this`, and arguments,
+  // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if
+  // available.
+  _.bind = function(func, context) {
+    var args, bound;
+    if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
+    if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function');
+    args = slice.call(arguments, 2);
+    bound = function() {
+      if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
+      Ctor.prototype = func.prototype;
+      var self = new Ctor;
+      Ctor.prototype = null;
+      var result = func.apply(self, args.concat(slice.call(arguments)));
+      if (_.isObject(result)) return result;
+      return self;
+    };
+    return bound;
+  };
+
+  // Partially apply a function by creating a version that has had some of its
+  // arguments pre-filled, without changing its dynamic `this` context. _ acts
+  // as a placeholder, allowing any combination of arguments to be pre-filled.
+  _.partial = function(func) {
+    var boundArgs = slice.call(arguments, 1);
+    return function() {
+      var position = 0;
+      var args = boundArgs.slice();
+      for (var i = 0, length = args.length; i < length; i++) {
+        if (args[i] === _) args[i] = arguments[position++];
+      }
+      while (position < arguments.length) args.push(arguments[position++]);
+      return func.apply(this, args);
+    };
+  };
+
+  // Bind a number of an object's methods to that object. Remaining arguments
+  // are the method names to be bound. Useful for ensuring that all callbacks
+  // defined on an object belong to it.
+  _.bindAll = function(obj) {
+    var i, length = arguments.length, key;
+    if (length <= 1) throw new Error('bindAll must be passed function names');
+    for (i = 1; i < length; i++) {
+      key = arguments[i];
+      obj[key] = _.bind(obj[key], obj);
+    }
+    return obj;
+  };
+
+  // Memoize an expensive function by storing its results.
+  _.memoize = function(func, hasher) {
+    var memoize = function(key) {
+      var cache = memoize.cache;
+      var address = hasher ? hasher.apply(this, arguments) : key;
+      if (!_.has(cache, address)) cache[address] = func.apply(this, arguments);
+      return cache[address];
+    };
+    memoize.cache = {};
+    return memoize;
+  };
+
+  // Delays a function for the given number of milliseconds, and then calls
+  // it with the arguments supplied.
+  _.delay = function(func, wait) {
+    var args = slice.call(arguments, 2);
+    return setTimeout(function(){
+      return func.apply(null, args);
+    }, wait);
+  };
+
+  // Defers a function, scheduling it to run after the current call stack has
+  // cleared.
+  _.defer = function(func) {
+    return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
+  };
+
+  // Returns a function, that, when invoked, will only be triggered at most once
+  // during a given window of time. Normally, the throttled function will run
+  // as much as it can, without ever going more than once per `wait` duration;
+  // but if you'd like to disable the execution on the leading edge, pass
+  // `{leading: false}`. To disable execution on the trailing edge, ditto.
+  _.throttle = function(func, wait, options) {
+    var context, args, result;
+    var timeout = null;
+    var previous = 0;
+    if (!options) options = {};
+    var later = function() {
+      previous = options.leading === false ? 0 : _.now();
+      timeout = null;
+      result = func.apply(context, args);
+      if (!timeout) context = args = null;
+    };
+    return function() {
+      var now = _.now();
+      if (!previous && options.leading === false) previous = now;
+      var remaining = wait - (now - previous);
+      context = this;
+      args = arguments;
+      if (remaining <= 0 || remaining > wait) {
+        clearTimeout(timeout);
+        timeout = null;
+        previous = now;
+        result = func.apply(context, args);
+        if (!timeout) context = args = null;
+      } else if (!timeout && options.trailing !== false) {
+        timeout = setTimeout(later, remaining);
+      }
+      return result;
+    };
+  };
+
+  // Returns a function, that, as long as it continues to be invoked, will not
+  // be triggered. The function will be called after it stops being called for
+  // N milliseconds. If `immediate` is passed, trigger the function on the
+  // leading edge, instead of the trailing.
+  _.debounce = function(func, wait, immediate) {
+    var timeout, args, context, timestamp, result;
+
+    var later = function() {
+      var last = _.now() - timestamp;
+
+      if (last < wait && last > 0) {
+        timeout = setTimeout(later, wait - last);
+      } else {
+        timeout = null;
+        if (!immediate) {
+          result = func.apply(context, args);
+          if (!timeout) context = args = null;
+        }
+      }
+    };
+
+    return function() {
+      context = this;
+      args = arguments;
+      timestamp = _.now();
+      var callNow = immediate && !timeout;
+      if (!timeout) timeout = setTimeout(later, wait);
+      if (callNow) {
+        result = func.apply(context, args);
+        context = args = null;
+      }
+
+      return result;
+    };
+  };
+
+  // Returns the first function passed as an argument to the second,
+  // allowing you to adjust arguments, run code before and after, and
+  // conditionally execute the original function.
+  _.wrap = function(func, wrapper) {
+    return _.partial(wrapper, func);
+  };
+
+  // Returns a negated version of the passed-in predicate.
+  _.negate = function(predicate) {
+    return function() {
+      return !predicate.apply(this, arguments);
+    };
+  };
+
+  // Returns a function that is the composition of a list of functions, each
+  // consuming the return value of the function that follows.
+  _.compose = function() {
+    var args = arguments;
+    var start = args.length - 1;
+    return function() {
+      var i = start;
+      var result = args[start].apply(this, arguments);
+      while (i--) result = args[i].call(this, result);
+      return result;
+    };
+  };
+
+  // Returns a function that will only be executed after being called N times.
+  _.after = function(times, func) {
+    return function() {
+      if (--times < 1) {
+        return func.apply(this, arguments);
+      }
+    };
+  };
+
+  // Returns a function that will only be executed before being called N times.
+  _.before = function(times, func) {
+    var memo;
+    return function() {
+      if (--times > 0) {
+        memo = func.apply(this, arguments);
+      } else {
+        func = null;
+      }
+      return memo;
+    };
+  };
+
+  // Returns a function that will be executed at most one time, no matter how
+  // often you call it. Useful for lazy initialization.
+  _.once = _.partial(_.before, 2);
+
+  // Object Functions
+  // ----------------
+
+  // Retrieve the names of an object's properties.
+  // Delegates to **ECMAScript 5**'s native `Object.keys`
+  _.keys = function(obj) {
+    if (!_.isObject(obj)) return [];
+    if (nativeKeys) return nativeKeys(obj);
+    var keys = [];
+    for (var key in obj) if (_.has(obj, key)) keys.push(key);
+    return keys;
+  };
+
+  // Retrieve the values of an object's properties.
+  _.values = function(obj) {
+    var keys = _.keys(obj);
+    var length = keys.length;
+    var values = Array(length);
+    for (var i = 0; i < length; i++) {
+      values[i] = obj[keys[i]];
+    }
+    return values;
+  };
+
+  // Convert an object into a list of `[key, value]` pairs.
+  _.pairs = function(obj) {
+    var keys = _.keys(obj);
+    var length = keys.length;
+    var pairs = Array(length);
+    for (var i = 0; i < length; i++) {
+      pairs[i] = [keys[i], obj[keys[i]]];
+    }
+    return pairs;
+  };
+
+  // Invert the keys and values of an object. The values must be serializable.
+  _.invert = function(obj) {
+    var result = {};
+    var keys = _.keys(obj);
+    for (var i = 0, length = keys.length; i < length; i++) {
+      result[obj[keys[i]]] = keys[i];
+    }
+    return result;
+  };
+
+  // Return a sorted list of the function names available on the object.
+  // Aliased as `methods`
+  _.functions = _.methods = function(obj) {
+    var names = [];
+    for (var key in obj) {
+      if (_.isFunction(obj[key])) names.push(key);
+    }
+    return names.sort();
+  };
+
+  // Extend a given object with all the properties in passed-in object(s).
+  _.extend = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    var source, prop;
+    for (var i = 1, length = arguments.length; i < length; i++) {
+      source = arguments[i];
+      for (prop in source) {
+        if (hasOwnProperty.call(source, prop)) {
+            obj[prop] = source[prop];
+        }
+      }
+    }
+    return obj;
+  };
+
+  // Return a copy of the object only containing the whitelisted properties.
+  _.pick = function(obj, iteratee, context) {
+    var result = {}, key;
+    if (obj == null) return result;
+    if (_.isFunction(iteratee)) {
+      iteratee = createCallback(iteratee, context);
+      for (key in obj) {
+        var value = obj[key];
+        if (iteratee(value, key, obj)) result[key] = value;
+      }
+    } else {
+      var keys = concat.apply([], slice.call(arguments, 1));
+      obj = new Object(obj);
+      for (var i = 0, length = keys.length; i < length; i++) {
+        key = keys[i];
+        if (key in obj) result[key] = obj[key];
+      }
+    }
+    return result;
+  };
+
+   // Return a copy of the object without the blacklisted properties.
+  _.omit = function(obj, iteratee, context) {
+    if (_.isFunction(iteratee)) {
+      iteratee = _.negate(iteratee);
+    } else {
+      var keys = _.map(concat.apply([], slice.call(arguments, 1)), String);
+      iteratee = function(value, key) {
+        return !_.contains(keys, key);
+      };
+    }
+    return _.pick(obj, iteratee, context);
+  };
+
+  // Fill in a given object with default properties.
+  _.defaults = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    for (var i = 1, length = arguments.length; i < length; i++) {
+      var source = arguments[i];
+      for (var prop in source) {
+        if (obj[prop] === void 0) obj[prop] = source[prop];
+      }
+    }
+    return obj;
+  };
+
+  // Create a (shallow-cloned) duplicate of an object.
+  _.clone = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+  };
+
+  // Invokes interceptor with the obj, and then returns obj.
+  // The primary purpose of this method is to "tap into" a method chain, in
+  // order to perform operations on intermediate results within the chain.
+  _.tap = function(obj, interceptor) {
+    interceptor(obj);
+    return obj;
+  };
+
+  // Internal recursive comparison function for `isEqual`.
+  var eq = function(a, b, aStack, bStack) {
+    // Identical objects are equal. `0 === -0`, but they aren't identical.
+    // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal).
+    if (a === b) return a !== 0 || 1 / a === 1 / b;
+    // A strict comparison is necessary because `null == undefined`.
+    if (a == null || b == null) return a === b;
+    // Unwrap any wrapped objects.
+    if (a instanceof _) a = a._wrapped;
+    if (b instanceof _) b = b._wrapped;
+    // Compare `[[Class]]` names.
+    var className = toString.call(a);
+    if (className !== toString.call(b)) return false;
+    switch (className) {
+      // Strings, numbers, regular expressions, dates, and booleans are compared by value.
+      case '[object RegExp]':
+      // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i')
+      case '[object String]':
+        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+        // equivalent to `new String("5")`.
+        return '' + a === '' + b;
+      case '[object Number]':
+        // `NaN`s are equivalent, but non-reflexive.
+        // Object(NaN) is equivalent to NaN
+        if (+a !== +a) return +b !== +b;
+        // An `egal` comparison is performed for other numeric values.
+        return +a === 0 ? 1 / +a === 1 / b : +a === +b;
+      case '[object Date]':
+      case '[object Boolean]':
+        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+        // millisecond representations. Note that invalid dates with millisecond representations
+        // of `NaN` are not equivalent.
+        return +a === +b;
+    }
+    if (typeof a != 'object' || typeof b != 'object') return false;
+    // Assume equality for cyclic structures. The algorithm for detecting cyclic
+    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+    var length = aStack.length;
+    while (length--) {
+      // Linear search. Performance is inversely proportional to the number of
+      // unique nested structures.
+      if (aStack[length] === a) return bStack[length] === b;
+    }
+    // Objects with different constructors are not equivalent, but `Object`s
+    // from different frames are.
+    var aCtor = a.constructor, bCtor = b.constructor;
+    if (
+      aCtor !== bCtor &&
+      // Handle Object.create(x) cases
+      'constructor' in a && 'constructor' in b &&
+      !(_.isFunction(aCtor) && aCtor instanceof aCtor &&
+        _.isFunction(bCtor) && bCtor instanceof bCtor)
+    ) {
+      return false;
+    }
+    // Add the first object to the stack of traversed objects.
+    aStack.push(a);
+    bStack.push(b);
+    var size, result;
+    // Recursively compare objects and arrays.
+    if (className === '[object Array]') {
+      // Compare array lengths to determine if a deep comparison is necessary.
+      size = a.length;
+      result = size === b.length;
+      if (result) {
+        // Deep compare the contents, ignoring non-numeric properties.
+        while (size--) {
+          if (!(result = eq(a[size], b[size], aStack, bStack))) break;
+        }
+      }
+    } else {
+      // Deep compare objects.
+      var keys = _.keys(a), key;
+      size = keys.length;
+      // Ensure that both objects contain the same number of properties before comparing deep equality.
+      result = _.keys(b).length === size;
+      if (result) {
+        while (size--) {
+          // Deep compare each member
+          key = keys[size];
+          if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break;
+        }
+      }
+    }
+    // Remove the first object from the stack of traversed objects.
+    aStack.pop();
+    bStack.pop();
+    return result;
+  };
+
+  // Perform a deep comparison to check if two objects are equal.
+  _.isEqual = function(a, b) {
+    return eq(a, b, [], []);
+  };
+
+  // Is a given array, string, or object empty?
+  // An "empty" object has no enumerable own-properties.
+  _.isEmpty = function(obj) {
+    if (obj == null) return true;
+    if (_.isArray(obj) || _.isString(obj) || _.isArguments(obj)) return obj.length === 0;
+    for (var key in obj) if (_.has(obj, key)) return false;
+    return true;
+  };
+
+  // Is a given value a DOM element?
+  _.isElement = function(obj) {
+    return !!(obj && obj.nodeType === 1);
+  };
+
+  // Is a given value an array?
+  // Delegates to ECMA5's native Array.isArray
+  _.isArray = nativeIsArray || function(obj) {
+    return toString.call(obj) === '[object Array]';
+  };
+
+  // Is a given variable an object?
+  _.isObject = function(obj) {
+    var type = typeof obj;
+    return type === 'function' || type === 'object' && !!obj;
+  };
+
+  // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp.
+  _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) {
+    _['is' + name] = function(obj) {
+      return toString.call(obj) === '[object ' + name + ']';
+    };
+  });
+
+  // Define a fallback version of the method in browsers (ahem, IE), where
+  // there isn't any inspectable "Arguments" type.
+  if (!_.isArguments(arguments)) {
+    _.isArguments = function(obj) {
+      return _.has(obj, 'callee');
+    };
+  }
+
+  // Optimize `isFunction` if appropriate. Work around an IE 11 bug.
+  if (typeof /./ !== 'function') {
+    _.isFunction = function(obj) {
+      return typeof obj == 'function' || false;
+    };
+  }
+
+  // Is a given object a finite number?
+  _.isFinite = function(obj) {
+    return isFinite(obj) && !isNaN(parseFloat(obj));
+  };
+
+  // Is the given value `NaN`? (NaN is the only number which does not equal itself).
+  _.isNaN = function(obj) {
+    return _.isNumber(obj) && obj !== +obj;
+  };
+
+  // Is a given value a boolean?
+  _.isBoolean = function(obj) {
+    return obj === true || obj === false || toString.call(obj) === '[object Boolean]';
+  };
+
+  // Is a given value equal to null?
+  _.isNull = function(obj) {
+    return obj === null;
+  };
+
+  // Is a given variable undefined?
+  _.isUndefined = function(obj) {
+    return obj === void 0;
+  };
+
+  // Shortcut function for checking if an object has a given property directly
+  // on itself (in other words, not on a prototype).
+  _.has = function(obj, key) {
+    return obj != null && hasOwnProperty.call(obj, key);
+  };
+
+  // Utility Functions
+  // -----------------
+
+  // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+  // previous owner. Returns a reference to the Underscore object.
+  _.noConflict = function() {
+    root._ = previousUnderscore;
+    return this;
+  };
+
+  // Keep the identity function around for default iteratees.
+  _.identity = function(value) {
+    return value;
+  };
+
+  _.constant = function(value) {
+    return function() {
+      return value;
+    };
+  };
+
+  _.noop = function(){};
+
+  _.property = function(key) {
+    return function(obj) {
+      return obj[key];
+    };
+  };
+
+  // Returns a predicate for checking whether an object has a given set of `key:value` pairs.
+  _.matches = function(attrs) {
+    var pairs = _.pairs(attrs), length = pairs.length;
+    return function(obj) {
+      if (obj == null) return !length;
+      obj = new Object(obj);
+      for (var i = 0; i < length; i++) {
+        var pair = pairs[i], key = pair[0];
+        if (pair[1] !== obj[key] || !(key in obj)) return false;
+      }
+      return true;
+    };
+  };
+
+  // Run a function **n** times.
+  _.times = function(n, iteratee, context) {
+    var accum = Array(Math.max(0, n));
+    iteratee = createCallback(iteratee, context, 1);
+    for (var i = 0; i < n; i++) accum[i] = iteratee(i);
+    return accum;
+  };
+
+  // Return a random integer between min and max (inclusive).
+  _.random = function(min, max) {
+    if (max == null) {
+      max = min;
+      min = 0;
+    }
+    return min + Math.floor(Math.random() * (max - min + 1));
+  };
+
+  // A (possibly faster) way to get the current timestamp as an integer.
+  _.now = Date.now || function() {
+    return new Date().getTime();
+  };
+
+   // List of HTML entities for escaping.
+  var escapeMap = {
+    '&': '&amp;',
+    '<': '&lt;',
+    '>': '&gt;',
+    '"': '&quot;',
+    "'": '&#x27;',
+    '`': '&#x60;'
+  };
+  var unescapeMap = _.invert(escapeMap);
+
+  // Functions for escaping and unescaping strings to/from HTML interpolation.
+  var createEscaper = function(map) {
+    var escaper = function(match) {
+      return map[match];
+    };
+    // Regexes for identifying a key that needs to be escaped
+    var source = '(?:' + _.keys(map).join('|') + ')';
+    var testRegexp = RegExp(source);
+    var replaceRegexp = RegExp(source, 'g');
+    return function(string) {
+      string = string == null ? '' : '' + string;
+      return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string;
+    };
+  };
+  _.escape = createEscaper(escapeMap);
+  _.unescape = createEscaper(unescapeMap);
+
+  // If the value of the named `property` is a function then invoke it with the
+  // `object` as context; otherwise, return it.
+  _.result = function(object, property) {
+    if (object == null) return void 0;
+    var value = object[property];
+    return _.isFunction(value) ? object[property]() : value;
+  };
+
+  // Generate a unique integer id (unique within the entire client session).
+  // Useful for temporary DOM ids.
+  var idCounter = 0;
+  _.uniqueId = function(prefix) {
+    var id = ++idCounter + '';
+    return prefix ? prefix + id : id;
+  };
+
+  // By default, Underscore uses ERB-style template delimiters, change the
+  // following template settings to use alternative delimiters.
+  _.templateSettings = {
+    evaluate    : /<%([\s\S]+?)%>/g,
+    interpolate : /<%=([\s\S]+?)%>/g,
+    escape      : /<%-([\s\S]+?)%>/g
+  };
+
+  // When customizing `templateSettings`, if you don't want to define an
+  // interpolation, evaluation or escaping regex, we need one that is
+  // guaranteed not to match.
+  var noMatch = /(.)^/;
+
+  // Certain characters need to be escaped so that they can be put into a
+  // string literal.
+  var escapes = {
+    "'":      "'",
+    '\\':     '\\',
+    '\r':     'r',
+    '\n':     'n',
+    '\u2028': 'u2028',
+    '\u2029': 'u2029'
+  };
+
+  var escaper = /\\|'|\r|\n|\u2028|\u2029/g;
+
+  var escapeChar = function(match) {
+    return '\\' + escapes[match];
+  };
+
+  // JavaScript micro-templating, similar to John Resig's implementation.
+  // Underscore templating handles arbitrary delimiters, preserves whitespace,
+  // and correctly escapes quotes within interpolated code.
+  // NB: `oldSettings` only exists for backwards compatibility.
+  _.template = function(text, settings, oldSettings) {
+    if (!settings && oldSettings) settings = oldSettings;
+    settings = _.defaults({}, settings, _.templateSettings);
+
+    // Combine delimiters into one regular expression via alternation.
+    var matcher = RegExp([
+      (settings.escape || noMatch).source,
+      (settings.interpolate || noMatch).source,
+      (settings.evaluate || noMatch).source
+    ].join('|') + '|$', 'g');
+
+    // Compile the template source, escaping string literals appropriately.
+    var index = 0;
+    var source = "__p+='";
+    text.replace(matcher, function(match, escape, interpolate, evaluate, offset) {
+      source += text.slice(index, offset).replace(escaper, escapeChar);
+      index = offset + match.length;
+
+      if (escape) {
+        source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'";
+      } else if (interpolate) {
+        source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'";
+      } else if (evaluate) {
+        source += "';\n" + evaluate + "\n__p+='";
+      }
+
+      // Adobe VMs need the match returned to produce the correct offest.
+      return match;
+    });
+    source += "';\n";
+
+    // If a variable is not specified, place data values in local scope.
+    if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n';
+
+    source = "var __t,__p='',__j=Array.prototype.join," +
+      "print=function(){__p+=__j.call(arguments,'');};\n" +
+      source + 'return __p;\n';
+
+    try {
+      var render = new Function(settings.variable || 'obj', '_', source);
+    } catch (e) {
+      e.source = source;
+      throw e;
+    }
+
+    var template = function(data) {
+      return render.call(this, data, _);
+    };
+
+    // Provide the compiled source as a convenience for precompilation.
+    var argument = settings.variable || 'obj';
+    template.source = 'function(' + argument + '){\n' + source + '}';
+
+    return template;
+  };
+
+  // Add a "chain" function. Start chaining a wrapped Underscore object.
+  _.chain = function(obj) {
+    var instance = _(obj);
+    instance._chain = true;
+    return instance;
+  };
+
+  // OOP
+  // ---------------
+  // If Underscore is called as a function, it returns a wrapped object that
+  // can be used OO-style. This wrapper holds altered versions of all the
+  // underscore functions. Wrapped objects may be chained.
+
+  // Helper function to continue chaining intermediate results.
+  var result = function(obj) {
+    return this._chain ? _(obj).chain() : obj;
+  };
+
+  // Add your own custom functions to the Underscore object.
+  _.mixin = function(obj) {
+    _.each(_.functions(obj), function(name) {
+      var func = _[name] = obj[name];
+      _.prototype[name] = function() {
+        var args = [this._wrapped];
+        push.apply(args, arguments);
+        return result.call(this, func.apply(_, args));
+      };
+    });
+  };
+
+  // Add all of the Underscore functions to the wrapper object.
+  _.mixin(_);
+
+  // Add all mutator Array functions to the wrapper.
+  _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+    var method = ArrayProto[name];
+    _.prototype[name] = function() {
+      var obj = this._wrapped;
+      method.apply(obj, arguments);
+      if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0];
+      return result.call(this, obj);
+    };
+  });
+
+  // Add all accessor Array functions to the wrapper.
+  _.each(['concat', 'join', 'slice'], function(name) {
+    var method = ArrayProto[name];
+    _.prototype[name] = function() {
+      return result.call(this, method.apply(this._wrapped, arguments));
+    };
+  });
+
+  // Extracts the result from a wrapped and chained object.
+  _.prototype.value = function() {
+    return this._wrapped;
+  };
+
+  // AMD registration happens at the end for compatibility with AMD loaders
+  // that may not enforce next-turn semantics on modules. Even though general
+  // practice for AMD registration is to be anonymous, underscore registers
+  // as a named module because, like jQuery, it is a base library that is
+  // popular enough to be bundled in a third party lib, but not be part of
+  // an AMD load request. Those cases could generate an error when an
+  // anonymous define() is called outside of a loader request.
+  if (typeof define === 'function' && define.amd) {
+    define('underscore', [], function() {
+      return _;
+    });
+  }
+}.call(this));
diff --git a/doc/html/_static/websupport.js b/doc/html/_static/websupport.js
index 98e7f40b6327e673e382068cdfb3bf3674a06cca..ffd9b2bfdcb71401f4f84b5eaa74ed2e7b306c1f 100644
--- a/doc/html/_static/websupport.js
+++ b/doc/html/_static/websupport.js
@@ -2,7 +2,7 @@
  * websupport.js
  * ~~~~~~~~~~~~~
  *
- * sphinx.websupport utilities for all documentation.
+ * sphinx.websupport utilties for all documentation.
  *
  * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index f83632f45740b0b6ed02b2d4176abe058c068625..e7468692a49c9dedac81e7799d21b97515b89738 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Users" href="../users.html" />
     <link rel="next" title="Building ProMod3" href="../buildsystem.html" />
     <link rel="prev" title="Getting Started" href="../gettingstarted.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -51,12 +50,12 @@ you can type <code class="docutils literal"><span class="pre">pm</span> <span cl
 <span id="promod-build-model"></span><h2>Building models<a class="headerlink" href="#building-models" title="Permalink to this headline">¶</a></h2>
 <p>You can run a full protein homology modelling pipeline from the command line
 with</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-f &lt;FILE&gt; <span class="p">|</span> -c &lt;FILE&gt; <span class="p">|</span> -j &lt;OBJECT&gt;<span class="p">|</span>&lt;FILE&gt;<span class="o">)</span>
-<span class="go">                 (-p &lt;FILE&gt; | -e &lt;FILE&gt;) [-o &lt;FILENAME&gt;]</span>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm build-model <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-f &lt;FILE&gt; <span class="p">|</span> -c &lt;FILE&gt; <span class="p">|</span> -j &lt;OBJECT&gt;<span class="p">|</span>&lt;FILE&gt;<span class="o">)</span>
+<span class="go">                 (-p &lt;FILE&gt; | -e &lt;FILE&gt;) [-s &lt;FILE&gt;] [-o &lt;FILENAME&gt;]</span>
 </pre></div>
 </div>
 <p>Example usage:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb
 </pre></div>
 </div>
 <p>This reads a target-template alignment from <code class="file docutils literal"><span class="pre">aln.fasta</span></code> and a matching
@@ -73,7 +72,7 @@ Notes on the input formats:</p>
 <li><p class="first">Leading/trailing whitespaces of sequence names will always be deleted</p>
 </li>
 <li><p class="first">FASTA input example:</p>
-<div class="highlight-none"><div class="highlight"><pre><span></span>&gt;target
+<div class="highlight-none"><div class="highlight"><pre>&gt;target
 HGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLG
 &gt;2jlp-1.A|55
 RAIHVHQFGDLSQGCESTGPHYNPLAVPH------PQHPG
@@ -94,7 +93,7 @@ Those in turn are objects with keys
 &#8216;seqres&#8217; (string for aligned sequence) and optionally for templates
 &#8216;offset&#8217; (number of residues to skip in structure file attached to it).
 Example:</p>
-<div class="highlight-json"><div class="highlight"><pre><span></span><span class="p">{</span><span class="nt">&quot;alignmentlist&quot;</span><span class="p">:</span> <span class="p">[</span> <span class="p">{</span>
+<div class="highlight-json"><div class="highlight"><pre><span class="p">{</span><span class="nt">&quot;alignmentlist&quot;</span><span class="p">:</span> <span class="p">[</span> <span class="p">{</span>
   <span class="nt">&quot;target&quot;</span><span class="p">:</span> <span class="p">{</span>
       <span class="nt">&quot;name&quot;</span><span class="p">:</span> <span class="s2">&quot;mytrg&quot;</span><span class="p">,</span>
       <span class="nt">&quot;seqres&quot;</span><span class="p">:</span> <span class="s2">&quot;HGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLG&quot;</span>
@@ -110,7 +109,7 @@ Example:</p>
 </li>
 </ul>
 <p>Structures can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
 chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
 <code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>. At least one structure must be
 given and you cannot mix file formats. Multiple structures can be given and each
@@ -132,6 +131,25 @@ residue in the aligned sequence. Leading/trailing whitespaces of &lt;CHAINID&gt;
 </ul>
 <p>Example: <code class="docutils literal"><span class="pre">...</span> <span class="pre">-p</span> <span class="pre">data/2jlp.pdb.gz</span></code>, where the pdb file has chains <code class="docutils literal"><span class="pre">A</span></code>,
 <code class="docutils literal"><span class="pre">B</span></code>, <code class="docutils literal"><span class="pre">C</span></code> and the template sequence is named <code class="docutils literal"><span class="pre">2jlp.A|55</span></code>.</p>
+<p>You can optionally specify sequence profiles to be added (<code class="docutils literal"><span class="pre">-s</span></code>) and linked
+to the corresponding target sequences. This has an impact on loop scoring with
+the database approach.
+The profiles can be provided as plain files or gzipped. Following file
+extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
+Consider to use <a class="reference external" href="https://www.openstructure.org/docs/dev/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+file in a3m format at hand.</p>
+<ul class="simple">
+<li>The profiles are mapped based on exact matches towards the gapless
+target sequences from the provided alignment files,
+i.e. one profile is mapped to several chains in case of homo-oligomers</li>
+<li>Every profile must have a unique sequence to avoid ambiguities</li>
+<li>All or nothing - You cannot provide profiles for only a subset of
+target sequences</li>
+</ul>
+<p>Example usage:</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
+</pre></div>
+</div>
 <p>Possible exit codes of the action:</p>
 <ul class="simple">
 <li>0: all went well</li>
@@ -142,6 +160,59 @@ residue in the aligned sequence. Leading/trailing whitespaces of &lt;CHAINID&gt;
 <li>other non-zero: failure in argument checking
 (see <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.pm3argparse.PM3ArgumentParser</span></code></a>)</li>
 </ul>
+</div>
+<div class="section" id="sidechain-modelling">
+<h2>Sidechain Modelling<a class="headerlink" href="#sidechain-modelling" title="Permalink to this headline">¶</a></h2>
+<p>You can (re-)construct the sidechains in a model from the command line.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> usage: build-sidechains <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-p &lt;FILE&gt; <span class="p">|</span> -e &lt;FILE&gt;<span class="o">)</span> <span class="o">[</span>-o &lt;FILENAME&gt;<span class="o">]</span> <span class="o">[</span>-k<span class="o">]</span> <span class="o">[</span>-n<span class="o">]</span>
+<span class="go">                          [-r] [-i] [-s]</span>
+</pre></div>
+</div>
+<p>Example usage:</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm build-sidechains -p input.pdb
+</pre></div>
+</div>
+<p>This reads a structure stored in in.pdb, strips all sidechains,
+detects and models disulfid bonds and reconstructs all sidechains with the
+flexible rotamer model. The result is stored as <code class="file docutils literal"><span class="pre">out.pdb</span></code>.
+The output filename can be controlled with the <code class="docutils literal"><span class="pre">-o</span></code> flag.</p>
+<p>A structure can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
+<a class="reference external" href="https://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
+chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
+<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>.</p>
+<p>Several flags control the modelling behaviour:</p>
+<dl class="option">
+<dt id="cmdoption-k">
+<span id="cmdoption--keep-sidechains"></span><code class="descname">-k</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--keep-sidechains</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-k" title="Permalink to this definition">¶</a></dt>
+<dd><p>Keep existing sidechains.</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-n">
+<span id="cmdoption--no-disulfids"></span><code class="descname">-n</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-disulfids</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-n" title="Permalink to this definition">¶</a></dt>
+<dd><p>Do not build disulfid bonds before sidechain optimization</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-r">
+<span id="cmdoption--rigid-rotamers"></span><code class="descname">-r</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--rigid-rotamers</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-r" title="Permalink to this definition">¶</a></dt>
+<dd><p>Do not use rotamers with subrotamers</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-i">
+<span id="cmdoption--backbone-independent"></span><code class="descname">-i</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--backbone-independent</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-i" title="Permalink to this definition">¶</a></dt>
+<dd><p>Use backbone independent rotamer library
+(from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.LoadLib()</span></code></a>) instead of the default backbone
+dependent one (from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.LoadBBDepLib()</span></code></a>)</p>
+</dd></dl>
+
+<dl class="option">
+<dt id="cmdoption-s">
+<span id="cmdoption--no-subrotamer-optimization"></span><code class="descname">-s</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-subrotamer-optimization</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-s" title="Permalink to this definition">¶</a></dt>
+<dd><p>Dont do subrotamer optimization if flexible rotamer model is used</p>
+</dd></dl>
+
 </div>
 </div>
 
@@ -155,6 +226,7 @@ residue in the aligned sequence. Leading/trailing whitespaces of &lt;CHAINID&gt;
   <ul>
 <li><a class="reference internal" href="#">ProMod3 Actions</a><ul>
 <li><a class="reference internal" href="#building-models">Building models</a></li>
+<li><a class="reference internal" href="#sidechain-modelling">Sidechain Modelling</a></li>
 </ul>
 </li>
 </ul>
@@ -184,6 +256,9 @@ residue in the aligned sequence. Leading/trailing whitespaces of &lt;CHAINID&gt;
       <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>
@@ -191,11 +266,11 @@ residue in the aligned sequence. Leading/trailing whitespaces of &lt;CHAINID&gt;
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/actions/index.txt"
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 7a72c1a6616b45888b696930be029d8e2cb467f2..cc45e8918df78dccd56b0f6955371f0109dfd7b5 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Developers" href="../developers.html" />
     <link rel="next" title="ProMod3‘s Share Of CMake" href="../cmake/index.html" />
     <link rel="prev" title="Contributing" href="../contributing.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -64,15 +63,15 @@ Python imports a module, its usually compiled into bytecode. This new file
 would clutter up the source repository, it would always show up as untracked
 file on <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code>. To prevent this, tell Python to stop producing
 bytecode right at the beginning of your test-script:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
 2
 3
 4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span>
 
 <span class="c1"># this is needed so there will be no test_actions.pyc created in the source</span>
 <span class="c1"># directory</span>
-<span class="hll"><span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="kc">True</span>
+<span class="hll"><span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="bp">True</span>
 </span></pre></div>
 </td></tr></table></div>
 <p>Line 5 does the trick. This needs to be set by you in every action unit test
@@ -103,20 +102,20 @@ called <code class="docutils literal"><span class="pre">do-awesome</span></code>
 action. So here we create a file <code class="file docutils literal"><span class="pre">test_action_do_awesome.py</span></code> (recognise
 the underscore between <code class="docutils literal"><span class="pre">do</span></code> and <code class="docutils literal"><span class="pre">awesome</span></code> instead of a hyphen, that&#8217;s
 <a class="reference external" href="https://www.python.org/dev/peps/pep-0008/">PEP 8</a>).</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch &lt;SOURCE&gt;/actions/tests/test_action_do_awesome.py
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch &lt;SOURCE&gt;/actions/tests/test_action_do_awesome.py
 <span class="gp">$</span>
 </pre></div>
 </div>
 <p>As a starter, we disable bytecode compilation in the script:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
 2
 3
 4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span>
 
 <span class="c1"># this is needed so there will be no test_actions.pyc created in the source</span>
 <span class="c1"># directory</span>
-<span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="kc">True</span>
+<span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="bp">True</span>
 </pre></div>
 </td></tr></table></div>
 </div>
@@ -132,7 +131,7 @@ add your new script:</p>
 4
 5
 6
-7</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">ACTION_UNIT_TESTS</span>
+7</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">ACTION_UNIT_TESTS</span>
   <span class="s">test_action_help.py</span>
 <span class="hll">  <span class="s">test_action_do_awesome.py</span>
 </span>  <span class="s">test_actions.py</span> <span class="c"># leave this as last item so it will be executed first!</span>
@@ -154,17 +153,17 @@ other action test script is run.</p>
 tests. By spawning off from this you inherit a bunch of useful methods for your
 testing. To make it work, the childclass needs to be set up properly. But
 first, <code class="file docutils literal"><span class="pre">test_actions.py</span></code> has to be loaded as a module:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>6</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">test_actions</span>
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>6</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">test_actions</span>
 </pre></div>
 </td></tr></table></div>
 <p>To showcase, the test cases, we explain how one would (and does) test the
 <code class="docutils literal"><span class="pre">help</span></code> action of <code class="docutils literal"><span class="pre">pm</span></code>.
 First, we create the childclass for the action.
 Go for <code class="xref py py-class docutils literal"><span class="pre">&lt;NAME&gt;ActionTests</span></code> as a naming scheme:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 7
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 7
  8
  9
-10</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">HelpActionTests</span><span class="p">(</span><span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="p">):</span>
+10</pre></div></td><td class="code"><div class="highlight"><pre><span class="k">class</span> <span class="nc">HelpActionTests</span><span class="p">(</span><span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="p">):</span>
     <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span> <span class="o">=</span> <span class="s1">&#39;help&#39;</span>
@@ -180,8 +179,8 @@ is derived from the <a class="reference external" href="https://docs.python.org/
 states will be placed in the userlevel documentation. This topic is already
 covered in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> by <a class="reference internal" href="#test_actions.ActionTestCase.RunExitStatusTest" title="test_actions.ActionTestCase.RunExitStatusTest"><code class="xref py py-meth docutils literal"><span class="pre">RunExitStatusTest()</span></code></a>.
 As an example, testing for <code class="docutils literal"><span class="pre">$?=0</span></code> could work like this:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
-12</pre></div></td><td class="code"><div class="highlight"><pre><span></span>    <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+12</pre></div></td><td class="code"><div class="highlight"><pre>    <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">())</span>
 </pre></div>
 </td></tr></table></div>
@@ -193,13 +192,13 @@ happens if a user throws dirty input data in.</p>
 </div>
 <div class="section" id="making-the-script-executable">
 <h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>&#8216;s <a class="reference external" href="https://www.openstructure.org/docs/dev/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python&#8216;s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>&#8216;s <a class="reference external" href="https://www.openstructure.org/docs/dev/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python&#8216;s
 <a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
 as a script:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
 14
-15</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
-    <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">testutils</span>
+15</pre></div></td><td class="code"><div class="highlight"><pre><span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
+    <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
     <span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
 </pre></div>
 </td></tr></table></div>
@@ -210,7 +209,7 @@ as a script:</p>
 <p>Unit tests are executed via <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code> and so are ProMod3 action tests.
 But for every test script, we also provide a private <code class="docutils literal"><span class="pre">make</span></code> target, ending
 with <code class="file docutils literal"><span class="pre">_run</span></code>. To solely run the tests for the awesome action, hit</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make test_action_do_awesome.py_run
 </pre></div>
 </div>
 </div>
@@ -227,20 +226,20 @@ parameter <code class="xref py py-attr docutils literal"><span class="pre">verbo
 output onto the command line. The idea is to turn it on for development, but
 once done, disable it to keep output of unit tests low.</p>
 <p>To get the test for exit code <code class="docutils literal"><span class="pre">0</span></code> talking to you, just do</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
-12</pre></div></td><td class="code"><div class="highlight"><pre><span></span>    <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">(),</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+12</pre></div></td><td class="code"><div class="highlight"><pre>    <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">(),</span> <span class="n">verbose</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
 </pre></div>
 </td></tr></table></div>
 <p>and</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
-12</pre></div></td><td class="code"><div class="highlight"><pre><span></span>    <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+12</pre></div></td><td class="code"><div class="highlight"><pre>    <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">())</span>
 </pre></div>
 </td></tr></table></div>
 <p>keeps it silent (<code class="xref py py-attr docutils literal"><span class="pre">verbose</span></code> is set to <code class="docutils literal"><span class="pre">False</span></code> by default). If enabled,
 output will be separated into <code class="file docutils literal"><span class="pre">stdout</span></code> and <code class="file docutils literal"><span class="pre">stderr</span></code>:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make test_action_do_awesome.py_run
 <span class="go">&lt;Lots of output from the build process&gt;</span>
 <span class="go">running checks test_action_do_awesome.py</span>
 <span class="go">stdout of &#39;&lt;BUILD&gt;/stage/bin/pm do-awesome&#39;</span>
@@ -403,6 +402,9 @@ file (also complains if a directory is found instead).</p>
       <input type="hidden" name="check_keywords" value="yes" />
       <input type="hidden" name="area" value="default" />
     </form>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
+    </p>
 </div>
 <script type="text/javascript">$('#searchbox').show(0);</script>
         </div>
@@ -410,11 +412,11 @@ file (also complains if a directory is found instead).</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/actions/index_dev.txt"
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 05f730f28a2e8349dffce5b4b7a0fcbfb68a61a0..5f862a43192321751e05856a85bbac77bac3e1c1 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
     <link rel="up" title="Documentation For Users" href="users.html" />
-    <link rel="next" title="modelling - Protein Modelling" href="modelling/index.html" />
+    <link rel="next" title="ProMod3 and Containers" href="container/index.html" />
     <link rel="prev" title="ProMod3 Actions" href="actions/index.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -70,7 +69,7 @@ and certain directories needed for building ProMod3. Basically it is called
 right from a shell with the directory containing the top-level
 <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> as an argument. The preferred approach is to generate a
 build folder and configure and compile in there:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">#</span> execute this in the ProMod3 root folder
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">#</span> execute this in the ProMod3 root folder
 <span class="gp">$</span> mkdir build
 <span class="gp">$</span> <span class="nb">cd</span> build
 <span class="gp">$</span> cmake .. -DOST_ROOT<span class="o">=</span>&lt;PATH TO OST&gt;
@@ -117,7 +116,7 @@ really got rebuild and similar things required.</p>
 <div class="section" id="running-make">
 <h2>Running Make<a class="headerlink" href="#running-make" title="Permalink to this headline">¶</a></h2>
 <p>After configuring, you want to build ProMod3 by</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make
 </pre></div>
 </div>
 <p>to populate the <code class="file docutils literal"><span class="pre">stage</span></code> directory with a ready-to-go version of the
@@ -141,7 +140,7 @@ builder</li>
 <h2>Installing ProMod3<a class="headerlink" href="#installing-project" title="Permalink to this headline">¶</a></h2>
 <p>If you wish to install ProMod3 (note that you can also safely keep it all in
 the <code class="file docutils literal"><span class="pre">stage</span></code> directory), you can use</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make install
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make install
 </pre></div>
 </div>
 <p>By default, this will copy the <code class="file docutils literal"><span class="pre">stage</span></code> directory to <code class="file docutils literal"><span class="pre">/usr/local</span></code>. To
@@ -177,7 +176,7 @@ safely delete the whole source folder.</p>
   <li><a href="index.html">Documentation overview</a><ul>
   <li><a href="users.html">Documentation For Users</a><ul>
       <li>Previous: <a href="actions/index.html" title="previous chapter">ProMod3 Actions</a></li>
-      <li>Next: <a href="modelling/index.html" title="next chapter"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+      <li>Next: <a href="container/index.html" title="next chapter">ProMod3 and Containers</a></li>
   </ul></li>
   </ul></li>
 </ul>
@@ -197,6 +196,9 @@ safely delete the whole source folder.</p>
       <input type="hidden" name="check_keywords" value="yes" />
       <input type="hidden" name="area" value="default" />
     </form>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
+    </p>
 </div>
 <script type="text/javascript">$('#searchbox').show(0);</script>
         </div>
@@ -204,11 +206,11 @@ safely delete the whole source folder.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/buildsystem.txt"
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 776b517f5d8af27418df83b927924c2b327d2a65..ee3fe26e8b52b3e319cb7640a69e70228fb70b3c 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -23,16 +23,15 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
-    <link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
+    <link rel="prev" title="References" href="references.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -41,6 +40,26 @@
             
   <div class="section" id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-1-3-0">
+<h2>Release 1.3.0<a class="headerlink" href="#release-1-3-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>Apply Apache Version 2.0 License to the project</li>
+<li>2010 Dunbrack rotamer library has been replaced by an own backbone dependent
+rotamer library. All scripts required to reproduce the data are in
+extras/data_generation/rotamer_library</li>
+<li>Penultimate rotamer library has been replaced by an own backbone independent
+rotamer library. All scripts required to reproduce the data are in
+extras/data_generation/rotamer_library</li>
+<li>SampleMonteCarlo function moved to Python. This makes it possible to provide
+sampler/closer/scorer/cooler objects implemented in both, Python and C++</li>
+<li>Action script for sidechain modelling</li>
+<li>Allow sequence profiles as input for build-model action script.</li>
+<li>Recipe for Docker / Singularity container</li>
+<li>Check peptide bonds when building a RawModel. Treat as gap if bond is
+stereochemically problematic despite being in sequence.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
+</ul>
+</div>
 <div class="section" id="release-1-2-0">
 <h2>Release 1.2.0<a class="headerlink" href="#release-1-2-0" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
@@ -111,6 +130,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
   <h3><a href="index.html">Table Of Contents</a></h3>
   <ul>
 <li><a class="reference internal" href="#">Changelog</a><ul>
+<li><a class="reference internal" href="#release-1-3-0">Release 1.3.0</a></li>
 <li><a class="reference internal" href="#release-1-2-0">Release 1.2.0</a></li>
 <li><a class="reference internal" href="#release-1-1-0">Release 1.1.0</a></li>
 <li><a class="reference internal" href="#release-1-0">Release 1.0</a></li>
@@ -121,7 +141,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
 <h3>Related Topics</h3>
 <ul>
   <li><a href="index.html">Documentation overview</a><ul>
-      <li>Previous: <a href="portableIO.html" title="previous chapter">Using Binary Files In ProMod3</a></li>
+      <li>Previous: <a href="references.html" title="previous chapter">References</a></li>
   </ul></li>
 </ul>
 </div>
@@ -140,6 +160,9 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
       <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>
@@ -147,11 +170,11 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/changelog.txt"
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index f80cc16828502e7b936f090bbb38cd803d3b88ee..78c3e04b30696fe180ec549bcb3bd85e5404a574 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Developers" href="../developers.html" />
     <link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
     <link rel="prev" title="test_actions - Testing Actions" href="../actions/index_dev.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -75,7 +74,7 @@ various <code class="file docutils literal"><span class="pre">CMakeLists.txt</sp
 <dl class="command">
 <dt id="command:module">
 <code class="descname">module</code><a class="headerlink" href="#command:module" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">module</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">module</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
        <span class="s">SOURCES</span> <span class="s">source1</span> <span class="s">source2</span>
        <span class="s">HEADERS</span> <span class="s">header1</span> <span class="s">header2</span> <span class="s">[IN_DIR</span> <span class="s">dir]</span>
                <span class="s">[header3</span> <span class="s">header4</span> <span class="s">[IN_DIR</span> <span class="s">dir]]</span>
@@ -116,7 +115,7 @@ libraries here, such as <code class="docutils literal"><span class="pre">${OST_L
 <dl class="command">
 <dt id="command:pymod">
 <code class="descname">pymod</code><a class="headerlink" href="#command:pymod" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
       <span class="s">CPP</span> <span class="s">source1</span> <span class="s">source2</span>
       <span class="s">PY</span> <span class="s">source</span> <span class="s">source2</span> <span class="s">[IN_DIR</span> <span class="s">dir]</span>
          <span class="s">[source3</span> <span class="s">source4</span> <span class="s">[IN_DIR</span> <span class="s">dir]]</span>
@@ -164,7 +163,7 @@ headers in the <code class="file docutils literal"><span class="pre">config</spa
 <dl class="command">
 <dt id="command:convert_module_data">
 <code class="descname">convert_module_data</code><a class="headerlink" href="#command:convert_module_data" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">convert_module_data</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">convert_module_data</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
                     <span class="s">FILE</span> <span class="s">file</span>
                     <span class="s">SCRIPT</span> <span class="s">script</span>
                     <span class="s">[ARGS</span> <span class="s">args]</span><span class="p">)</span>
@@ -186,7 +185,7 @@ If given, <code class="docutils literal"><span class="pre">args</span></code> ca
 <dl class="command">
 <dt id="command:promod3_unittest">
 <code class="descname">promod3_unittest</code><a class="headerlink" href="#command:promod3_unittest" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">promod3_unittest</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">promod3_unittest</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
                  <span class="s">SOURCES</span> <span class="s">source1</span> <span class="s">[source2</span> <span class="s">...]</span>
                  <span class="s">[LINK</span> <span class="s">library1/</span> <span class="s">linker</span> <span class="s">flag1</span> <span class="s">[library2/</span> <span class="s">linker</span> <span class="s">flag2</span> <span class="s">...]]</span>
                  <span class="s">[DATA</span> <span class="s">data1</span> <span class="s">[data2</span> <span class="s">...]]</span>
@@ -242,7 +241,7 @@ By default all unit tests are registered to be executed with the
 <dl class="command">
 <dt id="command:add_doc_source">
 <code class="descname">add_doc_source</code><a class="headerlink" href="#command:add_doc_source" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">add_doc_source</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">add_doc_source</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
                <span class="s">RST</span> <span class="s">rst1</span> <span class="s">[rst2...]</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -267,7 +266,7 @@ name or a CMake list.</dd>
 <dl class="command">
 <dt id="command:add_doc_dependency">
 <code class="descname">add_doc_dependency</code><a class="headerlink" href="#command:add_doc_dependency" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">add_doc_dependency</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">add_doc_dependency</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
                    <span class="s">DEP</span> <span class="s">dependency1</span> <span class="s">[dependency2...]</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -294,7 +293,7 @@ absolute path.</dd>
 <dl class="command">
 <dt id="command:pm_action">
 <code class="descname">pm_action</code><a class="headerlink" href="#command:pm_action" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">pm_action</span><span class="p">(</span><span class="s">ACTION</span> <span class="s">action-script</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">pm_action</span><span class="p">(</span><span class="s">ACTION</span> <span class="s">action-script</span>
           <span class="s">TARGET</span> <span class="s">target</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -365,6 +364,9 @@ target has to be created <strong>before</strong> any action may be attached to i
       <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>
@@ -372,11 +374,11 @@ target has to be created <strong>before</strong> any action may be attached to i
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/cmake/index.txt"
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
new file mode 100644
index 0000000000000000000000000000000000000000..bb4ef747ca46c389d8ebe2740955729f9fbafe9c
--- /dev/null
+++ b/doc/html/container/docker.html
@@ -0,0 +1,189 @@
+<!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>Docker &mdash; ProMod3 1.2.0 documentation</title>
+    
+    <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '1.2.0',
+        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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+    <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+    <link rel="up" title="ProMod3 and Containers" href="index.html" />
+    <link rel="next" title="Singularity" href="singularity.html" />
+    <link rel="prev" title="ProMod3 and Containers" href="index.html" />
+   
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head>
+  <body role="document">  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <div class="section" id="docker">
+<h1>Docker<a class="headerlink" href="#docker" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="build-docker-image">
+<h2>Build Docker Image<a class="headerlink" href="#build-docker-image" title="Permalink to this headline">¶</a></h2>
+<p>In order to build the image:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo docker build --tag &lt;IMAGE_NAME&gt; -f Dockerfile &lt;PATH_TO_DOCKERFILE_DIR&gt;
+</pre></div>
+</div>
+<p>You can chose any image name (tag) eg. promod.</p>
+</div>
+<div class="section" id="run-scripts-and-actions-with-ost-pm">
+<h2>Run scripts and actions with OST/PM<a class="headerlink" href="#run-scripts-and-actions-with-ost-pm" title="Permalink to this headline">¶</a></h2>
+<p>If script or action requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
+path. Eg. assuming that we have a struc.pdb file in /home/&lt;USER&gt;/pdbs directory and
+a script.py in /home/&lt;USER&gt; we could mount the /home/&lt;USER&gt; to /home in docker as
+above by specifying -v /home/&lt;USER&gt;:/home. To run the script we thus need to
+provide the (relative) path to the script and (relative) path to the file eg:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo docker run --rm -v /home/&lt;USER&gt;:/home &lt;IMAGE_NAME&gt; pm script.py pdbs/struct.pdb
+</pre></div>
+</div>
+<p>or with absolute paths:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo docker run --rm -v /home/&lt;USER&gt;:/home &lt;IMAGE_NAME&gt; pm /home/script.py /home/pdbs/struct.pdb
+</pre></div>
+</div>
+<p>An alternative is to mount the current working directory into the docker home:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home &lt;IMAGE_NAME&gt; pm script.py pdbs/struct.pdb
+</pre></div>
+</div>
+</div>
+<div class="section" id="the-compound-library">
+<span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
+Compound libraries contain information on chemical compounds, such as their
+connectivity, chemical class and one-letter-code. The compound library has
+several uses, but the most important one is to provide the connectivy
+information for the rule-based processor.</p>
+<p>The compound library is generated with the components.cif dictionary provided by
+the PDB. As the PDB updates regularly, the compound library shipped with the
+container is quickly outdated. For most use cases, this is not problematic.
+However, if you rely on correct connectivity information of the latest and
+greatest compounds, you have to keep the compound library up to date manually.</p>
+<p>The suggested way of doing this is to generate your own compound library and
+mount it into the container where the original compound lib resides to
+override it.</p>
+<p>The simplest way to create a compound library is to use the
+<strong class="program">chemdict_tool</strong> available in the container. The program allows you
+to import the chemical description of the compounds from a MMCIF dictionary,
+e.g. the components.cif dictionary provided by the PDB.
+The latest dictionary can be downloaded from the
+<a class="reference external" href="http://www.wwpdb.org/ccd.html">wwPDB site</a>.
+The files are rather large, it is therefore recommended to download the
+gzipped version.</p>
+<p>After downloading the file use <strong class="program">chemdict_tool</strong> in the container to
+convert the MMCIF  dictionary into our internal format:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo docker run --rm -v <span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span>:/home &lt;IMAGE_NAME&gt; chemdict_tool create components.cif.gz compounds.chemlib
+</pre></div>
+</div>
+<p>To run a script with the upated compound library, use the -v option for mounting/overriding:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo docker run --rm -v /home/&lt;USER&gt;:/home -v &lt;COMPLIB_DIR_LOCALHOST&gt;:&lt;COMPLIB_DIR_CONTAINER&gt; &lt;IMAGE_NAME&gt; pm script.py pdbs/struct.pdb
+</pre></div>
+</div>
+<p>with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated
+compound library with name compounds.chemlib and COMPLIB_DIR_CONTAINER the
+according path in the container.
+If you didnt change anything in the Dockerfile, the latter should be
+/usr/local/share/ost_complib</p>
+<p>You can check whether the default lib is successfully overriden by looking at the
+output when running a Python script with following code in the container:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">promod3</span> <span class="c1"># required to setup default lib</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
+<span class="n">lib</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">()</span>
+<span class="k">print</span> <span class="n">lib</span><span class="o">.</span><span class="n">GetCreationDate</span><span class="p">()</span>
+</pre></div>
+</div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+  <h3><a href="../index.html">Table Of Contents</a></h3>
+  <ul>
+<li><a class="reference internal" href="#">Docker</a><ul>
+<li><a class="reference internal" href="#build-docker-image">Build Docker Image</a></li>
+<li><a class="reference internal" href="#run-scripts-and-actions-with-ost-pm">Run scripts and actions with OST/PM</a></li>
+<li><a class="reference internal" href="#the-compound-library">The Compound Library</a></li>
+</ul>
+</li>
+</ul>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  <li><a href="../users.html">Documentation For Users</a><ul>
+  <li><a href="index.html">ProMod3 and Containers</a><ul>
+      <li>Previous: <a href="index.html" title="previous chapter">ProMod3 and Containers</a></li>
+      <li>Next: <a href="singularity.html" title="next chapter">Singularity</a></li>
+  </ul></li>
+  </ul></li>
+  </ul></li>
+</ul>
+</div>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/container/docker.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
+  <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="footer">
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
+      
+      |
+      <a href="../_sources/container/docker.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+    
+
+    
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..c564a55108949c1991d83c5b51904eb75a966fb6
--- /dev/null
+++ b/doc/html/container/index.html
@@ -0,0 +1,113 @@
+<!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 and Containers &mdash; ProMod3 1.2.0 documentation</title>
+    
+    <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '1.2.0',
+        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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+    <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+    <link rel="up" title="Documentation For Users" href="../users.html" />
+    <link rel="next" title="Docker" href="docker.html" />
+    <link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
+   
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head>
+  <body role="document">  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <div class="section" id="promod3-and-containers">
+<h1>ProMod3 and Containers<a class="headerlink" href="#promod3-and-containers" title="Permalink to this headline">¶</a></h1>
+<p>ProMod3 offers build recipes for Docker and Singularity in
+&lt;PATH_TO_PROMOD3_CHECKOUT&gt;/container. To avoid code duplication,
+the Singularity container bootstraps from the Docker one and adds
+some sugar on top.</p>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker</a></li>
+<li class="toctree-l1"><a class="reference internal" href="singularity.html">Singularity</a></li>
+</ul>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  <li><a href="../users.html">Documentation For Users</a><ul>
+      <li>Previous: <a href="../buildsystem.html" title="previous chapter">Building ProMod3</a></li>
+      <li>Next: <a href="docker.html" title="next chapter">Docker</a></li>
+  </ul></li>
+  </ul></li>
+</ul>
+</div>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/container/index.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
+  <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="footer">
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
+      
+      |
+      <a href="../_sources/container/index.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+    
+
+    
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
new file mode 100644
index 0000000000000000000000000000000000000000..97ef62cb079b566d42bfd80f0bd98b5cdb05dfde
--- /dev/null
+++ b/doc/html/container/singularity.html
@@ -0,0 +1,188 @@
+<!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>Singularity &mdash; ProMod3 1.2.0 documentation</title>
+    
+    <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '1.2.0',
+        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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+    <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+    <link rel="up" title="ProMod3 and Containers" href="index.html" />
+    <link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
+    <link rel="prev" title="Docker" href="docker.html" />
+   
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head>
+  <body role="document">  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <div class="section" id="singularity">
+<h1>Singularity<a class="headerlink" href="#singularity" title="Permalink to this headline">¶</a></h1>
+<p>We do not provide a &#8220;standalone&#8221; Singularity image, but rather bootstrap from a
+Docker image.</p>
+<div class="section" id="build-singularity-image">
+<h2>Build Singularity Image<a class="headerlink" href="#build-singularity-image" title="Permalink to this headline">¶</a></h2>
+<p>You can pull the Docker image to start with from two different sources.</p>
+<p>Option One:</p>
+<p>You built the Docker image locally and want to use it as a starting point. For
+this we have to fire up a local Docker registry and pull from there. Let&#8217;s
+assume you built the Docker image with tag promod.</p>
+<p>Fire the local Registry and push the promod image to it:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo docker run -d -p 5000:5000 --restart<span class="o">=</span>always --name registry registry:2
+sudo docker tag promod localhost:5000/promod
+sudo docker push localhost:5000/promod
+</pre></div>
+</div>
+<p>Make sure, that on top of your Singularity recipe you have something like:</p>
+<div class="highlight-bash"><div class="highlight"><pre>BootStrap: docker
+Registry: http://localhost:5000
+Namespace:
+From: promod:latest
+</pre></div>
+</div>
+<p>and build the image with:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo <span class="nv">SINGULARITY_NOHTTPS</span><span class="o">=</span><span class="m">1</span> singularity build promod.img Singularity
+</pre></div>
+</div>
+<p>Option Two:</p>
+<p>You pull a Docker image from an external Docker registry.
+Fill in a lot of words as soon as its on Dockerhub. Many words. The best words.</p>
+<p>and build the image with:</p>
+<div class="highlight-bash"><div class="highlight"><pre>sudo singularity build promod.img Singularity
+</pre></div>
+</div>
+</div>
+<div class="section" id="run-scripts-and-actions-with-ost-pm">
+<h2>Run scripts and actions with OST/PM<a class="headerlink" href="#run-scripts-and-actions-with-ost-pm" title="Permalink to this headline">¶</a></h2>
+<p>The created container can run the ost, pm or chemdict_tool executables.
+For convenience, a jupyter notebook playground with OST, ProMod3 and nglview is
+available.</p>
+<p>To run ost, pm or chemdict_tool executables, use the exec command.
+E.g. to run scripts with pm:</p>
+<div class="highlight-bash"><div class="highlight"><pre>singularity <span class="nb">exec</span> &lt;IMAGE&gt; pm my_script.py <span class="o">[</span>options<span class="o">]</span>
+</pre></div>
+</div>
+<p>The jupyter notebook is setup as an app in the container.
+To get help on how to run it:</p>
+<div class="highlight-bash"><div class="highlight"><pre>singularity run --app Notebook &lt;IMAGE&gt; --help
+</pre></div>
+</div>
+</div>
+<div class="section" id="the-compound-library">
+<h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
+<p>You&#8217;ll have the exact same problem with outdated compound libraries as in the
+raw Docker image. You can find more information on that matter in the Docker
+section of the documentation: <a class="reference internal" href="docker.html#docker-compound-lib"><span>The Compound Library</span></a>.</p>
+<p>The same trick of mounting an up to date compound library from the local host into
+the container applies. The two relevant commands for Singularity are building
+a new library and mount it.</p>
+<p>Build a new library:</p>
+<div class="highlight-bash"><div class="highlight"><pre>singularity <span class="nb">exec</span> &lt;IMAGE_NAME&gt; chemdict_tool create components.cif.gz compounds.chemlib
+</pre></div>
+</div>
+<p>Run some script with an updated compound library from localhost:</p>
+<div class="highlight-bash"><div class="highlight"><pre>singularity <span class="nb">exec</span> -B &lt;COMPLIB_DIR_LOCALHOST&gt;:&lt;COMPLIB_DIR_CONTAINER&gt; &lt;IMAGE_NAME&gt; pm my_script.py
+</pre></div>
+</div>
+<p>Same as for the Docker, if you didn&#8217;t meddle with the original Dockerfile,
+&lt;COMPLIB_DIR_CONTAINER&gt; should be /usr/local/share/ost_complib.
+&lt;COMPLIB_DIR_LOCALHOST&gt; is the directory that contains the compound lib with the
+name compounds.chemlib that you created before. Make sure that everything works
+as expected by executing the exact same lines of Python code as described
+in the Docker documentation: <a class="reference internal" href="docker.html#docker-compound-lib"><span>The Compound Library</span></a>.</p>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+  <h3><a href="../index.html">Table Of Contents</a></h3>
+  <ul>
+<li><a class="reference internal" href="#">Singularity</a><ul>
+<li><a class="reference internal" href="#build-singularity-image">Build Singularity Image</a></li>
+<li><a class="reference internal" href="#run-scripts-and-actions-with-ost-pm">Run scripts and actions with OST/PM</a></li>
+<li><a class="reference internal" href="#the-compound-library">The Compound Library</a></li>
+</ul>
+</li>
+</ul>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  <li><a href="../users.html">Documentation For Users</a><ul>
+  <li><a href="index.html">ProMod3 and Containers</a><ul>
+      <li>Previous: <a href="docker.html" title="previous chapter">Docker</a></li>
+      <li>Next: <a href="../modelling/index.html" title="next chapter"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+  </ul></li>
+  </ul></li>
+  </ul></li>
+</ul>
+</div>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../_sources/container/singularity.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
+  <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="footer">
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
+      
+      |
+      <a href="../_sources/container/singularity.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+    
+
+    
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 069ec304aa26f141410c4fe3bfd06b0b7624cbce..83fdf7685a07fb13d4514d1c11fb23d3abcd7d8e 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
     <link rel="up" title="Documentation For Developers" href="developers.html" />
     <link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
     <link rel="prev" title="ProMod3 Setup" href="dev_setup.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -55,27 +54,27 @@ the repository into a directory and just changed into it.</p>
 work fine with all the other new fellows waiting for release right from the
 beginning. Therefore you need to switch branches as a first step. Git will
 tell you for which branch you went, a story of failure otherwise.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout develop
 <span class="go">Switched to branch &#39;develop&#39;</span>
 </pre></div>
 </div>
 <p>Sitting on top of the right code basis, you should just spawn your own branch
 from it. As an example, your feature will go by the name of &#8216;sidechain&#8217;.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout -b sidechain
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout -b sidechain
 <span class="go">Switched to a new branch &#39;sidechain&#39;</span>
 </pre></div>
 </div>
 <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></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
 </pre></div>
 </div>
 <p>With that in place, changes which break our coding standards will abort any
 commit.</p>
 <p>Now create the directory structure where your project will live. Here is the
 list of directories which are likely to be used in every project.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir -p sidechain/doc
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> mkdir -p sidechain/doc
 <span class="gp">$</span> mkdir -p sidechain/pymod
 <span class="gp">$</span> mkdir -p sidechain/tests
 </pre></div>
@@ -83,7 +82,7 @@ list of directories which are likely to be used in every project.</p>
 <p>If you run <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code> at this point, you will see basically nothing. That
 is, Git does not admire empty directories. Before you bring your module under
 version control, create a couple of files which are always needed.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/pymod/__init__.py
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch sidechain/pymod/__init__.py
 <span class="gp">$</span> <span class="nb">echo</span> <span class="s2">&quot;:mod:\`~promod3.sidechain\` - ProMod3 side chain optimiser&quot;</span> &gt;&gt; sidechain/doc/index.rst
 <span class="gp">$</span> <span class="nb">echo</span> <span class="s2">&quot;================================================================================&quot;</span> &gt;&gt; sidechain/doc/index.rst
 </pre></div>
@@ -95,7 +94,7 @@ your documentation.</p>
 <p>For integration with <strong class="command">make</strong>, the build system needs to now about the
 new module and its members. This goes for setting up new CMake files and
 extending some around the directory root.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/CMakeLists.txt
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch sidechain/CMakeLists.txt
 <span class="gp">$</span> touch sidechain/pymod/CMakeLists.txt
 <span class="gp">$</span> touch sidechain/doc/CMakeLists.txt
 </pre></div>
@@ -103,7 +102,7 @@ extending some around the directory root.</p>
 <p>Each of those files still needs a bit of content. The simplest one comes from
 the module&#8217;s root, <code class="file docutils literal"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
 <div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
-2</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
+2</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
 <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
 </pre></div>
 </td></tr></table></div>
@@ -115,7 +114,7 @@ configurations. The next level in <code class="file docutils literal"><span clas
 2
 3
 4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_RST</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_RST</span>
 <span class="s">index.rst</span>
 <span class="p">)</span>
 
@@ -140,7 +139,7 @@ a couple of examples around in this repository. Here is the most basic
 2
 3
 4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_PYMOD</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_PYMOD</span>
 <span class="s">__init__.py</span>
 <span class="p">)</span>
 
@@ -168,7 +167,7 @@ top level <code class="file docutils literal"><span class="pre">CMakeLists.txt</
 12
 13
 14
-15</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="c">## &lt;lots of cmake commands...&gt;</span>
+15</pre></div></td><td class="code"><div class="highlight"><pre><span class="c">## &lt;lots of cmake commands...&gt;</span>
 
 <span class="c">## sub dirs to be recognised by CMake</span>
 <span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
@@ -200,7 +199,7 @@ still can stay in your repository while being out of the source tree by using
 sub-directories. ProMod3 comes with a dedicated prefix &#8216;build*&#8217; in
 <code class="file docutils literal"><span class="pre">.gitignore</span></code>. Have a directory <code class="file docutils literal"><span class="pre">build</span></code> and <code class="file docutils literal"><span class="pre">build-dbg</span></code> and it
 will not show up in <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code>.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir build
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> mkdir build
 <span class="gp">$</span> <span class="nb">cd</span> build
 </pre></div>
 </div>
@@ -210,7 +209,7 @@ those scripts only need to be pointed to an OST staging tree. Even if you
 are on a system not covered by available scripts, their code may help you at
 the CMake command. Once you managed to conquer a new system, feel free to add
 a new configuration script. The following example assumes Fedora 19.</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> ../conf-scripts/fedora-19-conf ../../ost.git/stage
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> ../conf-scripts/fedora-19-conf ../../ost.git/stage
 </pre></div>
 </div>
 <p>From this point, <strong class="command">make</strong> should work and you could start adding your
@@ -227,7 +226,7 @@ basic scheme is to import your module, subclass <a class="reference external" hr
 make the whole file runnable as script using the most common <a class="reference external" href="https://docs.python.org/2.7/library/__main__.html"><code class="xref py py-attr docutils literal"><span class="pre">__name__</span></code></a>
 attribute. As an example we test the
 <a class="reference internal" href="modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a> function:</p>
-<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
  2
  3
  4
@@ -245,9 +244,9 @@ attribute. As an example we test the
 16
 17
 18
-19</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">unittest</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
+19</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">unittest</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
 <span class="kn">import</span> <span class="nn">os</span>
 
 <span class="k">class</span> <span class="nc">ReconstructTests</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
@@ -256,13 +255,13 @@ attribute. As an example we test the
     	<span class="n">ref_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;data&#39;</span><span class="p">,</span> <span class="s1">&#39;1eye_rec.pdb&#39;</span><span class="p">)</span>
     	<span class="c1"># get and reconstruct 1eye</span>
     	<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">in_file</span><span class="p">)</span>
-    	<span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+    	<span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
     	<span class="c1"># compare with reference solution</span>
     	<span class="n">prot_rec</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">ref_file</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">GetAtomCount</span><span class="p">(),</span> <span class="n">prot_rec</span><span class="o">.</span><span class="n">GetAtomCount</span><span class="p">())</span>
 
 <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
-    <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">testutils</span>
+    <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
     <span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
 </pre></div>
 </td></tr></table></div>
@@ -272,7 +271,7 @@ First, tell CMake to search <code class="file docutils literal"><span class="pre
 by extending the list of sub-directories in <code class="file docutils literal"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
 <div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
 2
-3</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
+3</pre></div></td><td class="code"><div class="highlight"><pre> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
  <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
  <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">tests</span><span class="p">)</span>
 </pre></div>
@@ -291,7 +290,7 @@ you.</p>
  9
 10
 11
-12</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_UNIT_TESTS</span>
+12</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_UNIT_TESTS</span>
   <span class="s">test_reconstruct_sidechains.py</span>
 <span class="p">)</span>
 
@@ -316,10 +315,10 @@ you.</p>
 launcher found in your staging directory at <code class="file docutils literal"><span class="pre">stage/bin/pm</span></code>. This little
 guy helps keeping the shell environment in the right mood to carry out your
 job. So usually you will start an action by</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> stage/bin/pm <span class="nb">help</span>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> stage/bin/pm <span class="nb">help</span>
 </pre></div>
 </div>
-<p>To start your own action, follow <a class="reference internal" href="#how-to-start-your-own-module"><span class="std std-ref">How To Start Your Own Module</span></a> until
+<p>To start your own action, follow <a class="reference internal" href="#how-to-start-your-own-module"><span>How To Start Your Own Module</span></a> until
 creating a directory structure for a new module. Also <strong>do</strong> go for a dedicated
 branch for action-development. There you can produce intermediate commits while
 other branches stay clean in case you have to do some work there which needs to
@@ -327,7 +326,7 @@ get public.</p>
 <p>After preparing your repository its time to create a file for the action. That
 is a bit different than for modules. Assuming we are sitting in the
 repository&#8217;s root:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch action/pm-awesome-action
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch action/pm-awesome-action
 <span class="gp">$</span> chmod +x action/pm-awesome-action
 </pre></div>
 </div>
@@ -344,7 +343,7 @@ executable, which does not propagate if you do it <strong>after</strong> the fir
 4
 5
 6
-7</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="nb">add_custom_target</span><span class="p">(</span><span class="s">actions</span> <span class="s">ALL</span><span class="p">)</span>
+7</pre></div></td><td class="code"><div class="highlight"><pre> <span class="nb">add_custom_target</span><span class="p">(</span><span class="s">actions</span> <span class="s">ALL</span><span class="p">)</span>
  <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">tests</span><span class="p">)</span>
 
  <span class="nb">pm_action_init</span><span class="p">()</span>
@@ -378,7 +377,7 @@ that&#8217;s enough to get everything just right.</p>
 Your action will have own function definitions, variables and all the bells
 and whistles. Hiding behind <a class="reference external" href="https://docs.python.org/2.7/library/__main__.html"><code class="xref py py-attr docutils literal"><span class="pre">__main__</span></code></a> keeps everything separated and makes
 things easier when it gets to debugging. So just after</p>
-<div class="highlight-python"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">alot</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">alot</span>
 
 <span class="k">def</span> <span class="nf">functions_specific_to_your_action</span><span class="p">(</span><span class="o">...</span><span class="p">):</span>
 
@@ -465,7 +464,7 @@ and <code class="docutils literal"><span class="pre">ost</span></code> as in the
 folder and adapt it for your purposes. First, you will have to fix the paths
 to ProMod3 and OST in the <code class="file docutils literal"><span class="pre">Makefile</span></code> by changing the following
 lines:</p>
-<div class="highlight-make"><div class="highlight"><pre><span></span><span class="c"># path to OST and ProMod3 stage</span>
+<div class="highlight-make"><div class="highlight"><pre><span class="c"># path to OST and ProMod3 stage</span>
 <span class="nv">OST_ROOT</span> <span class="o">=</span> &lt;DEFINEME&gt;/ost/build/stage
 <span class="nv">PROMOD3_ROOT</span> <span class="o">=</span> &lt;DEFINEME&gt;/ProMod3/build/stage
 </pre></div>
@@ -518,29 +517,26 @@ needed to create the actual documentation is done by CMake and its makefiles.
 Hence, the <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> of the <code class="file docutils literal"><span class="pre">doc</span></code> directory of a module is
 crucial. For documentation which does not relate to a particular module, the
 repository comes with a top-level <code class="file docutils literal"><span class="pre">doc</span></code> directory.</p>
-<p>While you should not spend to much time thinking about how to format
-documentation, here is a helpful list of standard formatters:
-<a class="reference external" href="http://sphinx-doc.org/en/stable/markup/inline.html">http://sphinx-doc.org/en/stable/markup/inline.html</a></p>
 <p>If you write new functionality for ProMod3, or fix bugs, feel free to extend
 the <code class="file docutils literal"><span class="pre">CHANGELOG</span></code> file. It will be automatically pulled into the
 documentation.</p>
 <p>It is highly recommended to add code examples with your documentation. For that
-purpose, you should write a fully runnable script, which is to be placed in the
+purpose, you should write a fully runnable script which is to be placed in the
 <code class="file docutils literal"><span class="pre">doc/tests/scripts</span></code> directory. The script is to be runnable from within
 the <code class="file docutils literal"><span class="pre">doc/tests</span></code> directory as <code class="docutils literal"><span class="pre">pm</span> <span class="pre">SCRIPTPATH</span></code> and may use data stored in
 the <code class="file docutils literal"><span class="pre">doc/tests/data</span></code> directory. The script and any data needed by it, must
 then be referenced in the <code class="file docutils literal"><span class="pre">doc/tests/CMakeLists.txt</span></code> file. Afterwards,
-they can be included in the documentation using the
-<a class="reference external" href="http://www.sphinx-doc.org/en/stable/markup/code.html#includes">literalinclude</a>
-directive. For instance, if you add a new example code <code class="file docutils literal"><span class="pre">loop_main.py</span></code>,
+they can be included in the documentation using the literalinclude
+directive.
+For instance, if you add a new example code <code class="file docutils literal"><span class="pre">loop_main.py</span></code>,
 you would add it in your module documentation as follows:</p>
-<div class="highlight-rest"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../../tests/doc/scripts/loop_main.py
+<div class="highlight-rest"><div class="highlight"><pre><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../../tests/doc/scripts/loop_main.py
 </pre></div>
 </div>
 <p>If your example does not relate to a specific module and the documentation is
 in the top-level <code class="file docutils literal"><span class="pre">doc</span></code> directory, you need to drop one of the <code class="docutils literal"><span class="pre">..</span></code> as
 follows:</p>
-<div class="highlight-rest"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../tests/doc/scripts/hello_world.py
+<div class="highlight-rest"><div class="highlight"><pre><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../tests/doc/scripts/hello_world.py
 </pre></div>
 </div>
 <p>To ensure that the code examples keep on working, a unit test has to be defined
@@ -558,7 +554,7 @@ test.</li>
 there is no need to compile ProMod3 to read it. Our policy is to keep that
 folder in-sync with the latest documentation at least on the <code class="docutils literal"><span class="pre">master</span></code> branch
 (i.e. for every release). You can use the following commands to do the update:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">cd</span> &lt;PROMOD3_PATH&gt;/build
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> <span class="nb">cd</span> &lt;PROMOD3_PATH&gt;/build
 <span class="gp">$</span> make html
 <span class="gp">$</span> rsync -iv -az --exclude<span class="o">=</span><span class="s2">&quot;.*&quot;</span> --delete <span class="se">\</span>
 <span class="go">        &quot;stage/share/promod3/html/&quot; &quot;../doc/html&quot;</span>
@@ -641,6 +637,9 @@ contributions to web pages using ProMod3.</p>
       <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>
@@ -648,11 +647,11 @@ contributions to web pages using ProMod3.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/contributing.txt"
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 3cdcb509f583cc24facb60b9bcd5c19e7db01f34..ee31fc7f66fa665b132f6144ece8df392318a07c 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
     <link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
     <link rel="prev" title="helper - Shared Functionality For the Everything" href="helper.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -55,14 +54,14 @@
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Gromacs rule</li>
 <li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Desired number of positions (max. 3)</li>
-<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Anchor positions (max. 4)</li>
+<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Anchor positions (max. 4)</li>
 </ul>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -78,16 +77,16 @@
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C atom</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C-alpha atom</li>
 </ul>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -104,9 +103,9 @@ dihedral (A-B-C-D).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom A</li>
-<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom B</li>
-<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom C</li>
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of atom C</li>
 <li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Bond length (C-D)</li>
 <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Angle (B-C-D)</li>
 <li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Dihedral (A-B-C-D)</li>
@@ -116,7 +115,7 @@ dihedral (A-B-C-D).</p>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -127,22 +126,22 @@ dihedral (A-B-C-D).</p>
 <dt id="promod3.core.ConstructCBetaPos">
 <code class="descclassname">promod3.core.</code><code class="descname">ConstructCBetaPos</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCBetaPos" title="Permalink to this definition">¶</a></dt>
 <dd><p>Constructs position of C-beta atom given the positions of the backbone nitrogen,
-C-alpha and c atoms.</p>
+C-alpha and C atoms.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C-alpha atom</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Position of C atom</li>
 </ul>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -159,8 +158,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Axis of rotation</li>
-<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Anchor for rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Anchor for rotation</li>
 <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Angle (in radians in range [-pi,pi]) of rotation</li>
 </ul>
 </td>
@@ -168,7 +167,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -185,7 +184,7 @@ going through the origin.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Axis of rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Axis of rotation</li>
 <li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Angle (in radians in range [-pi,pi]) of rotation</li>
 </ul>
 </td>
@@ -193,7 +192,7 @@ going through the origin.</p>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -210,7 +209,7 @@ going through the origin.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue handle from which to extract N, CA and C coordinates.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue handle from which to extract N, CA and C coordinates.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>res</em> does not contain N, CA and C
 atoms.</td>
@@ -229,7 +228,7 @@ atoms.</td>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -339,6 +338,9 @@ angles and one distance and is used in the fragment database for fast lookups.</
       <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>
@@ -346,11 +348,11 @@ angles and one distance and is used in the fragment database for fast lookups.</
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/core/geometry.txt"
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index b99d92a070ce4ed9faef1242be310ea4eb2a9fe7..f3689561c61047d42abf48863b3213f1b1e4ab52 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
     <link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
     <link rel="prev" title="Runtime profiling" href="runtime_profiling.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -44,13 +43,13 @@
   <div class="section" id="graph-minimizer">
 <h1>Graph Minimizer<a class="headerlink" href="#graph-minimizer" title="Permalink to this headline">¶</a></h1>
 <p>The graph minimizer solves an energy minimization problem where we have n
-nodes <span class="math">N_i</span>, with each node having several possible solutions.
-Every solution has a self energy <span class="math">E_{self}</span> and pairwise energies in between nodes
+nodes <span class="math">\(N_i\)</span>, with each node having several possible solutions.
+Every solution has a self energy <span class="math">\(E_{self}\)</span> and pairwise energies in between nodes
 are possible. The goal is to select exactly one solution per node to obtain
-a set <span class="math">X=[x_1, x_2, ..., x_n]</span> that minimizes:</p>
+a set <span class="math">\(X=[x_1, x_2, ..., x_n]\)</span> that minimizes:</p>
 <div class="math">
-<p><span class="math">F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j&gt;i}E_{pair}(N_i[x_i], N_j[x_j])</span></p>
-</div><dl class="class">
+\[\begin{split}F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j&gt;i}E_{pair}(N_i[x_i], N_j[x_j])\end{split}\]</div>
+<dl class="class">
 <dt id="promod3.core.GraphMinimizer">
 <em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">GraphMinimizer</code><a class="headerlink" href="#promod3.core.GraphMinimizer" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="method">
@@ -111,7 +110,7 @@ inconsistent with the number of solutions in the specified nodes.</p>
 <code class="descname">ApplyDEE</code><span class="sig-paren">(</span><em>node_idx</em><span class="optional">[</span>, <em>e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyDEE" title="Permalink to this definition">¶</a></dt>
 <dd><p>Applies dead end elimination on one particular node and potentially
 deactivates certain solutions. The goldstein criterion is described in
-<a class="reference internal" href="#goldstein1994" id="id1">[goldstein1994]</a>.</p>
+<a class="reference internal" href="../references.html#goldstein1994" id="id1">[goldstein1994]</a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -138,7 +137,7 @@ a solution must be dominated by at least this <strong>e_cut</strong>.</li>
 <code class="descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em>edge_idx</em>, <em>epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
 <dd><p>Applies edge decomposition on one particular edge and potentially
 deactivates it. The exact decomposition  procedure is described in
-<a class="reference internal" href="../sidechain/index.html#krivov2009" id="id2">[krivov2009]</a>.</p>
+<a class="reference internal" href="../references.html#krivov2009" id="id2">[krivov2009]</a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -202,7 +201,7 @@ particular connected component is is larger <strong>max_complexity</strong>,
 this component is solved in a later iteration. The algorithm iterates until
 all connected components are solved and steadily increases the epsilon value
 resulting in a more and more agressive edge decomposition.
-Algorithm further descsribed in <a class="reference internal" href="../sidechain/index.html#krivov2009" id="id3">[krivov2009]</a>.</p>
+Algorithm further descsribed in <a class="reference internal" href="../references.html#krivov2009" id="id3">[krivov2009]</a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -241,7 +240,7 @@ runtime or even hit the <strong>max_visited_nodes</strong> parameter that caps t
 usage.
 To have a valid solution you have to take care that you set the <strong>e_cut</strong>
 parameter in the pruning function to <strong>e_tresh</strong>.
-Algorithm is described in <a class="reference internal" href="#leach1998" id="id4">[leach1998]</a>.</p>
+Algorithm is described in <a class="reference internal" href="../references.html#leach1998" id="id4">[leach1998]</a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -277,7 +276,7 @@ of that random selection relative to the current configuration is
 estimated. If the difference in energy is negative, the step is
 accepted. If not, the step is accepted with a probability given by
 the temperature dependent Metropolis criterion
-<span class="math">exp^{\left(\frac{-e_{diff}}{T}\right)}</span>.
+<span class="math">\(exp^{\left(\frac{-e_{diff}}{T}\right)}\)</span>.
 The temperature for every run starts with <strong>start_temperature</strong>
 and is multiplied every <strong>change_frequency</strong> steps with <strong>cooling_factor</strong>
 to achieve a simulated annealing effect.
@@ -330,18 +329,6 @@ The second element is the according energy value.</td>
 
 </dd></dl>
 
-<table class="docutils citation" frame="void" id="goldstein1994" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[goldstein1994]</a></td><td>Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="leach1998" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id4">[leach1998]</a></td><td>Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.</td></tr>
-</tbody>
-</table>
 </div>
 
 
@@ -377,6 +364,9 @@ The second element is the according energy value.</td>
       <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>
@@ -384,11 +374,11 @@ The second element is the according energy value.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/core/graph_minimizer.txt"
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 2ef049d9bc9fdc579ad7b7dffa6e9227371c6429..9e1caf9b893508c4ea9b8734be56dc504f28edf0 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
     <link rel="next" title="Geometry functions" href="geometry.html" />
     <link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -50,7 +49,7 @@ rather empty modules left alone.</p>
 </div>
 <div class="section" id="messages">
 <h2>Messages<a class="headerlink" href="#messages" title="Permalink to this headline">¶</a></h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">helper</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
 
 <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">&quot;Something failed!&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
 </pre></div>
@@ -83,9 +82,9 @@ traditionally reserved to successful commands.</li>
 <h2>File Tests<a class="headerlink" href="#file-tests" title="Permalink to this headline">¶</a></h2>
 <p>The following example parses an argument (call as <code class="docutils literal"><span class="pre">pm</span> <span class="pre">SCRIPTNAME</span> <span class="pre">FILENAME</span></code>) as
 a file name and checks whether it is a <code class="docutils literal"><span class="pre">pdb</span></code> or <code class="docutils literal"><span class="pre">mmcif</span></code> file.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="sd">&quot;&quot;&quot;Test for file reading.&quot;&quot;&quot;</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">helper</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">pm3argparse</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="sd">&quot;&quot;&quot;Test for file reading.&quot;&quot;&quot;</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
 
 <span class="n">p</span> <span class="o">=</span> <span class="n">pm3argparse</span><span class="o">.</span><span class="n">PM3ArgumentParser</span><span class="p">(</span><span class="n">__doc__</span><span class="p">)</span>
 <span class="n">p</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;file&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
@@ -96,7 +95,7 @@ a file name and checks whether it is a <code class="docutils literal"><span clas
 <span class="n">opts</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">ext</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileExtension</span><span class="p">(</span><span class="s1">&#39;Test file&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span>
                                                     <span class="n">opts</span><span class="o">.</span><span class="n">file</span><span class="p">,</span>
                                                     <span class="p">(</span><span class="s1">&#39;pdb&#39;</span><span class="p">,</span> <span class="s1">&#39;mmcif&#39;</span><span class="p">),</span>
-                                                    <span class="n">gzip</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                                                    <span class="n">gzip</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
 </pre></div>
 </div>
 <dl class="function">
@@ -239,6 +238,9 @@ script will terminate if a gzip file is found.</li>
       <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>
@@ -246,11 +248,11 @@ script will terminate if a gzip file is found.</li>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/core/helper.txt"
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 774d53ed424cd8915182a7f8216297a4fe85bde9..bb514aa8137b1a6dd020510b22901c305e8a3e62 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Users" href="../users.html" />
     <link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
     <link rel="prev" title="Loading Precomputed Objects" href="../loop/load_loop_objects.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -97,6 +96,9 @@ modeling per se but cover standard programming issues.</p>
       <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>
@@ -104,11 +106,11 @@ modeling per se but cover standard programming issues.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/core/index.txt"
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index c92c89603a57ec80a32e2435a5661d076d14f31a..580197b7cbbab45c2f8caccf62bfa4545c231a84 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 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="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -54,12 +53,12 @@ There <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentP
 simplification. It provides a set of standard arguments you just need to
 activate for your action plus it comes with some verification functionality for
 input.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="sd">&quot;&quot;&quot;</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">Place the description of your script right in the file and import</span>
 <span class="sd">it via &#39;__doc__&#39; as description to the parser (&#39;-h&#39;, &#39;--help&#39;).</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">pm3argparse</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
 
 <span class="c1"># make sure we see output when passing &#39;-h&#39;</span>
 <span class="kn">import</span> <span class="nn">ost</span>
@@ -156,7 +155,7 @@ sequence is used. File can be plain or gzipped.</li>
 <li><code class="docutils literal"><span class="pre">-j/--json</span> <span class="pre">&lt;OBJECT&gt;|&lt;FILE&gt;</span></code> - Alignments provided as JSON
 file/object. File can be plain or gzipped.</li>
 </ul>
-<p>See <a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details on the file formats.</p>
+<p>See <a class="reference internal" href="../actions/index.html#promod-build-model"><span>here</span></a> for details on the file formats.</p>
 <p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
 <ul class="simple">
 <li><code class="xref py py-attr docutils literal"><span class="pre">fasta</span></code> - filled with the input of the <code class="docutils literal"><span class="pre">--fasta</span></code> option, a
@@ -198,11 +197,51 @@ wrong type</li>
 </ul>
 </dd></dl>
 
+<dl class="method">
+<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">
+<code class="descname">AddProfile</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.AddProfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Commandline options for profiles</p>
+<p>Activate everything needed to load profiles to the argument parser.
+Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
+input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
+<p>Options/arguments added:</p>
+<ul class="simple">
+<li><code class="docutils literal"><span class="pre">-s/--seqprof</span> <span class="pre">&lt;FILE&gt;</span></code> - Sequence profile in any format readable
+by the <code class="xref py py-meth docutils literal"><span class="pre">ost.io.LoadSequenceProfile()</span></code> method. Format is chosen by 
+file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm, 
+.pssm.gz. Consider to use 
+<a class="reference external" href="https://www.openstructure.org/docs/dev/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file 
+in a3m format at hand.</li>
+</ul>
+<p>Notes:</p>
+<ul class="simple">
+<li>the profiles are mapped based on exact matches towards the gapless
+target sequences, i.e. one profile is mapped to several chains in
+case of homo-oligomers</li>
+<li>every profile must have a unique sequence to avoid ambiguities</li>
+<li>all or nothing - you cannot provide profiles for only a subset of
+target sequences</li>
+</ul>
+<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
+<ul class="simple">
+<li><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code> - <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>, 
+ordered to match the target sequences.</li>
+</ul>
+<p>Exit codes related to profile input:</p>
+<ul class="simple">
+<li>51 - a given profile file does not exist</li>
+<li>52 - failure to read a given profile file</li>
+<li>53 - a profile cannot be mapped to any target sequence</li>
+<li>54 - profile sequences are not unique</li>
+<li>55 - only subset of target sequences is covered by profile</li>
+</ul>
+</dd></dl>
+
 <dl class="method">
 <dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">
 <code class="descname">AddStructure</code><span class="sig-paren">(</span><em>attach_views=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.AddStructure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure" title="Permalink to this definition">¶</a></dt>
 <dd><p>Commandline options for structures.</p>
-<p>Activate everything needed to load alignments to the argument parser.
+<p>Activate everything needed to load structures to the argument parser.
 Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> and the
 input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -213,7 +252,7 @@ input is post processed and checked in <a class="reference internal" href="#prom
 to <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment"><code class="xref py py-meth docutils literal"><span class="pre">AddAlignment()</span></code></a>. Chains for each sequence
 are identified based on the sequence name of the
 templates in the alignments (see 
-<a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details).</td>
+<a class="reference internal" href="../actions/index.html#promod-build-model"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -336,6 +375,9 @@ and with the right constraints.</p>
       <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>
@@ -343,11 +385,11 @@ and with the right constraints.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/core/pm3argparse.txt"
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index 2466ad9d3f6e6d8de264e1874c43332677a3a97a..03dd39d1b39511fd097be0ed0e5c11bdbfdb1dd1 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
     <link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
     <link rel="prev" title="Geometry functions" href="geometry.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -193,6 +192,9 @@ will fail miserably if timers are currently running.</p>
       <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>
@@ -200,11 +202,11 @@ will fail miserably if timers are currently running.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/core/runtime_profiling.txt"
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index e0e9cb4d4256b35a60b91b487c28cbea9efd04cf..ce61a107cba4e00eaf86e1513fb394684be9a639 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Users" href="../users.html" />
     <link rel="next" title="Documentation For Developers" href="../developers.html" />
     <link rel="prev" title="Graph Minimizer" href="graph_minimizer.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -98,6 +97,9 @@ enabled globally.</p>
       <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>
@@ -105,11 +107,11 @@ enabled globally.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/core/setcompoundschemlib.txt"
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index f58b1ee6ad20de2cf87c9fc6bf8c81d1ba15d6b5..e1d54f0a89bff975c6b8b2c74a1c2a07d5b95517 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
     <link rel="up" title="Documentation For Developers" href="developers.html" />
     <link rel="next" title="Contributing" href="contributing.html" />
     <link rel="prev" title="Documentation For Developers" href="developers.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -87,7 +86,7 @@ created something that could go into a release, tidy things up according to the
 rules from above and merge it into <code class="docutils literal"><span class="pre">develop</span></code>. From there it will
 automatically find its way into the next release.</p>
 <p>To set up your own branch, start from a current <code class="docutils literal"><span class="pre">develop</span></code> branch:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop         <span class="c1"># switch to branch develop</span>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout develop         <span class="c1"># switch to branch develop</span>
 <span class="gp">$</span> git pull --rebase            <span class="c1"># update branch develop</span>
 <span class="gp">$</span> git checkout -b &lt;BRANCHNAME&gt; <span class="c1"># create branch &lt;BRANCHNAME&gt; and switch to it</span>
 </pre></div>
@@ -97,7 +96,7 @@ want to make use of in your project. Keeping your branch up to date is a three
 step process. Git does not allow updates on top of changed code, so either
 changes have to be committed, or if in the middle of implementing something,
 stored away temporarily. Making commits is straight forward:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit -m <span class="s1">&#39;&lt;DESCRIPTION&gt;&#39;</span> <span class="c1"># commit changes including a comment</span>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git commit -m <span class="s1">&#39;&lt;DESCRIPTION&gt;&#39;</span> <span class="c1"># commit changes including a comment</span>
 </pre></div>
 </div>
 <p>Hiding your changes away from Git just for updating files is a bit more
@@ -108,15 +107,15 @@ you have changed, too, and stashed away, this may end up in a non-resolvable
 merge conflict and your changes are lost. Usually the log tells you, which
 files were recently modified. Moving all current changes to the stack is
 achieved by:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash save
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git stash save
 </pre></div>
 </div>
 <p>To revive them, use:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash pop
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git stash pop
 </pre></div>
 </div>
 <p>After cleaning up your branch, switch to <code class="docutils literal"><span class="pre">develop</span></code>, update it and switch back:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout develop
 <span class="gp">$</span> git pull --rebase
 <span class="gp">$</span> git checkout &lt;BRANCHNAME&gt;
 </pre></div>
@@ -125,11 +124,11 @@ achieved by:</p>
 and rebasing. A rebase may only be done, if you <strong>never</strong> pushed your branch to
 the origin of the repository (otherwise you will mess up history, in the worst
 case <code class="docutils literal"><span class="pre">develop</span></code> may be unusable once you merge):</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git rebase develop
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git rebase develop
 </pre></div>
 </div>
 <p>For branches which are available to others, do a proper merge:</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git merge develop
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git merge develop
 </pre></div>
 </div>
 <p>This may require some manual conflict solving and will end up in a merge commit.</p>
@@ -138,17 +137,17 @@ case <code class="docutils literal"><span class="pre">develop</span></code> may
 <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></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
 </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
 <code class="file docutils literal"><span class="pre">extras/pre_commit/</span></code>. The checks can be manually executed with</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> python .git/hooks/pre-commit
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> python .git/hooks/pre-commit
 </pre></div>
 </div>
 <p>If you ever have to skip the hook,</p>
-<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit --no-verify
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git commit --no-verify
 </pre></div>
 </div>
 <p>does the trick. <strong>But</strong> checks are always run on the complete file containing
@@ -174,7 +173,7 @@ is invoked on unit test code, where we may go a little bit less restrictive.</p>
 everything together that belongs together&#8217;. That is, code, documentation and
 extra data should be gathered on a per-module basis immediately in the
 repository root. The directory structure of your module should look like this:</p>
-<div class="highlight-text"><div class="highlight"><pre><span></span>promod3.git/                            Project folder
+<div class="highlight-text"><div class="highlight"><pre>promod3.git/                            Project folder
       your_module/                      Module directory
             CMakeLists.txt              CMake configuration
             data/                       Extra data (if needed)
@@ -206,13 +205,13 @@ repository root. The directory structure of your module should look like this:</
 <p>Additionally to the module directories there are a few extra folders:</p>
 <ul class="simple">
 <li><code class="file docutils literal"><span class="pre">actions</span></code>: Scripts callable as <code class="docutils literal"><span class="pre">pm</span> <span class="pre">&lt;ACTION_NAME&gt;</span></code>.
-See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span class="std std-ref">here</span></a> for details.</li>
+See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span>here</span></a> for details.</li>
 <li><code class="file docutils literal"><span class="pre">cmake_support</span></code>: Helper functions for CMake.
-See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a> for details.</li>
+See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span>here</span></a> for details.</li>
 <li><code class="file docutils literal"><span class="pre">doc</span></code>: High-level documentation, test scripts (<code class="file docutils literal"><span class="pre">doc/tests</span></code>) and a
 copy of the generated html documentation (<code class="file docutils literal"><span class="pre">doc/html</span></code>). The latter must
 be kept up-to-date at least on the <code class="docutils literal"><span class="pre">master</span></code> branch.
-See <a class="reference internal" href="contributing.html#writing-documentation"><span class="std std-ref">here</span></a> for details.</li>
+See <a class="reference internal" href="contributing.html#writing-documentation"><span>here</span></a> for details.</li>
 <li><code class="file docutils literal"><span class="pre">extras</span></code>: Extra data and information that doesn&#8217;t fit anywhere
 else (e.g. Git hooks or scripts to recreate the binary files).</li>
 <li><code class="file docutils literal"><span class="pre">scripts</span></code>: Input for scripts that end up in <code class="file docutils literal"><span class="pre">stage/bin</span></code></li>
@@ -227,7 +226,7 @@ Python modules are declared there as well as which files belong to the
 documentation. CMake is a rather complex topic (unfortunately all usable
 build systems seem to be) so we skip a detailed view, here, and just advice you
 to go by example. There is a tiny bit of documentation on our additions to
-CMake <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a>. If you really need to make changes to the
+CMake <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span>here</span></a>. If you really need to make changes to the
 build system, other than adding new files and modules, you have to dive into
 CMake documentation all by yourself and on your own responsibility. You have
 been warned.</p>
@@ -285,6 +284,9 @@ modules from there, use the binaries from <code class="file docutils literal"><s
       <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>
@@ -292,11 +294,11 @@ modules from there, use the binaries from <code class="file docutils literal"><s
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/dev_setup.txt"
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 89882a9474b79f60d2d36dbbc47bec5394e3ccc3..930ffb34523ae56bcb4f270040a1eff3211bf7c1 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -23,17 +23,16 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
     <link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
     <link rel="prev" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -116,6 +115,9 @@ new features.</p>
       <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>
@@ -123,11 +125,11 @@ new features.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/developers.txt"
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 4e5da3b46b5ba10cbb6458cf8b9eee2e6aeedac4..a375c1a39e95f3d98da12fabb2a22d34e7711010 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -24,15 +24,14 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -43,7 +42,8 @@
 <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
- <a href="#_"><strong>_</strong></a>
+ <a href="#Symbols"><strong>Symbols</strong></a>
+ | <a href="#_"><strong>_</strong></a>
  | <a href="#A"><strong>A</strong></a>
  | <a href="#B"><strong>B</strong></a>
  | <a href="#C"><strong>C</strong></a>
@@ -66,6 +66,69 @@
  | <a href="#U"><strong>U</strong></a>
  
 </div>
+<h2 id="Symbols">Symbols</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt>
+    -i, --backbone-independent
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="actions/index.html#cmdoption-i">command line option</a>
+  </dt>
+
+      </dl></dd>
+      
+  <dt>
+    -k, --keep-sidechains
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="actions/index.html#cmdoption-k">command line option</a>
+  </dt>
+
+      </dl></dd>
+      
+  <dt>
+    -n, --no-disulfids
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="actions/index.html#cmdoption-n">command line option</a>
+  </dt>
+
+      </dl></dd>
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt>
+    -r, --rigid-rotamers
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="actions/index.html#cmdoption-r">command line option</a>
+  </dt>
+
+      </dl></dd>
+      
+  <dt>
+    -s, --no-subrotamer-optimization
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="actions/index.html#cmdoption-s">command line option</a>
+  </dt>
+
+      </dl></dd>
+  </dl></td>
+</tr></table>
+
 <h2 id="_">_</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
@@ -282,6 +345,10 @@
   </dt>
 
       
+  <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">AddProfile() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+  </dt>
+
+      
   <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.AddRotamer">AddRotamer() (promod3.sidechain.BBDepRotamerLib method)</a>
   </dt>
 
@@ -737,12 +804,12 @@
   </dt>
 
       </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="modelling/gap_handling.html#promod3.modelling.ClearGaps">ClearGaps() (in module promod3.modelling)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearPos">ClearPos() (promod3.loop.AllAtomPositions method)</a>
   </dt>
@@ -761,6 +828,18 @@
   </dt>
 
         
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser.Close">(promod3.modelling.CTerminalCloser method)</a>
+  </dt>
+
+        
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase.Close">(promod3.modelling.CloserBase method)</a>
+  </dt>
+
+        
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser.Close">(promod3.modelling.DeNovoCloser method)</a>
+  </dt>
+
+        
   <dt><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser.Close">(promod3.modelling.DirtyCCDCloser method)</a>
   </dt>
 
@@ -772,6 +851,10 @@
   <dt><a href="modelling/monte_carlo.html#promod3.modelling.KICCloser.Close">(promod3.modelling.KICCloser method)</a>
   </dt>
 
+        
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.NTerminalCloser.Close">(promod3.modelling.NTerminalCloser method)</a>
+  </dt>
+
       </dl></dd>
       
   <dt><a href="modelling/pipeline.html#promod3.modelling.CloseGaps">CloseGaps() (in module promod3.modelling)</a>
@@ -782,6 +865,10 @@
   </dt>
 
       
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.CloserBase">CloserBase (class in promod3.modelling)</a>
+  </dt>
+
+      
   <dt><a href="modelling/pipeline.html#promod3.modelling.CloseSmallDeletions">CloseSmallDeletions() (in module promod3.modelling)</a>
   </dt>
 
@@ -821,6 +908,33 @@
 
       </dl></dd>
       
+  <dt>
+    command line option
+  </dt>
+
+      <dd><dl>
+        
+  <dt><a href="actions/index.html#cmdoption-i">-i, --backbone-independent</a>
+  </dt>
+
+        
+  <dt><a href="actions/index.html#cmdoption-k">-k, --keep-sidechains</a>
+  </dt>
+
+        
+  <dt><a href="actions/index.html#cmdoption-n">-n, --no-disulfids</a>
+  </dt>
+
+        
+  <dt><a href="actions/index.html#cmdoption-r">-r, --rigid-rotamers</a>
+  </dt>
+
+        
+  <dt><a href="actions/index.html#cmdoption-s">-s, --no-subrotamer-optimization</a>
+  </dt>
+
+      </dl></dd>
+      
   <dt><a href="scoring/backbone_score_env.html#promod3.scoring.ConstraintFunction">ConstraintFunction (class in promod3.scoring)</a>
   </dt>
 
@@ -890,6 +1004,10 @@
 
       </dl></dd>
       
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase">CoolerBase (class in promod3.modelling)</a>
+  </dt>
+
+      
   <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo">CoordInfo (class in promod3.loop)</a>
   </dt>
 
@@ -946,6 +1064,14 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.DeNovoCloser">DeNovoCloser (class in promod3.modelling)</a>
+  </dt>
+
+      
+  <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.DihedralConfiguration">DihedralConfiguration (class in promod3.sidechain)</a>
+  </dt>
+
+      
   <dt><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser">DirtyCCDCloser (class in promod3.modelling)</a>
   </dt>
 
@@ -969,12 +1095,12 @@
   <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.disulfid_bridges">disulfid_bridges (promod3.modelling.SidechainReconstructionData attribute)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoExternalScores">DoExternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
   </dt>
@@ -1542,6 +1668,10 @@
   </dt>
 
       
+  <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetDihedralConfiguration">GetDihedralConfiguration() (in module promod3.sidechain)</a>
+  </dt>
+
+      
   <dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetDistBinSize">GetDistBinSize() (promod3.loop.FragDB method)</a>
   </dt>
 
@@ -1892,12 +2022,20 @@
   </dt>
 
       
-  <dt><a href="modelling/monte_carlo.html#promod3.modelling.GetScore">GetScore() (in module promod3.modelling)</a>
+  <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.GetRotamericConfiguration">GetRotamericConfiguration() (in module promod3.sidechain)</a>
+  </dt>
+
+      
+  <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">GetScore() (promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
   </dt>
 
       <dd><dl>
         
-  <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">(promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer.GetScore">(promod3.modelling.LinearScorer method)</a>
+  </dt>
+
+        
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase.GetScore">(promod3.modelling.ScorerBase method)</a>
   </dt>
 
       </dl></dd>
@@ -1984,11 +2122,15 @@
   </dt>
 
       
-  <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.GetTemperature">GetTemperature() (promod3.modelling.ExponentialCooler method)</a>
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.GetTemperature">GetTemperature() (promod3.modelling.CoolerBase method)</a>
   </dt>
 
       <dd><dl>
         
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.GetTemperature">(promod3.modelling.ExponentialCooler method)</a>
+  </dt>
+
+        
   <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetTemperature">(promod3.sidechain.FRMRotamer method)</a>
   </dt>
 
@@ -2145,6 +2287,10 @@
   </dt>
 
         
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.Initialize">(promod3.modelling.SamplerBase method)</a>
+  </dt>
+
+        
   <dt><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.Initialize">(promod3.modelling.SoftSampler method)</a>
   </dt>
 
@@ -2270,6 +2416,10 @@
   </dt>
 
       
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer">LinearScorer (class in promod3.modelling)</a>
+  </dt>
+
+      
   <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.lj_pairs">lj_pairs (promod3.loop.ForcefieldConnectivity attribute)</a>
   </dt>
 
@@ -2348,6 +2498,10 @@
   </dt>
 
       
+  <dt><a href="sidechain/loading.html#promod3.sidechain.LoadBBDepLib">LoadBBDepLib() (in module promod3.sidechain)</a>
+  </dt>
+
+      
   <dt><a href="modelling/algorithms.html#promod3.modelling.FraggerHandle.LoadCached">LoadCached() (promod3.modelling.FraggerHandle method)</a>
   </dt>
 
@@ -2371,22 +2525,18 @@
   <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadDefaultBackboneOverallScorer">LoadDefaultBackboneOverallScorer() (in module promod3.scoring)</a>
   </dt>
 
-      
-  <dt><a href="sidechain/loading.html#promod3.sidechain.LoadDunbrackLib">LoadDunbrackLib() (in module promod3.sidechain)</a>
-  </dt>
-
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="loop/load_loop_objects.html#promod3.loop.LoadFragDB">LoadFragDB() (in module promod3.loop)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadHBondScorer">LoadHBondScorer() (in module promod3.scoring)</a>
   </dt>
 
       
-  <dt><a href="sidechain/loading.html#promod3.sidechain.LoadPenultimateLib">LoadPenultimateLib() (in module promod3.sidechain)</a>
+  <dt><a href="sidechain/loading.html#promod3.sidechain.LoadLib">LoadLib() (in module promod3.sidechain)</a>
   </dt>
 
       
@@ -2788,6 +2938,10 @@
   </dt>
 
         
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase.ProposeStep">(promod3.modelling.SamplerBase method)</a>
+  </dt>
+
+        
   <dt><a href="modelling/monte_carlo.html#promod3.modelling.SoftSampler.ProposeStep">(promod3.modelling.SoftSampler method)</a>
   </dt>
 
@@ -2903,6 +3057,10 @@
 
       <dd><dl>
         
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.CoolerBase.Reset">(promod3.modelling.CoolerBase method)</a>
+  </dt>
+
+        
   <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.Reset">(promod3.modelling.ExponentialCooler method)</a>
   </dt>
 
@@ -3010,6 +3168,10 @@
   </dt>
 
       
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.SamplerBase">SamplerBase (class in promod3.modelling)</a>
+  </dt>
+
+      
   <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.Save">Save() (promod3.loop.ForcefieldLookup method)</a>
   </dt>
 
@@ -3146,6 +3308,10 @@
   </dt>
 
       
+  <dt><a href="modelling/monte_carlo.html#promod3.modelling.ScorerBase">ScorerBase (class in promod3.modelling)</a>
+  </dt>
+
+      
   <dt><a href="modelling/gap_handling.html#promod3.modelling.ScoringGapExtender">ScoringGapExtender (class in promod3.modelling)</a>
   </dt>
 
@@ -3383,12 +3549,12 @@
   <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetOLC">SetOLC() (promod3.loop.BackboneList method)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity">SetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
       
   <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.SetPolarDirection">SetPolarDirection() (promod3.sidechain.Particle method)</a>
   </dt>
@@ -3708,6 +3874,9 @@
       <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>
@@ -3715,11 +3884,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index f984958d7fd43ff0e604a8031e37bb8b44e74eec..383cc28ba66f74863d5bc7ad8beb8e391d54b852 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
     <link rel="up" title="Documentation For Users" href="users.html" />
     <link rel="next" title="ProMod3 Actions" href="actions/index.html" />
     <link rel="prev" title="Documentation For Users" href="users.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -48,22 +47,22 @@
 <p>First steps to get ProMod3 up and running:</p>
 <ol class="arabic simple">
 <li>Obtain all dependencies and compile ProMod3 with <code class="docutils literal"><span class="pre">cmake</span></code> and <code class="docutils literal"><span class="pre">make</span></code>
-(see <a class="reference internal" href="buildsystem.html#building-promod"><span class="std std-ref">here</span></a>).</li>
+(see <a class="reference internal" href="buildsystem.html#building-promod"><span>here</span></a>).</li>
 <li>Ensure that you have a <code class="docutils literal"><span class="pre">stage/bin</span></code> folder which includes a <code class="docutils literal"><span class="pre">pm</span></code> executable.
 For convenience, add the folder to your <code class="docutils literal"><span class="pre">PATH</span></code> env. variable.</li>
 <li>You can now execute ProMod3 by running the following in your terminal:</li>
 </ol>
 <blockquote>
-<div><div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm &lt;COMMAND&gt;
+<div><div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm &lt;COMMAND&gt;
 </pre></div>
 </div>
 <p>Here <code class="docutils literal"><span class="pre">&lt;COMMAND&gt;</span></code> can be:</p>
 <ul>
-<li><p class="first">a predefined &#8220;action&#8221; (see <a class="reference internal" href="actions/index.html#promod-actions"><span class="std std-ref">here</span></a>)</p>
+<li><p class="first">a predefined &#8220;action&#8221; (see <a class="reference internal" href="actions/index.html#promod-actions"><span>here</span></a>)</p>
 </li>
 <li><p class="first">the path to a python script, such as the following example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<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>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
 
 <span class="c1"># generate backbone with dihedrals of a helix and store it</span>
 <span class="n">sequence</span> <span class="o">=</span> <span class="s2">&quot;HELLYEAH&quot;</span>
@@ -88,7 +87,7 @@ is conserved</li>
 <li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> module)</li>
 <li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> module)</li>
 <li>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
 </ul>
 <p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
 try to use the fast and multi-threaded &#8220;CPU&#8221; platform of OpenMM (should be
@@ -140,6 +139,9 @@ not set, 1 thread will be used by default.</p>
       <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>
@@ -147,11 +149,11 @@ not set, 1 thread will be used by default.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/gettingstarted.txt"
diff --git a/doc/html/index.html b/doc/html/index.html
index 9a9a20281972b758a64c9e1976765ce31fd410cc..34717b01d44a8fe487e6b10904aed475244505e7 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! &mdash; ProMod3 1.2.0 documentation</title>
+    <title>ProMod3 &mdash; ProMod3 1.2.0 documentation</title>
     
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -23,31 +23,38 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="#" />
     <link rel="next" title="Documentation For Users" href="users.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
         <div class="bodywrapper">
           <div class="body" role="main">
             
-  <div class="section" id="welcome-to-promod3-s-documentation">
-<h1>Welcome To ProMod3&#8217;s Documentation!<a class="headerlink" href="#welcome-to-promod3-s-documentation" title="Permalink to this headline">¶</a></h1>
-<p>Contents:</p>
+  <div class="section" id="promod3">
+<h1>ProMod3<a class="headerlink" href="#promod3" title="Permalink to this headline">¶</a></h1>
+<p>ProMod3 is a modelling engine based on the OpenStructure <a class="reference internal" href="references.html#biasini2013" id="id1">[biasini2013]</a>
+computational structural biology framework that can perform all steps required
+to generate a protein model by homology. Its modular design aims at
+implementing flexible modelling pipelines and fast prototyping of novel
+algorithms.</p>
+</div>
+<div class="section" id="documentation">
+<h1>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="users.html">Users</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
 <li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</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="container/index.html">ProMod3 and Containers</a></li>
 <li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
 <li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
 <li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
@@ -56,29 +63,16 @@
 <li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="dev_setup.html">ProMod3 Setup</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="actions/index_dev.html"><code class="docutils literal"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cmake/index.html">ProMod3&#8216;s Share Of CMake</a></li>
-<li class="toctree-l2"><a class="reference internal" href="portableIO.html">Using Binary Files In ProMod3</a></li>
-</ul>
-</li>
 </ul>
 </div>
 <div class="toctree-wrapper compound">
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
 </ul>
 </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>
-<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
-<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
-<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
-</ul>
 </div>
 
 
@@ -89,10 +83,10 @@
         <div class="sphinxsidebarwrapper">
   <h3><a href="#">Table Of Contents</a></h3>
   <ul>
-<li><a class="reference internal" href="#">Welcome To ProMod3&#8217;s Documentation!</a><ul>
+<li><a class="reference internal" href="#">ProMod3</a></li>
+<li><a class="reference internal" href="#documentation">Documentation</a><ul>
 </ul>
 </li>
-<li><a class="reference internal" href="#indices-and-tables">Indices And Tables</a></li>
 </ul>
 <div class="relations">
 <h3>Related Topics</h3>
@@ -117,6 +111,9 @@
       <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>
@@ -124,11 +121,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/index.txt"
diff --git a/doc/html/license.html b/doc/html/license.html
new file mode 100644
index 0000000000000000000000000000000000000000..3a642030045fad96522780fdbc1780d948f9e81b
--- /dev/null
+++ b/doc/html/license.html
@@ -0,0 +1,312 @@
+<!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>License &mdash; ProMod3 1.2.0 documentation</title>
+    
+    <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '1.2.0',
+        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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+    <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+    <link rel="next" title="References" href="references.html" />
+    <link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
+   
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head>
+  <body role="document">  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <div class="section" id="license">
+<h1>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h1>
+<div class="highlight-python"><div class="highlight"><pre>
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      &quot;License&quot; shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      &quot;Licensor&quot; shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      &quot;Legal Entity&quot; shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      &quot;control&quot; means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      &quot;You&quot; (or &quot;Your&quot;) shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      &quot;Source&quot; form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      &quot;Object&quot; form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
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+
+      &quot;Work&quot; shall mean the work of authorship, whether in Source or
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+      (an example is provided in the Appendix below).
+
+      &quot;Derivative Works&quot; shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      &quot;Contribution&quot; shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
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+      &quot;Contributor&quot; shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
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+
+   2. Grant of Copyright License. Subject to the terms and conditions of
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+      defend, and hold each Contributor harmless for any liability
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+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets &quot;[]&quot;
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+      file or class name and description of purpose be included on the
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+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an &quot;AS IS&quot; BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+
+ProMod3 bundles the file &quot;FindEigen3.cmake&quot;, which is availabe under a 
+&quot;2-clause BSD&quot; license. For details, see cmake_support/FindEigen3.cmake.
+
+ProMod3 bundles the file &quot;cmake.py&quot;, which is available under a 
+&quot;3-clause BSD&quot; license. For details, see doc/cmake.py and 
+doc/Copyright_cmake.py.txt
+</pre></div>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+      <li>Previous: <a href="portableIO.html" title="previous chapter">Using Binary Files In ProMod3</a></li>
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diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index df65f9c542ab9108208ba0e8740ebb02e80413e0..7dc41f2fdff64e339e14bb14a9bfca31b39bdae8 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="loop - Loop Handling" href="index.html" />
     <link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
     <link rel="prev" title="Structural Data" href="structure_db.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -48,8 +47,8 @@
 positions of all their heavy atoms and an environment (<a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) to
 handle changes during loop modelling.</p>
 <p>The example below showcases some operations on the two classes:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">geom</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
 
 <span class="c1"># load example (has res. numbering starting at 1)</span>
 <span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">&quot;data/1CRN.pdb&quot;</span><span class="p">)</span>
@@ -90,8 +89,8 @@ new loop is being added.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) &#8211; Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) &#8211; Internal SEQRES to be set (single chain or list with one per
 chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
 </tr>
 </tbody>
@@ -113,7 +112,7 @@ concatenated one after each other (indexing starts at 0)</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structral data to be set as environment. The chains
 in <em>env_structure</em> are expected to be in the same
 order as the SEQRES items provided in constructor.</td>
 </tr>
@@ -143,7 +142,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
 <li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnvPositions</span></code></a>) &#8211; Structural data to be set as environment.</li>
 <li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) &#8211; Structural data to be set as environment.</li>
 <li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; Backbone data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Res. number defining the start position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Res. number defining the start position in the SEQRES.</li>
 <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index of chain the structural data belongs to.</li>
 </ul>
 </td>
@@ -220,7 +219,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -354,7 +353,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue providing atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue providing atoms</li>
 </ul>
 </td>
 </tr>
@@ -400,7 +399,7 @@ out of bounds or if residues in the two containers are inconsistent
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Set position at that index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Set position to <em>pos</em>.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Set position to <em>pos</em>.</li>
 </ul>
 </td>
 </tr>
@@ -450,7 +449,7 @@ out of bounds or if residues in the two containers are inconsistent
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Atom position index.</td>
 </tr>
@@ -554,7 +553,7 @@ if <em>atom_name</em> is not one of that residue&#8217;s heavy atoms.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index</td>
 </tr>
@@ -833,9 +832,9 @@ atom (N, CA, C, O).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -855,8 +854,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index</li>
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) &#8211; Chain into which we insert</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Residue number for the inserted residue</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) &#8211; Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Residue number for the inserted residue</li>
 </ul>
 </td>
 </tr>
@@ -949,7 +948,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
 <dt id="promod3.loop.AminoAcidLookup">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
 <dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
+(<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
 hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
 <dl class="staticmethod">
 <dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -962,7 +961,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
 </tr>
 </tbody>
 </table>
@@ -984,7 +983,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
 <li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Atom index (in [0, GetNumAtoms(aa)-1])</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
 </ul>
@@ -1014,7 +1013,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
 <li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Atom index (in [0, GetNumHydrogens(aa)-1])</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
 </ul>
@@ -1043,7 +1042,7 @@ atom.</p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
 </ul>
 </td>
@@ -1071,7 +1070,7 @@ and atom.</p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</li>
 <li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Atom name</li>
 </ul>
 </td>
@@ -1095,7 +1094,7 @@ hydrogens of <em>aa</em>.</p>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
 </tr>
 </tbody>
 </table>
@@ -1127,7 +1126,7 @@ hydrogens of <em>aa</em>.</p>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
 </tr>
 </tbody>
 </table>
@@ -1160,7 +1159,7 @@ hydrogens of <em>aa</em>.</p>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
@@ -1254,7 +1253,7 @@ when residue is peptide bound.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. PRO)</td>
 </tr>
@@ -1278,7 +1277,7 @@ when residue is N terminal.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) &#8211; Amino acid type</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. H3 for PRO)</td>
 </tr>
@@ -1335,6 +1334,9 @@ when residue is N terminal.</td>
       <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>
@@ -1342,11 +1344,11 @@ when residue is N terminal.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/loop/all_atom.txt"
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 096e988e0855d432d670e2d868e5e9d6da9309ab..357d1bd34d6320248ac91726e150e47866652729 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="loop - Loop Handling" href="index.html" />
     <link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
     <link rel="prev" title="loop - Loop Handling" href="index.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -46,10 +45,10 @@
 <p>The most simple representation of structural information in ProMod3 is the
 <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
 residues. They provide structural manipulations, they can be manipulated and
-converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</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>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
 
 <span class="n">sequence</span> <span class="o">=</span> <span class="s2">&quot;AAAAAAAA&quot;</span>
 
@@ -59,11 +58,11 @@ converted from, to, or inserted to a <a class="reference external" href="https:/
 
 <span class="c1"># let&#39;s have a look at the set dihedral angles</span>
 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)):</span>
-    <span class="nb">print</span> <span class="s2">&quot;Looking at position </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">i</span>
+    <span class="k">print</span> <span class="s2">&quot;Looking at position </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">i</span>
     <span class="k">if</span> <span class="n">i</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="nb">print</span> <span class="s2">&quot;phi: </span><span class="si">%.4f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPhiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+        <span class="k">print</span> <span class="s2">&quot;phi: </span><span class="si">%.4f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPhiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
-        <span class="nb">print</span> <span class="s2">&quot;psi: </span><span class="si">%.4f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPsiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+        <span class="k">print</span> <span class="s2">&quot;psi: </span><span class="si">%.4f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPsiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
 
 
 <span class="c1"># we now use a TorsionSampler to set random dihedral angles</span>
@@ -160,7 +159,7 @@ code which is not one of the 20 default amino acids or if
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Sequence of created BackboneList</li>
-<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; List of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; List of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
 which the backbone positions are extracted.</li>
 </ul>
 </td>
@@ -184,7 +183,7 @@ a residue not providing all necessary positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -194,7 +193,7 @@ a residue not providing all necessary positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; </li>
-<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; </li>
 <li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; </li>
 <li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; </li>
 </ul>
@@ -213,7 +212,7 @@ a residue not providing all necessary positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -230,8 +229,8 @@ be replaced, otherwise they will be added to the entity.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) &#8211; The chain</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Residue number defining the start location of insertion</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) &#8211; The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Residue number defining the start location of insertion</li>
 </ul>
 </td>
 </tr>
@@ -247,7 +246,7 @@ be replaced, otherwise they will be added to the entity.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) &#8211; </li>
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) &#8211; </li>
 <li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; </li>
 <li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; </li>
 </ul>
@@ -266,7 +265,7 @@ be replaced, otherwise they will be added to the entity.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; </td>
 </tr>
@@ -299,7 +298,8 @@ be replaced, otherwise they will be added to the entity.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Set amino acid sequence to this.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>sequence</em> contains a one letter
-code which is not one of the 20 default amino acids.</td>
+code which is not one of the 20 default amino acids or size of
+<em>sequence</em> does not match.</td>
 </tr>
 </tbody>
 </table>
@@ -369,7 +369,7 @@ actual fragment at specified <em>index</em></p>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
 atom for residue at given index.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</td>
 </tr>
@@ -394,7 +394,7 @@ atom for residue at given index.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen / alpha carbon / beta carbon / carbon
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen / alpha carbon / beta carbon / carbon
 / oxygen atom to this.</li>
 </ul>
 </td>
@@ -446,7 +446,7 @@ atom for residue at given index.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</td>
 </tr>
@@ -463,7 +463,7 @@ atom for residue at given index.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Set amino acid type of the residue to this.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Set amino acid type of the residue to this.</li>
 </ul>
 </td>
 </tr>
@@ -489,12 +489,12 @@ and set the amino acid type according to the given one letter code.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) &#8211; Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) &#8211; Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of oxygen atom to this.</li>
 <li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) &#8211; Set one letter code of the residue to this.</li>
 </ul>
 </td>
@@ -564,12 +564,12 @@ to the given one letter code.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) &#8211; Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) &#8211; Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) &#8211; Set position of oxygen atom to this.</li>
 <li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) &#8211; Set one letter code of the residue to this.</li>
 </ul>
 </td>
@@ -633,7 +633,7 @@ reconstructed if the residue handle is valid.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue following the C stem (C stem residue is last
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue following the C stem (C stem residue is last
 element of this backbone list)</td>
 </tr>
 </tbody>
@@ -650,7 +650,7 @@ element of this backbone list)</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</li>
 </ul>
 </td>
 </tr>
@@ -670,7 +670,7 @@ element of this backbone list)</td>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Start index.</li>
 <li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; End index (one past last residue to transform).</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</li>
 </ul>
 </td>
 </tr>
@@ -686,7 +686,7 @@ element of this backbone list)</td>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; The transformation</td>
 </tr>
 </tbody>
 </table>
@@ -706,12 +706,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
 positions of the N, CA and C atoms.</p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
 </td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The other residue.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The other residue.</li>
 <li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; The other backbone list.</li>
 <li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Residue index in <em>other</em> backbone list.</li>
 </ul>
@@ -731,7 +731,7 @@ positions of the N, CA and C atoms.</p>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
 list onto CA positions of <em>other</em> backbone list.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; The other backbone list.</td>
 </tr>
@@ -847,8 +847,8 @@ smaller than 3.</p>
 <dl class="method">
 <dt id="promod3.loop.BackboneList.SetBackrub">
 <code class="descname">SetBackrub</code><span class="sig-paren">(</span><em>index</em>, <em>primary_rot_angle</em>, <em>flanking_rot_angle_one</em>, <em>flanking_rot_angle_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetBackrub" title="Permalink to this definition">¶</a></dt>
-<dd><p>Applies a backrub motion at residue defined by <strong>index</strong>. The first
-rotation axis is defined by the CA positions from residues at
+<dd><p>Applies a backrub motion <a class="reference internal" href="../references.html#davis2006" id="id1">[davis2006]</a> at residue defined by <strong>index</strong>.
+The first rotation axis is defined by the CA positions from residues at
 <strong>index</strong> -1 and <strong>index</strong> +1. All atoms in between get rotated around this
 axis by <strong>primary_rot_angle</strong>. To restore the the hydrogen bond network
 of the two transformed oxygens, the backrub motion gets completed by
@@ -996,6 +996,9 @@ backbone list.</td>
       <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>
@@ -1003,11 +1006,11 @@ backbone list.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/loop/backbone.txt"
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 4ceff047a047b214b7ec544b3426b6026963b818..ab4e5e12d61677e6b6356a9c5daced26e748eec7 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Users" href="../users.html" />
     <link rel="next" title="Representing Loops" href="backbone.html" />
     <link rel="prev" title="Other Scoring Functions" href="../scoring/other_scoring_functions.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -46,8 +45,8 @@
 <p>Tools and algorithms for loop handling. This module provides ways for
 representation of peptides and to obtain fragments to potentially use as
 loops. The following example should give you an idea of what can be done:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
 
 <span class="c1"># load an example structure</span>
 <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
@@ -65,26 +64,26 @@ loops. The following example should give you an idea of what can be done:</p>
 <span class="c1"># extract potential loops from fragment database based on geometry</span>
 <span class="n">frag_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
 <span class="n">fragments</span> <span class="o">=</span> <span class="n">frag_db</span><span class="o">.</span><span class="n">SearchDB</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">frag_length</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s2">&quot;Num. fragments found in FragDB: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragments</span><span class="p">)</span>
+<span class="k">print</span> <span class="s2">&quot;Num. fragments found in FragDB: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragments</span><span class="p">)</span>
 <span class="c1"># compare with reference</span>
 <span class="n">struct_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fragments</span><span class="p">)):</span>
     <span class="c1"># get structure from structural database</span>
     <span class="n">bb_list</span> <span class="o">=</span> <span class="n">struct_db</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span>
                                         <span class="n">fragments</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">frag_seq</span><span class="p">)</span>
-    <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
-    <span class="nb">print</span> <span class="s2">&quot;-&gt; fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
+    <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
+    <span class="k">print</span> <span class="s2">&quot;-&gt; fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
 
 <span class="c1"># extract potential loops from fragment database based on sequence</span>
 <span class="n">fragger</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">Fragger</span><span class="p">(</span><span class="n">frag_seq</span><span class="p">)</span>
 <span class="c1"># for simplicity we just use a sequence similarity score</span>
 <span class="n">fragger</span><span class="o">.</span><span class="n">AddSeqSimParameters</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">seq</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">BLOSUM62</span><span class="p">)</span>
 <span class="n">fragger</span><span class="o">.</span><span class="n">Fill</span><span class="p">(</span><span class="n">struct_db</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s2">&quot;Num. fragments found in Fragger: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)</span>
+<span class="k">print</span> <span class="s2">&quot;Num. fragments found in Fragger: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)</span>
 <span class="c1"># compare fraggers with reference</span>
 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)):</span>
-    <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
-    <span class="nb">print</span> <span class="s2">&quot;-&gt; fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
+    <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
+    <span class="k">print</span> <span class="s2">&quot;-&gt; fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
 </pre></div>
 </div>
 <p>Contents:</p>
@@ -155,6 +154,9 @@ loops. The following example should give you an idea of what can be done:</p>
       <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>
@@ -162,11 +164,11 @@ loops. The following example should give you an idea of what can be done:</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/loop/index.txt"
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 8425953c8165937468f1c690d1e44d38250cfe99..b8422dc5bda27ed0694076129b00848e52828bfd 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="loop - Loop Handling" href="index.html" />
     <link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
     <link rel="prev" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -49,7 +48,7 @@ ProMod3 offers to load precomputed instances for direct usage.</p>
 <dt id="promod3.loop.LoadTorsionSampler">
 <code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSampler</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSampler" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis &amp; Rachovsky [1] that has been trained on
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id1">[solis2006]</a> that has been trained on
 non-redundant protein structures.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -69,7 +68,7 @@ non-redundant protein structures.</p>
 <dt id="promod3.loop.LoadTorsionSamplerCoil">
 <code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerCoil</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerCoil" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis &amp; Rachovsky [1] that has been trained on coil
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id2">[solis2006]</a> that has been trained on coil
 residues of  non-redundant protein structures.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -89,7 +88,7 @@ residues of  non-redundant protein structures.</p>
 <dt id="promod3.loop.LoadTorsionSamplerHelical">
 <code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerHelical</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerHelical" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis &amp; Rachovsky [1] that has been trained on helical
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id3">[solis2006]</a> that has been trained on helical
 residues of  non-redundant protein structures.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -109,7 +108,7 @@ residues of  non-redundant protein structures.</p>
 <dt id="promod3.loop.LoadTorsionSamplerExtended">
 <code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerExtended</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerExtended" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by Solis &amp; Rachovsky [1] that has been trained on extended
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id4">[solis2006]</a> that has been trained on extended
 residues of  non-redundant protein structures.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -126,48 +125,41 @@ residues of  non-redundant protein structures.</p>
 </dd></dl>
 
 <dl class="method">
-<dt id="promod3.loop.LoadFragDB">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads and returns a FragDB containing fragments up to the length of 14,
-therefore capable of bridging gaps up to the length of 12.</p>
+<dt id="promod3.loop.LoadStructureDB">
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadStructureDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads and returns a structure db containing roughly 21000 chains form the
+PDB with seqid redundancy cutoff of 60%</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Fragment database</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure db</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
 <dl class="method">
-<dt id="promod3.loop.LoadStructureDB">
-<code class="descclassname">promod3.loop.</code><code class="descname">LoadStructureDB</code><span class="sig-paren">(</span><em>load_frequencies=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads and returns a structure db containing roughly 24000 chains form the
-PDB with redundancy cutoff of 90%</p>
+<dt id="promod3.loop.LoadFragDB">
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads and returns a FragDB containing fragments up to the length of 14,
+therefore capable of bridging gaps up to the length of 12. The returned
+databases contains the location of fragments in the <a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>
+returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" title="promod3.loop.LoadStructureDB"><code class="xref py py-meth docutils literal"><span class="pre">LoadStructureDB()</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>load_frequencies</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; If True, the full database including profile
-information gets loaded (see
-<a class="reference internal" href="structure_db.html#promod3.loop.StructureDB.Load" title="promod3.loop.StructureDB.Load"><code class="xref py py-meth docutils literal"><span class="pre">StructureDB.Load()</span></code></a>).</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The structure db</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Fragment database</td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
-<dl class="docutils">
-<dt>[1] A. D. Solis and S. Rackovsky. Improvement of statistical potentials and</dt>
-<dd>threading score functions using information maximization.
-Proteins, 62(4):892–908, Mar 2006.</dd>
-</dl>
 </div>
 
 
@@ -203,6 +195,9 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
       <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>
@@ -210,11 +205,11 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/loop/load_loop_objects.txt"
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 38cdf31e4748d13ed4624067799504894827ea98..73512c3235bfc8f6b421cd22dc9534b987f5ba01 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="loop - Loop Handling" href="index.html" />
     <link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
     <link rel="prev" title="Handling All Atom Positions" href="all_atom.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -42,13 +41,13 @@
           <div class="body" role="main">
             
   <div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
 proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal"><span class="pre">MmSystemCreator</span></code></a>) and a
 specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>).</p>
 <p>The example below showcases the creation and use of an MM system:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">geom</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
 
 <span class="c1"># setup system creator</span>
 <span class="n">ff_lookup</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">ForcefieldLookup</span><span class="o">.</span><span class="n">GetDefault</span><span class="p">()</span>
@@ -68,8 +67,8 @@ specialized forcefield lookup for amino acids (<a class="reference internal" hre
 <span class="n">loop_start_indices</span> <span class="o">=</span> <span class="p">[</span><span class="mi">10</span><span class="p">,</span> <span class="mi">20</span><span class="p">]</span>
 <span class="n">loop_lengths</span> <span class="o">=</span> <span class="p">[</span><span class="mi">6</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span>
 <span class="c1"># define which of the res_indices is terminal</span>
-<span class="n">is_n_ter</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="kc">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
-<span class="n">is_c_ter</span> <span class="o">=</span> <span class="p">[</span><span class="kc">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="p">[</span><span class="kc">True</span><span class="p">]</span>
+<span class="n">is_n_ter</span> <span class="o">=</span> <span class="p">[</span><span class="bp">True</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="bp">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">is_c_ter</span> <span class="o">=</span> <span class="p">[</span><span class="bp">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="p">[</span><span class="bp">True</span><span class="p">]</span>
 <span class="c1"># get disulfid bridges</span>
 <span class="n">disulfid_bridges</span> <span class="o">=</span> <span class="n">mm_sys</span><span class="o">.</span><span class="n">GetDisulfidBridges</span><span class="p">(</span><span class="n">all_atoms</span><span class="p">,</span> <span class="n">res_indices</span><span class="p">)</span>
 <span class="c1"># setup MM system</span>
@@ -78,9 +77,9 @@ specialized forcefield lookup for amino acids (<a class="reference internal" hre
 
 <span class="c1"># run simulation</span>
 <span class="n">sim</span> <span class="o">=</span> <span class="n">mm_sys</span><span class="o">.</span><span class="n">GetSimulation</span><span class="p">()</span>
-<span class="nb">print</span> <span class="s2">&quot;Potential energy before: </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
+<span class="k">print</span> <span class="s2">&quot;Potential energy before: </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
 <span class="n">sim</span><span class="o">.</span><span class="n">ApplySD</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s2">&quot;Potential energy after: </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
+<span class="k">print</span> <span class="s2">&quot;Potential energy after: </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
 
 <span class="c1"># extract new loop positions and store it</span>
 <span class="n">mm_sys</span><span class="o">.</span><span class="n">ExtractLoopPositions</span><span class="p">(</span><span class="n">all_atoms</span><span class="p">,</span> <span class="n">res_indices</span><span class="p">)</span>
@@ -288,7 +287,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>. Use this to run
 MM simulations.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -435,7 +434,7 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
 <dl class="class">
 <dt id="promod3.loop.ForcefieldLookup">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
 <ul class="simple">
 <li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
 <em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -513,7 +512,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -525,7 +524,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.loop.ForcefieldLookup.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -548,7 +547,7 @@ for details.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) &#8211; Forcefield-specific amino acid type</td>
 </tr>
@@ -664,7 +663,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
 </tr>
@@ -680,7 +679,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
 </tr>
@@ -695,7 +694,7 @@ for details.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -719,7 +718,7 @@ for details.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -744,7 +743,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -769,7 +768,7 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -915,7 +914,7 @@ for details.</p>
 <dt id="promod3.loop.ForcefieldAminoAcid">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
 <dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
 there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
 (<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
 types. The full list of values is:</p>
@@ -932,7 +931,7 @@ types. The full list of values is:</p>
 <dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
 are the combination of all bonds and 1,3 pairs of angles and are not stored
 separately). Each type of connectivity has it&#8217;s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
 The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
 = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
 residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the
@@ -1042,7 +1041,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldBondInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldBondInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1104,7 +1103,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1181,7 +1180,7 @@ False, False)</em>.</p>
 <dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
 <dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1286,8 +1285,8 @@ False, False)</em>.</p>
 <dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
 <dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1391,7 +1390,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1481,7 +1480,7 @@ False, False)</em>.</p>
 <dl class="class">
 <dt id="promod3.loop.ForcefieldLJPairInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
 <dl class="attribute">
 <dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
 <code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1585,6 +1584,9 @@ False, False)</em>.</p>
       <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>
@@ -1592,11 +1594,11 @@ False, False)</em>.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/loop/mm_system_creation.txt"
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 9e2c5705f18ee62396096e5fb1a4622a9ff814dc..1393cd8e34a778a3cf5516c1bf02e564096622a1 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="loop - Loop Handling" href="index.html" />
     <link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
     <link rel="prev" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -43,7 +42,7 @@
             
   <div class="section" id="structural-data">
 <h1>Structural Data<a class="headerlink" href="#structural-data" title="Permalink to this headline">¶</a></h1>
-<p>The structural database serves as a container for structural backbone and
+<p>The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> serves as a container for structural backbone and
 sequence data. Custom accessor objects can be implemented that relate
 arbitrary features to structural data. Examples provided by ProMod3 include
 accession using matching stem geometry (see: <a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) or sequence
@@ -66,10 +65,10 @@ to the OUTER surface. To determine whether an atom is part of that outer
 surface, the full structure is placed into a 3D grid and a flood fill
 algorithm is used to determine the atoms of interest.
 Internal cavities are excluded by using this approach. This is a simplified
-version of the residue depth as discussed in <a class="reference internal" href="#chakravarty1999" id="id1">[chakravarty1999]</a> and gets
+version of the residue depth as discussed in <a class="reference internal" href="../references.html#chakravarty1999" id="id1">[chakravarty1999]</a> and gets
 directly calculated when structural information is added to the StructureDB.</li>
 <li>The amino acid frequency derived from structural alignments as described
-in <a class="reference internal" href="#zhou2005" id="id2">[zhou2005]</a> - Since the calculation of such a profile already requires a
+in <a class="reference internal" href="../references.html#zhou2005" id="id2">[zhou2005]</a> - Since the calculation of such a profile already requires a
 StructureDB, we end up in a hen and egg problem here... When adding
 structural information to the StructureDB, the according memory gets
 just allocated and set to zero. The usage of this information
@@ -83,7 +82,7 @@ and manually set them (or load the provided default database).</li>
 <dt id="promod3.loop.CoordInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">CoordInfo</code><a class="headerlink" href="#promod3.loop.CoordInfo" title="Permalink to this definition">¶</a></dt>
 <dd><p>The CoordInfo gets automatically generated when new chains are added to
-the structural database. It contains internal information of how a
+a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>. It contains internal information of how a
 connected stretch of residues is stored in the database.</p>
 <dl class="attribute">
 <dt id="promod3.loop.CoordInfo.id">
@@ -118,14 +117,14 @@ structure. (<a class="reference external" href="https://docs.python.org/2.7/libr
 <code class="descname">start_resnum</code><a class="headerlink" href="#promod3.loop.CoordInfo.start_resnum" title="Permalink to this definition">¶</a></dt>
 <dd><p>Residue number of first residue in the added stretch. The residue number
 is relative to the SEQRES provided in the input profile when adding the
-stuff to the structure db.</p>
+stuff to the structure db. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="promod3.loop.CoordInfo.shift">
 <code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
 <dd><p>Translation from original coordinates that has been applied before storing
-structural information in db.</p>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
 </dd></dl>
 
 </dd></dl>
@@ -133,7 +132,7 @@ structural information in db.</p>
 <dl class="class">
 <dt id="promod3.loop.FragmentInfo">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragmentInfo</code><span class="sig-paren">(</span><em>chain_index</em>, <em>offset</em>, <em>length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>The FragmentInfo defines any fragment in the structural database. If you
+<dd><p>The FragmentInfo defines any fragment in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>. If you
 implement your own accessor object, thats the information you want to store.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -151,8 +150,8 @@ implement your own accessor object, thats the information you want to store.</p>
 <dl class="attribute">
 <dt id="promod3.loop.FragmentInfo.chain_index">
 <code class="descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
-<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a>) in the structure db
-this particle belongs to. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a>) in the
+<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> this particle belongs to. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
 </dd></dl>
 
 <dl class="attribute">
@@ -174,8 +173,8 @@ this particle belongs to. (<a class="reference external" href="https://docs.pyth
 <h2>The Structure Database<a class="headerlink" href="#the-structure-database" title="Permalink to this headline">¶</a></h2>
 <p>The following code example demonstrates how to create a structural database
 and fill it with content.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
 <span class="kn">import</span> <span class="nn">os</span>
 
 <span class="c1"># StructureDB where all data get extracted</span>
@@ -194,8 +193,8 @@ and fill it with content.</p>
 <span class="n">prof_dir</span> <span class="o">=</span> <span class="s2">&quot;data&quot;</span>
 
 <span class="c1"># The naming of the files in the directories is e.g. 1CRN.pdb for </span>
-<span class="c1"># the structure and 1CRNA.hhm for the profile. Please note, </span>
-<span class="c1"># that the structure can contain several chains, whereas the hhm </span>
+<span class="c1"># the structure and 1CRNA.hhm for the profile. </span>
+<span class="c1"># The structure possibly contain several chains, whereas the hhm </span>
 <span class="c1"># file is only for that specific chain.</span>
 <span class="n">structure_ids</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;1CRN&quot;</span><span class="p">,</span> <span class="s2">&quot;1AKI&quot;</span><span class="p">]</span>
 <span class="n">chain_names</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;A&quot;</span><span class="p">,</span> <span class="s2">&quot;A&quot;</span><span class="p">]</span>
@@ -227,11 +226,14 @@ and fill it with content.</p>
 
                                 
 <span class="c1"># We now have two structures in both databases...</span>
-
-<span class="c1"># Please note, that there is no profile derived from structures</span>
-<span class="c1"># assigned yet to structure_db_one, the memory is only allocated</span>
-<span class="c1"># and set to zero. In structure_db_two, there&#39;ll never be stored a </span>
-<span class="c1"># structure profile as we did not initialize it accordingly. </span>
+<span class="c1"># Lets get a summary of whats actually in there</span>
+<span class="n">structure_db_one</span><span class="o">.</span><span class="n">PrintStatistics</span><span class="p">()</span>
+<span class="n">structure_db_two</span><span class="o">.</span><span class="n">PrintStatistics</span><span class="p">()</span>
+
+<span class="c1"># There is no profile derived from structures assigned to </span>
+<span class="c1"># structure_db_one yet, the memory is only allocated and set to </span>
+<span class="c1"># zero. In structure_db_two, there&#39;ll never be stored a structure </span>
+<span class="c1"># profile as we did not initialize it accordingly. </span>
 <span class="c1"># However, we can still use its coordinates and residue depths to</span>
 <span class="c1"># generate profiles!  </span>
 <span class="c1"># To demonstrate, we use our structure_db_two to derive profiles </span>
@@ -271,7 +273,7 @@ database, you might want to consider two things:</p>
 <ol class="arabic simple">
 <li>Use a database of limited size to generate the actual profiles (something
 in between 5000 and 10000 nonredundant chains is enough)</li>
-<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
 running in parallel</li>
 </ol>
 <dl class="class">
@@ -282,7 +284,7 @@ StructureDB in order to define what data you want to store additionally
 to backbone coordinates and sequence.
 If you want to store all data possible, use All. If you only want a subset,
 you can combine some of the datatypes with a bitwise or operation
-(see example script for StructureDB). One important note:
+(see example script for <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>). One important note:
 If you enable AAFrequenciesStruct, the actual information is not automatically
 assigned. Only the according memory is allocated and set to zero, the actual
 information must be assigned manually (see example script again...).</p>
@@ -293,8 +295,8 @@ AAFrequenciesStruct</p>
 <dl class="class">
 <dt id="promod3.loop.StructureDB">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDB</code><span class="sig-paren">(</span><em>data_to_store</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
-<dd><p>Generates an empty StructureDB that can be filled with content through
-<a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
+<dd><p>Generates an empty <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> that can be filled with content
+through <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
 <em>data_to_store</em>. Have a look at the <a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>
 documentation and at the example script...</p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -325,7 +327,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -337,7 +339,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.loop.StructureDB.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -405,10 +407,10 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; identifier of the added structure (e.g. pdb id)</li>
 <li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Name of the chain in <em>ent</em> you want to add</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) &#8211; The full entity that must contain a chain named
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) &#8211; The full entity that must contain a chain named
 as specified by <em>chain_name</em>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The reference sequence of chain with name <em>chain_name</em></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile information for the chain with name
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The reference sequence of chain with name <em>chain_name</em></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile information for the chain with name
 <em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li>
 <li><strong>only_longest_stretch</strong> &#8211; Flag whether you want to add only the longest
 connected stretch of residues are all connected
@@ -460,7 +462,7 @@ accordingly!</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The StructureDB indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1]) of
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])
 of all coords (connected stretches) with matching
 <em>id</em> / <em>chain_name</em>.</p>
 </td>
@@ -490,7 +492,7 @@ index <em>idx</em>.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; The StructureDB index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
 </tr>
 </tbody>
 </table>
@@ -536,9 +538,9 @@ the database.</td>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) &#8211; Fragment definition from which to extract positions.</li>
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Sequence to set for the returned backbone list.</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Positions on which the backbone list&#8217;s N-terminus should be
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Positions on which the backbone list&#8217;s N-terminus should be
 superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Positions on which the backbone list&#8217;s C-terminus should be
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Positions on which the backbone list&#8217;s C-terminus should be
 superposed onto.</li>
 </ul>
 </td>
@@ -649,7 +651,8 @@ connected stretches of residues in the database.</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Solvent accessibility for each residue of <em>fragment</em> in square A
-as calculated by dssp.</td>
+as calculated by <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">Accessibility()</span></code></a> when adding
+the structure to the database.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
 </tr>
@@ -675,7 +678,7 @@ connected stretches of residues in the database.</td>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The sequence profile for the residues defined by <em>fragment</em> with
 the BLOSUM62 probabilities as NULL model.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) &#8211; Fragment definition from which to extract the sequence
 profile</td>
@@ -699,7 +702,7 @@ connected stretches of residues in the database.</td>
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure profile for the residues defined by <em>fragment</em> with
 the BLOSUM62 probabilities as NULL model.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) &#8211; Fragment definition from which to extract the structure
 profile</td>
@@ -734,7 +737,7 @@ containing that data.</li>
 probabilities as NULL model.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and
@@ -756,7 +759,7 @@ frequencies in entry with <em>coord_idx</em></p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Source of profile frequencies</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Source of profile frequencies</li>
 <li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; StructureDB index of entry for which to set frequencies
 (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</li>
 </ul>
@@ -785,7 +788,7 @@ to make sure that you have no close homologue in the database.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; StructureDB indices to be added to the sub database (in [0,
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; Indices of chains to be added to the sub database (in [0,
 <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if you provide an invalid index</td>
@@ -807,8 +810,8 @@ between the N-stem C atom and the C-stem N atom). It can therefore be searched
 for fragments matching a certain geometry of N and C stems. The bins are
 accessed through a hash table, making searching the database ultra fast.</p>
 <p>This example illustrates how to create a custom FragDB based on a StructureDB:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<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>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
 
 <span class="c1"># let&#39;s load the default structure_db </span>
 <span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="o">.</span><span class="n">LoadPortable</span><span class="p">(</span><span class="s2">&quot;data/port_str_db.dat&quot;</span><span class="p">)</span>
@@ -877,7 +880,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -889,7 +892,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.loop.FragDB.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -906,7 +909,8 @@ for details.</p>
 <dl class="method">
 <dt id="promod3.loop.FragDB.GetAngularBinSize">
 <code class="descname">GetAngularBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetAngularBinSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>The size of the bins for the 4 angles describing the stem geometry and used to organize the fragments in the database.</p>
+<dd><p>The size of the bins for the 4 angles describing the stem geometry and used
+to organize the fragments in the database.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -922,7 +926,8 @@ for details.</p>
 <dl class="method">
 <dt id="promod3.loop.FragDB.GetDistBinSize">
 <code class="descname">GetDistBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetDistBinSize" title="Permalink to this definition">¶</a></dt>
-<dd><p>The size of the bins for the distance describing the stem geometry and used to organize the fragments in the database.</p>
+<dd><p>The size of the bins for the distance describing the stem geometry and used
+to organize the fragments in the database.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -938,8 +943,13 @@ for details.</p>
 <dl class="method">
 <dt id="promod3.loop.FragDB.AddFragments">
 <code class="descname">AddFragments</code><span class="sig-paren">(</span><em>fragment_length</em>, <em>rmsd_cutoff</em>, <em>structure_db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.AddFragments" title="Permalink to this definition">¶</a></dt>
-<dd><p>Iterates over all fragments of length <strong>fragment_length</strong> in the given structural database and adds them to the fragment database. Fragments will be skipped if there is already a fragment in the database that has an RMSD to the one being added smaller than <strong>rmsd_cutoff</strong>.
-As the fragments are added they are organized in bins described by their length and the geometry of their N and C stem.</p>
+<dd><p>Iterates over all fragments of length <strong>fragment_length</strong> in
+<strong>structure_db</strong> and adds them to the fragment database.
+Fragments will be skipped if there is already a fragment in the database
+that has an RMSD smaller than <strong>rmsd_cutoff</strong>, where RMSD is calculated
+upon superposing the stem residues.
+As the fragments are added they are organized in bins described by their
+length and the geometry of their N and C stem.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -958,7 +968,7 @@ As the fragments are added they are organized in bins described by their length
 <dl class="method">
 <dt id="promod3.loop.FragDB.PrintStatistics">
 <code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
-<dd><p>Prints statistics about the fragment databse, notably:</p>
+<dd><p>Prints statistics about the fragment database, notably:</p>
 <ol class="arabic simple">
 <li>the number of different stem groups (number of bins used to group the
 fragments according to the geometry of their stem residues)</li>
@@ -1019,7 +1029,7 @@ a given length.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; The length of the fragments</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">True if fragments of given length exist. This function is quick.</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">True if fragments of given length exist.</td>
 </tr>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
 </tr>
@@ -1034,7 +1044,7 @@ a given length.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Maximal fragment length contained in db. This function is quick.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Maximal fragment length contained in db.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
 </tr>
@@ -1052,8 +1062,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The N-stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The C-stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The C-stem</li>
 <li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of residues of the fragment</li>
 <li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Whether to extend the search to include fragments from
 <em>extra_bins</em> additional bins surrounding the bin given by
@@ -1080,7 +1090,7 @@ function.</p>
 for fragments that possibly represent the structural conformation of interest.
 The <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> searches a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> for n fragments,
 that maximize a certain score and gathers a set of fragments with a guaranteed
-structural diversity based on an rmsd_threshold. You can use the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a>
+structural diversity based on an rmsd threshold. You can use the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a>
 wrapped in a full fletched pipeline implemented in
 <a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal"><span class="pre">FraggerHandle</span></code></a> or search for fragments from scratch
 using an arbitrary linear combination of scores:</p>
@@ -1093,9 +1103,9 @@ Calculates the avg. substitution matrix based sequence similarity of amino acids
 when comparing a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> and the target
 sequence</li>
 <li><strong>SSAgree</strong>:
-Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="#jones1999" id="id3">[Jones1999]</a>
-and the dssp <a class="reference internal" href="#kabsch1983" id="id4">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.
-The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="#soding2005" id="id5">[soding2005]</a>.</li>
+Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id3">[Jones1999]</a>
+and the dssp <a class="reference internal" href="../references.html#kabsch1983" id="id4">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.
+The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="../references.html#soding2005" id="id5">[soding2005]</a>.</li>
 <li><strong>TorsionProbability</strong>:
 Calculates the avg. probability of observing the phi/psi dihedral angles of a potential
 fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> given the target sequence. The probabilities are
@@ -1110,8 +1120,8 @@ fragment from the <a class="reference internal" href="#promod3.loop.StructureDB"
 in between them. The scores are calculated as L1 distances between the profile columns.
 In this case, the amino acid frequencies extracted from structural alignments are used.</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
 
 <span class="c1"># load an example structure</span>
 <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
@@ -1141,13 +1151,13 @@ In this case, the amino acid frequencies extracted from structural alignments ar
 <span class="c1"># let&#39;s see how good the fragments are...</span>
 <span class="n">below_three</span> <span class="o">=</span> <span class="mi">0</span>
 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)):</span>
-    <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span><span class="kc">True</span><span class="p">)</span>
-    <span class="nb">print</span> <span class="s2">&quot;Fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
+    <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span><span class="bp">True</span><span class="p">)</span>
+    <span class="k">print</span> <span class="s2">&quot;Fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">ca_rmsd</span> <span class="o">&lt;</span> <span class="mf">3.0</span><span class="p">:</span>
         <span class="n">below_three</span> <span class="o">+=</span> <span class="mi">1</span>
 
 <span class="n">fraction</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">below_three</span><span class="p">)</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s2">&quot;Fraction of fragments below 3A: </span><span class="si">%.2f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">fraction</span>
+<span class="k">print</span> <span class="s2">&quot;Fraction of fragments below 3A: </span><span class="si">%.2f</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">fraction</span>
 
 <span class="c1"># add into a cached map with ID based on frag_pos</span>
 <span class="n">fragger_map</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">FraggerMap</span><span class="p">()</span>
@@ -1277,7 +1287,7 @@ linked to this object.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile for the fraggers target_sequence</li>
 </ul>
 </td>
 </tr>
@@ -1295,7 +1305,7 @@ linked to this object.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile for the fraggers target_sequence</li>
 </ul>
 </td>
 </tr>
@@ -1511,7 +1521,7 @@ coordinates. This file will hence be much larger than the one saved with
 <dl class="class">
 <dt id="promod3.loop.PsipredPrediction">
 <em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">PsipredPrediction</code><a class="headerlink" href="#promod3.loop.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
-<dd><p>A container for the secondary structure prediction by Psipred.</p>
+<dd><p>A container for the secondary structure prediction by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id6">[Jones1999]</a>.</p>
 <dl class="method">
 <dt id="promod3.loop.PsipredPrediction.PsipredPrediction">
 <code class="descname">PsipredPrediction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
@@ -1694,36 +1704,6 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
 
 </dd></dl>
 
-<table class="docutils citation" frame="void" id="soding2005" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id5">[soding2005]</a></td><td>Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="chakravarty1999" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[chakravarty1999]</a></td><td>Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="zhou2005" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[zhou2005]</a></td><td>Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="jones1999" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id3">[Jones1999]</a></td><td>Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="kabsch1983" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id4">[kabsch1983]</a></td><td>Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.</td></tr>
-</tbody>
-</table>
 </div>
 </div>
 
@@ -1772,6 +1752,9 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
       <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>
@@ -1779,11 +1762,11 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/loop/structure_db.txt"
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index c9d75287ca27196ad6349d2f16c1aeb7a3c7df34..123e1b9f6a52fe78e7fff7a4d35c7cd736ea9a0c 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="loop - Loop Handling" href="index.html" />
     <link rel="next" title="Structural Data" href="structure_db.html" />
     <link rel="prev" title="Representing Loops" href="backbone.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -56,14 +55,14 @@ most methods which need to access a specific distribution can either take 3
 residue names or an index as input.</p>
 <p>As a showcase example, we randomly sample from a given torsion sample and
 store the resulting samples as a scatter plot:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
 <span class="c1"># this requires matplotlib and numpy</span>
 <span class="kn">import</span> <span class="nn">matplotlib</span>
 <span class="c1"># change next line, if you wish to use a GUI-based plot-output</span>
 <span class="n">matplotlib</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s2">&quot;Agg&quot;</span><span class="p">)</span>
-<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
-<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
 
 <span class="c1"># load a default sampler</span>
 <span class="n">t_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSampler</span><span class="p">()</span>
@@ -138,7 +137,7 @@ acids not matching any of the group definitions.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) &#8211; structure from which parameters will be extracted</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) &#8211; structure from which parameters will be extracted</td>
 </tr>
 </tbody>
 </table>
@@ -175,7 +174,7 @@ less machine-dependent).</p>
 </td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</p>
 </td>
 </tr>
 </tbody>
@@ -188,7 +187,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.loop.TorsionSampler.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -210,9 +209,9 @@ for details.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for the central residue</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
 </ul>
 </td>
 </tr>
@@ -252,9 +251,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which torsion angles will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which torsion angles will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
 </ul>
 </td>
 </tr>
@@ -290,9 +289,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the <em>phi</em> will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the <em>phi</em> will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; <em>psi</em> angle</li>
 </ul>
 </td>
@@ -334,9 +333,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the <em>psi</em> angle will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the <em>psi</em> angle will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; <em>phi</em> angle</li>
 </ul>
 </td>
@@ -378,9 +377,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; phi angle</li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; psi angle</li>
 </ul>
@@ -424,9 +423,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; phi angle</li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; psi angle</li>
 </ul>
@@ -448,9 +447,9 @@ standard amino acid</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; id of the residue after <em>central</em></li>
 <li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; phi angle</li>
 <li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; psi angle</li>
 </ul>
@@ -582,6 +581,9 @@ standard amino acid</td>
       <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>
@@ -589,11 +591,11 @@ standard amino acid</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/loop/torsion_sampler.txt"
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 0cd8be8702bde9b8f390725a811a36e6c272ea21..a6d307d115ec4bc8a417e80684512c2d35f69e69 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
     <link rel="prev" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -94,7 +93,7 @@ of the solutions</li>
 indices of the common subsets (rigid blocks) relative
 to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
 and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
 superpose the according positions in <strong>bb_list_one</strong>
 onto <strong>bb_list_two</strong></p>
 </td>
@@ -112,7 +111,7 @@ onto <strong>bb_list_two</strong></p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) &#8211; An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) &#8211; An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
 objects from which the positions are extracted</li>
 <li><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; The idx of the first sequence from which the CA
 positions will be extracted</li>
@@ -133,9 +132,9 @@ of the solutions</li>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> with the first element being a
 <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">list</span></code> defining the
 column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
 and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
 superpose the according positions from the first
 sequence onto the second sequence.</p>
 </td>
@@ -172,7 +171,7 @@ of the solutions</li>
 indices of the common subsets (rigid blocks) relative
 to the input <code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code> objects
 and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
 superpose the according positions in <strong>pos_one</strong>
 onto <strong>pos_two</strong></p>
 </td>
@@ -235,8 +234,8 @@ Weird things are happening otherwise.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; SEQRES for this chain</li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Sequence profile for this chain.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Sequence profile for this chain.</li>
 <li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) &#8211; Psipred prediction for this chain.</li>
 <li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Length (num. residues) of fragments to be extracted.</li>
 <li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of fragments to be extracted at each
@@ -328,7 +327,7 @@ want to generate</li>
 <li><strong>avg_sampling_per_position</strong> &#8211; Number of Monte Carlo sampling steps
 the total number is: 
 len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
-<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; The sequence profile for <strong>sequence</strong>. This increases the 
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; The sequence profile for <strong>sequence</strong>. This increases the 
 fragment search performance.</li>
 <li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) &#8211; The psipred prediction for <strong>sequence</strong>. This
 increases the fragment search performance</li>
@@ -404,6 +403,9 @@ with the keys of the scores in <strong>scorer</strong></li>
       <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>
@@ -411,11 +413,11 @@ with the keys of the scores in <strong>scorer</strong></li>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/algorithms.txt"
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 032f3350c35708976935479acb04659939e587f6..186d5fed2099d5423d7bd8f40f00133260ef10b1 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
     <link rel="prev" title="Model Checking" href="model_checking.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -60,8 +59,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
-<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
 <li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal"><span class="pre">seq</span></code></a></li>
 </ul>
 </td>
@@ -116,7 +115,7 @@ are valid and:</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -267,13 +266,13 @@ extend the gap past another gap.</p>
 <dl class="attribute">
 <dt id="promod3.modelling.StructuralGap.before">
 <code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
 </dd></dl>
 
 <dl class="attribute">
 <dt id="promod3.modelling.StructuralGap.after">
 <code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
 </dd></dl>
 
 <dl class="attribute">
@@ -300,7 +299,7 @@ False if no new extension possible.</p>
 <dt id="promod3.modelling.GapExtender">
 <em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">GapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender" title="Permalink to this definition">¶</a></dt>
 <dd><p>The extender cycles through the following steps:</p>
-<div class="highlight-none"><div class="highlight"><pre><span></span>   -
+<div class="highlight-none"><div class="highlight"><pre>   -
   --
    --
  ---
@@ -318,7 +317,7 @@ False if no new extension possible.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) &#8211; The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The full sequence of the chain, the gap is associated with.</li>
 </ul>
 </td>
 </tr>
@@ -359,7 +358,7 @@ valid termini.</td>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) &#8211; The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The full sequence of the chain, the gap is associated with.</li>
 <li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; <ul>
 <li>If -1, all possible non-terminal gaps are returned.</li>
 <li>If &gt;= 0, this restricts the max. gap-length
@@ -412,7 +411,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
 <li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) &#8211; The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
 <li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Penalty for length of gap.</li>
 <li><strong>penalties</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Penalty for each residue added to gap.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The full sequence of the chain, the gap is associated with.</li>
 <li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; <ul>
 <li>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a>
 (i.e. it stops at gaps and termini).</li>
@@ -645,6 +644,9 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
       <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>
@@ -652,11 +654,11 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/gap_handling.txt"
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index 79fbb0d1cc6ff30dd9e85dc0aebdb05f2097a5e4..aaf344b9b133cb58df7c9a3259bb3f21ef765de8 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Users" href="../users.html" />
     <link rel="next" title="Modelling Pipeline" href="pipeline.html" />
-    <link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
+    <link rel="prev" title="Singularity" href="../container/singularity.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -50,8 +49,8 @@ capabilities to extract useful template data for the target and to fill the
 remaining structural data to create a full model of the target. In its simplest
 form, you can use a target-template alignment and a template structure to create
 a model fully automatically as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
+<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>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
 
 <span class="c1"># get raw model</span>
 <span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1crn_cut.pdb&#39;</span><span class="p">)</span>
@@ -129,7 +128,7 @@ a model fully automatically as follows:</p>
 <ul>
   <li><a href="../index.html">Documentation overview</a><ul>
   <li><a href="../users.html">Documentation For Users</a><ul>
-      <li>Previous: <a href="../buildsystem.html" title="previous chapter">Building ProMod3</a></li>
+      <li>Previous: <a href="../container/singularity.html" title="previous chapter">Singularity</a></li>
       <li>Next: <a href="pipeline.html" title="next chapter">Modelling Pipeline</a></li>
   </ul></li>
   </ul></li>
@@ -150,6 +149,9 @@ a model fully automatically as follows:</p>
       <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>
@@ -157,11 +159,11 @@ a model fully automatically as follows:</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/index.txt"
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index b1803ae6baaba3a96330a07192ae2987307a9f9b..f9a06ae834a22e2af5e9b7a6affd5e3f5d84aec7 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
     <link rel="prev" title="Handling Gaps" href="gap_handling.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -49,8 +48,8 @@ filled manually or generated using static filling functions using the
 functionality from the <a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a> or Monte Carlo algorithms.
 Once it contains candidates you can apply closing, scoring or clustering
 algorithms on all loop candidates. Example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
+<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>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
 
 <span class="c1"># let&#39;s load a crambin structure from the pdb</span>
 <span class="n">crambin</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
@@ -132,8 +131,8 @@ a fragment database.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the N-terminal end of the loop</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the C-terminal end of the loop</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the N-terminal end of the loop</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the C-terminal end of the loop</li>
 <li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; The sequence of residues to be added including the
 <em>n_stem</em> and <em>c_stem</em></li>
 <li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) &#8211; The fragment database</li>
@@ -183,10 +182,10 @@ original state once the sampling is done.</p>
 <li><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of loop candidates to return</li>
 <li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of MC steps to perform for each loop candidate
 generated</li>
-<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) &#8211; Used to generate a new configuration at each MC step</li>
-<li><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) &#8211; Used to close the loop after each MC step</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) &#8211; Used to score the generated configurations at each MC step</li>
-<li><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) &#8211; Controls the temperature profile of the simulated annealing</li>
+<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span>Sampler Object</span></a>) &#8211; Used to generate a new configuration at each MC step</li>
+<li><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span>Closer Object</span></a>) &#8211; Used to close the loop after each MC step</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span>Scorer Object</span></a>) &#8211; Used to score the generated configurations at each MC step</li>
+<li><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span>Cooler Object</span></a>) &#8211; Controls the temperature profile of the simulated annealing</li>
 <li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Seed to feed the random number generator for
 accepting/rejecting proposed monte carlo steps.
 For every monte carlo run, the random number generator
@@ -244,9 +243,9 @@ not depending on a metropolis criterium.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n-stem positions every candidate
 should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c-stem positions every candidate
 should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
 <li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
 of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) &#8211; A torsion sampler (used for all residues) or a list
@@ -288,9 +287,9 @@ candidate. This leads to an increase in number of loops.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n-stem positions every candidate
 should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c-stem positions every candidate
 should match</li>
 <li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; First pivot residue</li>
 <li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Second pivot residue</li>
@@ -364,7 +363,7 @@ anything is raised when calculating the scores.</p>
 <code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
 with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
 details, <em>prof.null_model</em> is used for weighting).</p>
 <p>Note that for profile scores a higher &#8220;score&#8221; is better! So take care when
 combining this to other scores, where it is commonly the other way around.</p>
@@ -380,7 +379,7 @@ with this DB).</p>
 <li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) &#8211; Add scores to this score container using the default
 key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
 <li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) &#8211; Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a></li>
-<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile information for target.</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; Profile information for target.</li>
 <li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Loop starts at index <em>offset</em> in <em>prof</em>.</li>
 </ul>
 </td>
@@ -412,8 +411,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) &#8211; Add scores to this score container using the default
 key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the N-terminal end of the loop.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the C-terminal end of the loop.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the N-terminal end of the loop.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; The residue at the C-terminal end of the loop.</li>
 </ul>
 </td>
 </tr>
@@ -998,8 +997,8 @@ gap for a model. This shows the combined usage of <a class="reference internal"
 keep a consistent modelling environment, <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a> with its
 scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a> for keeping track of scores and
 <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> to combine scores:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
 
 <span class="c1"># setup raw model</span>
 <span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1crn_cut.pdb&#39;</span><span class="p">)</span>
@@ -1009,7 +1008,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
                           <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">&#39;tpl&#39;</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
 <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
 <span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Number of gaps in raw model: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Number of gaps in raw model: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
 
 <span class="c1"># setup default scorers for modelling handle</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">SetupDefaultBackboneScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
@@ -1022,7 +1021,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
 
 <span class="c1"># get data for gap to close</span>
 <span class="n">gap</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Gap to close: </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap</span><span class="p">))</span>
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Gap to close: </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap</span><span class="p">))</span>
 <span class="n">n_stem</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">before</span>
 <span class="n">c_stem</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">after</span>
 <span class="n">start_resnum</span> <span class="o">=</span> <span class="n">n_stem</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
@@ -1031,19 +1030,19 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
 <span class="c1"># get loop candidates from FragDB</span>
 <span class="n">candidates</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">LoopCandidates</span><span class="o">.</span><span class="n">FillFromDatabase</span><span class="p">(</span>\
                 <span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">frag_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">)</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Number of loop candidates: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Number of loop candidates: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
 
 <span class="c1"># all scores will be kept in a score container which we update</span>
 <span class="n">all_scores</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoreContainer</span><span class="p">()</span>
 <span class="c1"># the keys used to identify scores are globally defined</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Stem RMSD key = &#39;</span><span class="si">%s</span><span class="s2">&#39;&quot;</span> \
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Stem RMSD key = &#39;</span><span class="si">%s</span><span class="s2">&#39;&quot;</span> \
       <span class="o">%</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetStemRMSDsKey</span><span class="p">())</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Profile keys = [&#39;</span><span class="si">%s</span><span class="s2">&#39;, &#39;</span><span class="si">%s</span><span class="s2">&#39;]&quot;</span> \
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Profile keys = [&#39;</span><span class="si">%s</span><span class="s2">&#39;, &#39;</span><span class="si">%s</span><span class="s2">&#39;]&quot;</span> \
       <span class="o">%</span> <span class="p">(</span><span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetSequenceProfileScoresKey</span><span class="p">(),</span>
          <span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetStructureProfileScoresKey</span><span class="p">()))</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Backbone scoring keys = </span><span class="si">%s</span><span class="s2">&quot;</span> \
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Backbone scoring keys = </span><span class="si">%s</span><span class="s2">&quot;</span> \
       <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetBackboneScoringKeys</span><span class="p">()))</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;All atom scoring keys = </span><span class="si">%s</span><span class="s2">&quot;</span> \
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;All atom scoring keys = </span><span class="si">%s</span><span class="s2">&quot;</span> \
       <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetAllAtomScoringKeys</span><span class="p">()))</span>
 
 <span class="c1"># get stem RMSDs for each candidate (i.e. how well does it fit?)</span>
@@ -1052,7 +1051,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
 
 <span class="c1"># close the candidates with CCD</span>
 <span class="n">orig_indices</span> <span class="o">=</span> <span class="n">candidates</span><span class="o">.</span><span class="n">ApplyCCD</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">)</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Number of closed loop candidates: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Number of closed loop candidates: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
 
 <span class="c1"># get subset of previously computed scores</span>
 <span class="n">all_scores</span> <span class="o">=</span> <span class="n">all_scores</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">orig_indices</span><span class="p">)</span>
@@ -1069,20 +1068,20 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
 <span class="n">candidates</span><span class="o">.</span><span class="n">CalculateAllAtomScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">mhandle</span><span class="p">,</span> <span class="n">start_resnum</span><span class="p">)</span>
 
 <span class="c1"># use default weights to combine scores</span>
-<span class="n">weights</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-                                              <span class="n">with_aa</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<span class="n">weights</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
+                                              <span class="n">with_aa</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
 <span class="n">scores</span> <span class="o">=</span> <span class="n">all_scores</span><span class="o">.</span><span class="n">LinearCombine</span><span class="p">(</span><span class="n">weights</span><span class="p">)</span>
 
 <span class="c1"># rank them (best = lowest &quot;score&quot;)</span>
 <span class="n">arg_sorted_scores</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">([(</span><span class="n">v</span><span class="p">,</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">scores</span><span class="p">)])</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Ranked candidates: score, index&quot;</span><span class="p">)</span>
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Ranked candidates: score, index&quot;</span><span class="p">)</span>
 <span class="k">for</span> <span class="n">v</span><span class="p">,</span><span class="n">i</span> <span class="ow">in</span> <span class="n">arg_sorted_scores</span><span class="p">:</span>
-  <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%g</span><span class="s2">, </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">,</span><span class="n">i</span><span class="p">))</span>
+  <span class="k">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%g</span><span class="s2">, </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">,</span><span class="n">i</span><span class="p">))</span>
 
 <span class="c1"># insert best into model, update scorers and clear gaps</span>
 <span class="n">best_candidate</span> <span class="o">=</span> <span class="n">candidates</span><span class="p">[</span><span class="n">arg_sorted_scores</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]]</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">InsertLoopClearGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">best_candidate</span><span class="p">,</span> <span class="n">gap</span><span class="p">)</span>
-<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Number of gaps in closed model: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
+<span class="k">print</span><span class="p">(</span><span class="s2">&quot;Number of gaps in closed model: </span><span class="si">%d</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
 <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="s2">&quot;model.pdb&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
@@ -1132,6 +1131,9 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
       <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>
@@ -1139,11 +1141,11 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/loop_candidates.txt"
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index d6e5827539347b83e178f2de00f6fbfc0a8fd73c..7db018c134fded5b40bda21e4ac46b65cc172117 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
     <link rel="prev" title="Handling Loop Candidates" href="loop_candidates.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -47,8 +46,8 @@
 stem residues. ProMod3 implements two algorithms performing this task:</p>
 <blockquote>
 <div><ul class="simple">
-<li>Cyclic coordinate descent (CCD) <a class="reference internal" href="#canutescu2003" id="id1">[canutescu2003]</a></li>
-<li>Kinematic closure (KIC) <a class="reference internal" href="#mandell2009" id="id2">[mandell2009]</a></li>
+<li>Cyclic coordinate descent (CCD) <a class="reference internal" href="../references.html#canutescu2003" id="id1">[canutescu2003]</a></li>
+<li>Kinematic closure (KIC) <a class="reference internal" href="../references.html#coutsias2005" id="id2">[coutsias2005]</a></li>
 </ul>
 </div></blockquote>
 <p>In case of small gaps or small issues in the loop you might also consider the
@@ -83,11 +82,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Sequence of the backbones to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n_stem.
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n_stem.
 If the residue before <em>n_stem</em> doesn&#8217;t exist, the
 torsion sampler will use a default residue (ALA) and
 and phi angle (-1.0472) to evaluate the first angle.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c_stem.
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c_stem.
 If the residue after <em>c_stem</em> doesn&#8217;t exist, the
 torsion sampler will use a default residue (ALA) and
 psi angle (-0.7854) to evaluate the last angle.</li>
@@ -124,8 +123,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n_stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c_stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue defining the c_stem</li>
 <li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Maximal number of iterations</li>
 <li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The algorithm stops as soon as the c_stem of the loop to
 be  closed has RMSD below the given <em>c_stem</em></li>
@@ -326,7 +325,7 @@ size or sequence as the initial one.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -348,7 +347,7 @@ size or sequence as the initial one.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -371,7 +370,7 @@ doesn&#8217;t do anything if specified residue is a glycine</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -393,7 +392,7 @@ doesn&#8217;t do anything if specified residue is a glycine</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -415,7 +414,7 @@ doesn&#8217;t do anything if specified residue is a glycine</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Restraint Position (in Angstrom)</li>
 <li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Force constant in kJ/mol/nm^2</li>
 </ul>
 </td>
@@ -470,8 +469,8 @@ means no cutoff.</td>
 <a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a>, it may be desired to
 quickly relax the loop. The <a class="reference internal" href="#promod3.modelling.AllAtomRelaxer" title="promod3.modelling.AllAtomRelaxer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomRelaxer</span></code></a> class takes care of that.</p>
 <p>Example usage:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<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>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
 
 <span class="c1"># load example (has res. numbering starting at 1)</span>
 <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
@@ -492,7 +491,7 @@ quickly relax the loop. The <a class="reference internal" href="#promod3.modelli
 <span class="n">relaxer</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">AllAtomRelaxer</span><span class="p">(</span><span class="n">sc_result</span><span class="p">,</span> <span class="n">mm_sys</span><span class="p">)</span>
 <span class="c1"># relax loop</span>
 <span class="n">pot_e</span> <span class="o">=</span> <span class="n">relaxer</span><span class="o">.</span><span class="n">Run</span><span class="p">(</span><span class="n">sc_result</span><span class="p">,</span> <span class="mi">300</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s2">&quot;Potential energy after: </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">pot_e</span>
+<span class="k">print</span> <span class="s2">&quot;Potential energy after: </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="n">pot_e</span>
 <span class="c1"># update environment with solution</span>
 <span class="n">env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">sc_result</span><span class="o">.</span><span class="n">env_pos</span><span class="p">)</span>
 <span class="c1"># store all positions of environment</span>
@@ -588,19 +587,6 @@ the one given in the constructor.</td>
 
 </dd></dl>
 
-<p class="rubric">Citations</p>
-<table class="docutils citation" frame="void" id="canutescu2003" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[canutescu2003]</a></td><td>Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="mandell2009" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[mandell2009]</a></td><td>Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.</td></tr>
-</tbody>
-</table>
 </div>
 </div>
 
@@ -648,6 +634,9 @@ the one given in the constructor.</td>
       <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>
@@ -655,11 +644,11 @@ the one given in the constructor.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/loop_closing.txt"
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 914620c01d9b7ab91692936ea61927682e9a7a87..72ee3c891aedcbda0112e003c61ff2c8be5d170b 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="Handling Gaps" href="gap_handling.html" />
     <link rel="prev" title="Modelling Pipeline" href="pipeline.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -57,14 +56,14 @@ three of the atoms exist (center and radii are estimated then).</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect rings.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect rings.</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of rings to perform ring checks. Each ring is a named
 tuple with:
-center (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
 radius (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
 </tr>
 </tbody>
 </table>
@@ -80,11 +79,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rings</strong> &#8211; List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect punches.</li>
 </ul>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
 have a punched ring.</p>
 </td>
 </tr>
@@ -103,7 +102,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rings</strong> &#8211; List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) &#8211; Structure for which to detect punches.</li>
 </ul>
 </td>
 </tr>
@@ -128,7 +127,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>candidates</strong> (<code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code>) &#8211; Loop candidates meant to fill <em>gap</em> within <em>model</em>.
 Offending candidates are removed from this list.</li>
-<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) &#8211; Model for which loop is to be filled.</li>
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) &#8211; Model for which loop is to be filled.</li>
 <li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>.) &#8211; Gap for which loop is to be filled.</li>
 <li><strong>orig_indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; Mapping to old indexing of candidates. If given, it
 must have as many elements as <em>candidates</em>.</li>
@@ -154,7 +153,7 @@ See <a class="reference internal" href="#promod3.modelling.FilterCandidates" tit
 <code class="descclassname">promod3.modelling.</code><code class="descname">RunMolProbity</code><span class="sig-paren">(</span><em>target_pdb</em>, <em>molprobity_bin=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_molprobity.html#RunMolProbity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.RunMolProbity" title="Permalink to this definition">¶</a></dt>
 <dd><p>Run <code class="docutils literal"><span class="pre">MolProbity</span></code> from <code class="docutils literal"><span class="pre">Phenix</span></code> on a given PDB file.</p>
 <p>MolProbity score computation: (formula from molprobity source code)</p>
-<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">clashscore</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">&quot;Clashscore&quot;</span><span class="p">]</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="n">clashscore</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">&quot;Clashscore&quot;</span><span class="p">]</span>
 <span class="n">rota_out</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">&quot;Rotamer outliers&quot;</span><span class="p">]</span>
 <span class="n">rama_iffy</span> <span class="o">=</span> <span class="mf">100.</span> <span class="o">-</span> <span class="n">result</span><span class="p">[</span><span class="s2">&quot;Ramachandran favored&quot;</span><span class="p">]</span>
 <span class="n">mpscore</span> <span class="o">=</span> <span class="p">((</span> <span class="mf">0.426</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">clashscore</span><span class="p">)</span> <span class="p">)</span> <span class="o">+</span>
@@ -193,7 +192,7 @@ with <code class="docutils literal"><span class="pre">MolProbity</span> <span cl
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a></p>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the &#8220;phenix.molprobity&#8221;
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the &#8220;phenix.molprobity&#8221;
 executable is not found.</p>
 </td>
 </tr>
@@ -210,7 +209,7 @@ executable is not found.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) &#8211; OST entity on which to do analysis.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) &#8211; OST entity on which to do analysis.</td>
 </tr>
 </tbody>
 </table>
@@ -275,6 +274,9 @@ executable is not found.</p>
       <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>
@@ -282,11 +284,11 @@ executable is not found.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/model_checking.txt"
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 6732e2a0fa011a0b43ada5c9968d35caabf3e393..ff74d9bd4fa6768b5fd7df9ed3b4c4f53d29ad09 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
     <link rel="prev" title="Fitting Loops Into Gaps" href="loop_closing.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -48,19 +47,19 @@ novo structure candidates for loops or N-/C-Termini. Every iteration of the
 sampling process consists basically of four steps and we define objects for
 each step:</p>
 <ul class="simple">
-<li><a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>: Propose new conformation</li>
-<li><a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>: Adapt new conformation to the environment</li>
-<li><a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>: Score the new conformation</li>
-<li><a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>: Accept/Reject new conformation based on the score and
+<li><a class="reference internal" href="#mc-sampler-object"><span>Sampler Object</span></a>: Propose new conformation</li>
+<li><a class="reference internal" href="#mc-closer-object"><span>Closer Object</span></a>: Adapt new conformation to the environment</li>
+<li><a class="reference internal" href="#mc-scorer-object"><span>Scorer Object</span></a>: Score the new conformation</li>
+<li><a class="reference internal" href="#mc-cooler-object"><span>Cooler Object</span></a>: Accept/Reject new conformation based on the score and
 a temperature controlled Metropolis criterion</li>
 </ul>
 <p>These steps can be arbitrarily combined to generate custom Monte Carlo sampling
 pipelines. This combination either happens manually or by using the convenient
 <a class="reference internal" href="#promod3.modelling.SampleMonteCarlo" title="promod3.modelling.SampleMonteCarlo"><code class="xref py py-func docutils literal"><span class="pre">SampleMonteCarlo()</span></code></a> function. For example, here we show how to apply Monte
 Carlo sampling to the N-terminal part of crambin:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
-<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<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>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
 
 <span class="c1"># setup protein</span>
 <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
@@ -105,34 +104,35 @@ Carlo sampling to the N-terminal part of crambin:</p>
 
 <span class="c1"># shake it!</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">SampleMonteCarlo</span><span class="p">(</span><span class="n">mc_sampler</span><span class="p">,</span> <span class="n">mc_closer</span><span class="p">,</span> <span class="n">mc_scorer</span><span class="p">,</span>
-                           <span class="n">mc_cooler</span><span class="p">,</span> <span class="mi">10000</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+                           <span class="n">mc_cooler</span><span class="p">,</span> <span class="mi">10000</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="bp">False</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
 
 <span class="c1"># save down the result</span>
 <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">&quot;sampled_frag.pdb&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
-<dl class="method">
+<dl class="function">
 <dt id="promod3.modelling.SampleMonteCarlo">
-<code class="descclassname">promod3.modelling.</code><code class="descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>steps</em>, <em>bb_list</em>, <em>initialize=True</em>, <em>seed=0</em>, <em>lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>steps</em>, <em>bb_list</em>, <em>initialize</em>, <em>seed=0</em>, <em>lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_monte_carlo.html#SampleMonteCarlo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
 <dd><p>A convenient function to perform Monte Carlo sampling using a simulated
-annealing scheme. In every iteration, a new loop conformation gets proposed by
-the provided <em>sampler</em> and closed by the <em>closer</em>. Upon scoring, this new
-conformation gets accepted/rejected using a metropolis criterion based on the
-temperature given by the <em>cooler</em>
+annealing scheme. In every iteration, a new loop conformation gets proposed 
+by the provided <em>sampler</em> and closed by the <em>closer</em>. Upon scoring, this new
+conformation gets accepted/rejected using a metropolis criterion based on 
+the temperature given by the <em>cooler</em> 
 =&gt; acceptance probability: exp(-delta_score/T).
-The result is stored in <em>bb_list</em> and is either the lowest energy conformation
-ever encountered or the last accepted proposal.</p>
+The result is stored in <em>bb_list</em> (passed by reference, so NO return value) 
+and is either the lowest energy conformation ever encountered or the last 
+accepted proposal.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) &#8211; Sampler object capable of initializing and altering
+<li><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span>Sampler Object</span></a>) &#8211; Sampler object capable of initializing and altering
 conformations.</li>
-<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) &#8211; Closer object to adapt a new conformation to
+<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span>Closer Object</span></a>) &#8211; Closer object to adapt a new conformation to
 the environment.</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) &#8211; Scorer object to score new loop conformations.</li>
-<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) &#8211; Cooler object to control the temperature of the
+<li><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span>Scorer Object</span></a>) &#8211; Scorer object to score new loop conformations.</li>
+<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span>Cooler Object</span></a>) &#8211; Cooler object to control the temperature of the 
 Monte Carlo trajectory.</li>
 <li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of Monte Carlo iterations to be performed.</li>
 <li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; The chosen conformation gets stored here.</li>
@@ -141,8 +141,8 @@ point, based on the samplers Initialize function.
 The input <em>bb_list</em> gets used otherwise.</li>
 <li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Seed for internal random number generator.</li>
 <li><strong>lowest_energy_conformation</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; If True, we choose the lowest scoring
-conformation of the trajectory. Otherwise,
-the last accepted proposal.</li>
+conformation of the trajectory. 
+Otherwise, the last accepted proposal.</li>
 </ul>
 </td>
 </tr>
@@ -154,7 +154,61 @@ the last accepted proposal.</li>
 <span id="mc-sampler-object"></span><h2>Sampler Object<a class="headerlink" href="#sampler-object" title="Permalink to this headline">¶</a></h2>
 <p>The sampler objects can be used to generate initial conformations and
 propose new conformations for a sequence of interest. They build the basis
-for any Monte Carlo sampling pipeline.</p>
+for any Monte Carlo sampling pipeline. You can either use one of the
+provided samplers or any object that implements the functionality of
+<a class="reference internal" href="#promod3.modelling.SamplerBase" title="promod3.modelling.SamplerBase"><code class="xref py py-class docutils literal"><span class="pre">SamplerBase</span></code></a>.</p>
+<dl class="class">
+<dt id="promod3.modelling.SamplerBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SamplerBase</code><a class="headerlink" href="#promod3.modelling.SamplerBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+sampler.</p>
+<dl class="method">
+<dt id="promod3.modelling.SamplerBase.Initialize">
+<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.Initialize" title="Permalink to this definition">¶</a></dt>
+<dd><p>Supposed to initialize structural information from scratch. The sequence
+of the generated <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is taken from <em>bb_list</em>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) &#8211; Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to this
+parameter. Sequence / length stay the same.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">None</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.SamplerBase.ProposeStep">
+<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<dd><p>Takes current positions and proposes a new conformation. There is no
+guarantee on maintining any special RT state. The <a class="reference internal" href="#mc-closer-object"><span>Closer Object</span></a>
+is supposed to sort that out.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) &#8211; Starting point, must not change when calling this
+function.</li>
+<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) &#8211; Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
+this parameter.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
 <dl class="class">
 <dt id="promod3.modelling.PhiPsiSampler">
 <em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">PhiPsiSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>torsion_sampler</em>, <em>n_stem_phi=-1.0472</em>, <em>c_stem_psi=-0.78540</em>, <em>prev_aa='A'</em>, <em>next_aa='A'</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler" title="Permalink to this definition">¶</a></dt>
@@ -337,7 +391,7 @@ by any fragger remain rigid.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Overall sequence</li>
-<li><strong>fraggers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects. The first
+<li><strong>fraggers</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) &#8211; A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects. The first
 fragger covers the region starting at the letter
 <em>sampling_start_index</em> of the <em>sequence</em> and so on.
 All fraggers must contain fragments of equal size.</li>
@@ -345,7 +399,7 @@ All fraggers must contain fragments of equal size.</li>
 sampling. The default gets constructed using the default
 constructor of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> and
 results in a helix.</li>
-<li><strong>sampling_start_index</strong> &#8211; Defines the beginning of the region, that actually
+<li><strong>sampling_start_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Defines the beginning of the region, that actually
 gets sampled.</li>
 <li><strong>init_fragments</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; When calling the Initialize function, the positions get set
 to the ones of <em>init_bb_list</em>. This is the number of
@@ -400,7 +454,44 @@ fragger object to alter the conformation.</p>
 conformations typically have to undergo some structural changes, so they
 fit to a given environment. This can either be structural changes, that
 the stems of the sampled conformation overlap with given stem residues or
-or simple stem superposition in case of terminal sampling.</p>
+or simple stem superposition in case of terminal sampling. You can either
+use any of the provided closers or any object that implements the
+functionality of <a class="reference internal" href="#promod3.modelling.CloserBase" title="promod3.modelling.CloserBase"><code class="xref py py-class docutils literal"><span class="pre">CloserBase</span></code></a>.</p>
+<dl class="class">
+<dt id="promod3.modelling.CloserBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CloserBase</code><a class="headerlink" href="#promod3.modelling.CloserBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+closer.</p>
+<dl class="method">
+<dt id="promod3.modelling.CloserBase.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloserBase.Close" title="Permalink to this definition">¶</a></dt>
+<dd><p>Takes current positions and proposes a new conformation that fits to a
+given environment.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) &#8211; Starting point, must not change when calling this
+function.</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) &#8211; Passed by reference, so the resulting
+<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
+this parameter.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Whether closing procedure was successful</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
 <dl class="class">
 <dt id="promod3.modelling.CCDCloser">
 <em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>sequence</em>, <em>torsion_sampler</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser" title="Permalink to this definition">¶</a></dt>
@@ -413,9 +504,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
 should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
 should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
 <li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Sequence of the conformation to be closed.</li>
 <li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
@@ -456,15 +547,16 @@ conformation to be closed.</li>
 <em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DirtyCCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser" title="Permalink to this definition">¶</a></dt>
 <dd><p>The DirtyCCDCloser applies the CCD algorithm to the sampled conformation
 to enforce the match between the conformations stem residue and
-the stems given by the closer.</p>
+the stems given by the closer. There is no check for reasonable backbone
+dihedral angles as it is the case for the <a class="reference internal" href="#promod3.modelling.CCDCloser" title="promod3.modelling.CCDCloser"><code class="xref py py-class docutils literal"><span class="pre">CCDCloser</span></code></a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
 should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation
 should adapt.</li>
 </ul>
 </td>
@@ -504,9 +596,9 @@ solutions. The KICCloser simply picks the first one.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
 adapt.</li>
-<li><strong>c_stem</strong> &#8211; Defining stem positions the closed conformation should
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
 adapt.</li>
 <li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Seed for internal random generators.</li>
 </ul>
@@ -539,49 +631,128 @@ adapt.</li>
 <dl class="class">
 <dt id="promod3.modelling.NTerminalCloser">
 <em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">NTerminalCloser</code><span class="sig-paren">(</span><em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser" title="Permalink to this definition">¶</a></dt>
-<dd><p>The NTerminalCloser simply takes the conformation and closes by superposing
-the c_stem with the desired positions.</p>
+<dd><p>The <a class="reference internal" href="#promod3.modelling.NTerminalCloser" title="promod3.modelling.NTerminalCloser"><code class="xref py py-class docutils literal"><span class="pre">NTerminalCloser</span></code></a> simply takes the conformation and closes by
+superposing the c_stem with the desired positions.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
 adapt.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether closing was successful</td>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.modelling.NTerminalCloser.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; Conformation to be closed (or in this case
+transformed in space).</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; Closed (transformed) conformation gets stored in
+here.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
+</td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
+</dd></dl>
+
 <dl class="class">
 <dt id="promod3.modelling.CTerminalCloser">
 <em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CTerminalCloser</code><span class="sig-paren">(</span><em>n_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser" title="Permalink to this definition">¶</a></dt>
-<dd><p>The CTerminalCloser simply takes the conformation and closes by superposing
-the n_stem with the desired positions.</p>
+<dd><p>The <a class="reference internal" href="#promod3.modelling.CTerminalCloser" title="promod3.modelling.CTerminalCloser"><code class="xref py py-class docutils literal"><span class="pre">CTerminalCloser</span></code></a> simply takes the conformation and closes by
+superposing the n_stem with the desired positions.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Defining stem positions the closed conformation should
 adapt.</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether closing was successful</td>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.modelling.CTerminalCloser.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; Conformation to be closed (or in this case
+transformed in space).</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; Closed (transformed) conformation gets stored in
+here.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
+</td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.modelling.DeNovoCloser">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DeNovoCloser</code><a class="headerlink" href="#promod3.modelling.DeNovoCloser" title="Permalink to this definition">¶</a></dt>
+<dd><p>In case of sampling a full stretch, you dont have external constraints. The
+closer has a rather boring job in this case.</p>
+<dl class="method">
+<dt id="promod3.modelling.DeNovoCloser.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeNovoCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><p>Does absolutely nothing, except copying over the coordinates from
+<em>actual_positions</em> to <em>closed_positions</em> and return true.</p>
+</dd></dl>
+
+</dd></dl>
+
 </div>
 <div class="section" id="scorer-object">
 <span id="mc-scorer-object"></span><h2>Scorer Object<a class="headerlink" href="#scorer-object" title="Permalink to this headline">¶</a></h2>
 <p>The scorer asses a proposed conformation and are intended to return a pseudo
-energy, the lower the better.</p>
+energy, the lower the better. You can either use the provided scorer or any
+object implementing the functionality defined in <a class="reference internal" href="#promod3.modelling.ScorerBase" title="promod3.modelling.ScorerBase"><code class="xref py py-class docutils literal"><span class="pre">ScorerBase</span></code></a>.</p>
 <dl class="class">
-<dt>
-<code class="descname">LinearScorer(scorer, scorer_env, start_resnum, num_residues,</code></dt>
-<dt>
-<code class="descname">chain_idx, linear_weights)</code></dt>
+<dt id="promod3.modelling.ScorerBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScorerBase</code><a class="headerlink" href="#promod3.modelling.ScorerBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+scorer.</p>
+<dl class="method">
+<dt id="promod3.modelling.ScorerBase.GetScore">
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScorerBase.GetScore" title="Permalink to this definition">¶</a></dt>
+<dd><p>Takes coordinates and spits out a score given some internal structural
+environment.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>) &#8211; Coordinates to be scored</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The score</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.modelling.LinearScorer">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">LinearScorer</code><span class="sig-paren">(</span><em>scorer</em>, <em>scorer_env</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em>, <em>linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer" title="Permalink to this definition">¶</a></dt>
 <dd><p>The LinearScorer allows to combine the scores available from
 <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a> in a linear manner. See
 <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination"><code class="xref py py-meth docutils literal"><span class="pre">CalculateLinearCombination()</span></code></a> for a
@@ -589,7 +760,7 @@ detailed description of the arguments.</p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
 <p class="last">The provided <em>scorer_env</em> will be altered in every
-<a class="reference internal" href="#promod3.modelling.GetScore" title="promod3.modelling.GetScore"><code class="xref py py-func docutils literal"><span class="pre">GetScore()</span></code></a> call.
+<a class="reference internal" href="#promod3.modelling.LinearScorer.GetScore" title="promod3.modelling.LinearScorer.GetScore"><code class="xref py py-func docutils literal"><span class="pre">GetScore()</span></code></a> call.
 You might consider the Stash / Pop mechanism of the
 <a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
 original state once the sampling is done.</p>
@@ -617,8 +788,8 @@ which no scorer exists</p>
 </tbody>
 </table>
 <dl class="method">
-<dt id="promod3.modelling.GetScore">
-<code class="descclassname">promod3.modelling.</code><code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetScore" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.modelling.LinearScorer.GetScore">
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer.GetScore" title="Permalink to this definition">¶</a></dt>
 <dd><table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -640,13 +811,44 @@ which no scorer exists</p>
 <span id="mc-cooler-object"></span><h2>Cooler Object<a class="headerlink" href="#cooler-object" title="Permalink to this headline">¶</a></h2>
 <p>The cooler objects control the temperature of the Monte Carlo trajectory.
 They&#8217;re intended to deliver steadily decreasing temperatures with calls
-to their GetTemperature function.</p>
+to their GetTemperature function. You can either use the provided cooler
+or any object implementing the functionality defined in
+<a class="reference internal" href="#promod3.modelling.CoolerBase" title="promod3.modelling.CoolerBase"><code class="xref py py-class docutils literal"><span class="pre">CoolerBase</span></code></a>.</p>
+<dl class="class">
+<dt id="promod3.modelling.CoolerBase">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CoolerBase</code><a class="headerlink" href="#promod3.modelling.CoolerBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Abstract base class defining the functions that must be implemented by any
+cooler.</p>
+<dl class="method">
+<dt id="promod3.modelling.CoolerBase.GetTemperature">
+<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Temperature</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.CoolerBase.Reset">
+<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.Reset" title="Permalink to this definition">¶</a></dt>
+<dd><p>Resets to original state, so a new Monte Carlo trajectory can be generated</p>
+</dd></dl>
+
+</dd></dl>
+
 <dl class="class">
 <dt id="promod3.modelling.ExponentialCooler">
 <em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ExponentialCooler</code><span class="sig-paren">(</span><em>change_frequency</em>, <em>start_temperature</em>, <em>cooling_factor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler" title="Permalink to this definition">¶</a></dt>
 <dd><p>The exponential cooler starts with a given <em>start_temperature</em> and counts the
-calls to its GetTemperature function. According to the <em>change_frequency</em>,
-the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
+calls to its <a class="reference internal" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="promod3.modelling.ExponentialCooler.GetTemperature"><code class="xref py py-meth docutils literal"><span class="pre">GetTemperature()</span></code></a> function. According to the
+<em>change_frequency</em>, the returned temperature gets multiplied by the
+<em>cooling_factor</em>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -676,7 +878,8 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
 <dl class="method">
 <dt id="promod3.modelling.ExponentialCooler.Reset">
 <code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.Reset" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets current temperature back to <em>start_temperature</em></p>
+<dd><p>Sets current temperature back to <em>start_temperature</em> and the
+internal counter to 0</p>
 </dd></dl>
 
 </dd></dl>
@@ -728,6 +931,9 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
       <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>
@@ -735,11 +941,11 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/monte_carlo.txt"
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 9973f610b7e21bd5badbd8e66be478d0bc0272bd..3fee1ffc297b97f36e5b297a5941bddbdff75750 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="Model Checking" href="model_checking.html" />
     <link rel="prev" title="modelling - Protein Modelling" href="index.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -60,8 +59,8 @@ heuristics)</li>
 with the <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a> function. If you want to run and tweak the
 internal steps, you can start with the  following code and adapt it to your
 purposes:</p>
-<div class="highlight-default" id="modelling-steps-example"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-python" id="modelling-steps-example"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
 
 <span class="c1"># setup</span>
 <span class="n">merge_distance</span> <span class="o">=</span> <span class="mi">4</span>
@@ -117,7 +116,7 @@ chain follows afterwards.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -143,13 +142,13 @@ Gaps of different chains are appended one after another.</p>
 <dl class="attribute">
 <dt id="promod3.modelling.ModellingHandle.seqres">
 <code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
 of the target protein.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -158,7 +157,7 @@ of the target protein.</p>
 <dl class="attribute">
 <dt id="promod3.modelling.ModellingHandle.profiles">
 <code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
 the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>). Please note, that this
 attribute won&#8217;t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>. You have
 to fill it manually or even better by the convenient function
@@ -167,7 +166,7 @@ to fill it manually or even better by the convenient function
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -321,7 +320,7 @@ alignment handle or an alignment handle list. Every list item is treated as a
 single chain in the final raw model.</p>
 <p>Each alignment handle must contain exactly two sequences and the second
 sequence is considered the template sequence, which must have a
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
 <p>This is a basic protein core modelling algorithm that copies backbone
 coordinates based on the sequence alignment. For matching residues, the
 side chain coordinates are also copied. Gaps are ignored. Hydrogen an
@@ -349,7 +348,7 @@ as information about insertions and deletions in the gaps list.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) &#8211; Single alignment handle for raw model with single chain or
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) &#8211; Single alignment handle for raw model with single chain or
 list of alignment handles for raw model with multiple chains.</li>
 <li><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; True, if we wish to include ligands in the model. This
 searches for ligands in all OST handles of the views
@@ -375,7 +374,7 @@ in SMTL). All ligands are added to a new chain named
 <li>the second sequence does not have an attached structure</li>
 <li>the residues of the template structure do not match with the
 alignment sequence (note that you can set an &#8220;offset&#8221; (see
-<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
 template sequence (but not for the target))</li>
 <li>the target sequence has a non-zero offset (cannot be honored as
 the resulting model will always start its residue numbering at 1)</li>
@@ -395,7 +394,7 @@ the resulting model will always start its residue numbering at 1)</li>
 <dd><p>Build a model starting with a raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a>).</p>
 <p>This function implements a recommended pipeline to generate complete models
 from a raw model. The steps are shown in detail in the code example
-<a class="reference internal" href="#modelling-steps-example"><span class="std std-ref">above</span></a>. If you wish to use your own
+<a class="reference internal" href="#modelling-steps-example"><span>above</span></a>. If you wish to use your own
 pipeline, you can use that code as a starting point for your own custom
 modelling pipeline. For reproducibility, we recommend that you keep copies
 of custom pipelines.</p>
@@ -413,12 +412,12 @@ return an incomplete model.</p>
 <li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) &#8211; The prepared template coordinates loaded with the input
 alignment.</li>
 <li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
 Both do a similarly good job without ligands (CHARMM
 slightly better), but you will want to be consistent
 with the optional force fields in <cite>extra_force_fields</cite>.</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) &#8211; Additional list of force fields to use if a 
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) &#8211; Additional list of force fields to use if a 
 (ligand) residue cannot be parametrized with the
 default force field. The force fields are tried
 in the order as given and ligands without an
@@ -429,7 +428,7 @@ existing parametrization are skipped.</li>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -604,7 +603,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
 <li><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; This is the chain where the info goes to</li>
 <li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; First residue of the copied stretch</li>
 <li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Last residue of the copied stretch</li>
-<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; Transformation to be applied to all atom positions when
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) &#8211; Transformation to be applied to all atom positions when
 they&#8217;re copied over</li>
 </ul>
 </td>
@@ -635,7 +634,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) &#8211; Will have the profiles attached afterwards</li>
-<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; The sequence profiles to attach</li>
+<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) &#8211; The sequence profiles to attach</li>
 </ul>
 </td>
 </tr>
@@ -735,8 +734,8 @@ Before diving into the more demanding tasks in modeling, those may be closed
 already in the raw-model. After closure some checks are done to see if the
 solution is stereochemically sensible.</p>
 <p>Closed gaps are removed from <code class="xref py py-attr docutils literal"><span class="pre">mhandle.gaps</span></code>.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
 
 <span class="c1"># setup</span>
 <span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/gly.pdb&#39;</span><span class="p">)</span>
@@ -745,9 +744,9 @@ solution is stereochemically sensible.</p>
 <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
 <span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
 <span class="c1"># close small deletion</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">CloseSmallDeletions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 </pre></div>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
@@ -769,7 +768,7 @@ For the scondary-structure-penalty to work,
 the model-template must have the appropriate
 information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a> is
 called (e.g. with 
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.8.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
 <li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
 of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>. Also works in combination
 with <cite>use_scoring_extender</cite>. This allows the gap
@@ -802,8 +801,8 @@ stretch of original gaps and the deleted region. Original gaps will be
 removed. Stem residues count to the gap, so <strong>A-A-A</strong> has a distance of 0.</p>
 <p>IMPORTANT: we assume here that <em>mhandle</em> stores gaps sequentially.
 Non-sequential gaps are ignored!</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
 
 <span class="c1"># setup</span>
 <span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1crn_cut.pdb&#39;</span><span class="p">)</span>
@@ -814,9 +813,9 @@ Non-sequential gaps are ignored!</p>
 <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
 <span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
 <span class="c1"># merge gaps</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">MergeGapsByDistance</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 </pre></div>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
@@ -846,8 +845,8 @@ both in this resnum range.</li>
 database. Do not expect a gap being filled in between its actual stem
 residues.
 This function cannot fill gaps at C- or N-terminal.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
 
 <span class="c1"># setup</span>
 <span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1crn_cut.pdb&#39;</span><span class="p">)</span>
@@ -858,11 +857,11 @@ This function cannot fill gaps at C- or N-terminal.</p>
 <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
 <span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
 <span class="c1"># close gaps</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">(),</span>
                               <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">(),</span>
                               <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">())</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 </pre></div>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
@@ -952,8 +951,8 @@ more loop candidates to be found.</p>
 <em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> lists. The latter
 is only used if the gap length is &gt;= the length of fragments stored.</p>
 <p>This function cannot fill gaps at C- or N-terminal.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
 
 <span class="c1"># setup</span>
 <span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1crn_cut.pdb&#39;</span><span class="p">)</span>
@@ -964,10 +963,10 @@ is only used if the gap length is &gt;= the length of fragments stored.</p>
 <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
 <span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
 <span class="c1"># close gaps</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">FillLoopsByMonteCarlo</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span>
                               	<span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">())</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 </pre></div>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
@@ -1060,8 +1059,8 @@ but we do not assume that the resulting termini are of high quality!</p>
 <em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> lists. The latter
 is only used if the gap length is &gt;= the length of fragments stored.</p>
 <p>Terminal gaps of length 1 are ignored by this function!</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
 
 <span class="c1"># setup</span>
 <span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/gly.pdb&#39;</span><span class="p">)</span>
@@ -1072,10 +1071,10 @@ is only used if the gap length is &gt;= the length of fragments stored.</p>
 <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
 <span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
 <span class="c1"># close gaps</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps before: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 <span class="n">modelling</span><span class="o">.</span><span class="n">ModelTermini</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span>
                        <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">())</span>
-<span class="nb">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="k">print</span> <span class="s1">&#39;Number of gaps after: </span><span class="si">%d</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
 </pre></div>
 </div>
 <table class="docutils field-list" frame="void" rules="none">
@@ -1100,7 +1099,7 @@ fragger handle for each chain in <em>mhandle</em>.</li>
 
 <dl class="function">
 <dt id="promod3.modelling.BuildSidechains">
-<code class="descclassname">promod3.modelling.</code><code class="descname">BuildSidechains</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_pipeline.html#BuildSidechains"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">BuildSidechains</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>rotamer_library=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_pipeline.html#BuildSidechains"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
 <dd><p>Build sidechains for model.</p>
 <p>This is a wrapper for <a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>, 
 followed by a check for ring punches. If ring punches are found it 
@@ -1123,6 +1122,10 @@ if None.</li>
 <li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) &#8211; Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>
 if ring punches are found. A default one is loaded
 if None.</li>
+<li><strong>rotamer_library</strong> (<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a> or
+<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) &#8211; Used as parameter for 
+<code class="xref py py-func docutils literal"><span class="pre">modelling.ReconstructSidechains()</span></code>, a default 
+one is loaded if None.</li>
 </ul>
 </td>
 </tr>
@@ -1134,7 +1137,7 @@ if None.</li>
 <dt id="promod3.modelling.MinimizeModelEnergy">
 <code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_pipeline.html#MinimizeModelEnergy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
 <dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.8.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
 It will iteratively (at most <em>max_iterations</em> times):</p>
 <ul class="simple">
 <li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
@@ -1158,7 +1161,7 @@ If the variable is not set, 1 thread will be used by default.</p>
 <li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Max. number of iterations within LBFGS method</li>
 <li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; if True, use the AMBER force field instead of the def.
 CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) &#8211; Additional list of force fields to use (see
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) &#8211; Additional list of force fields to use (see
 <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
 </ul>
 </td>
@@ -1166,7 +1169,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
 </td>
 </tr>
 </tbody>
@@ -1233,6 +1236,9 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
       <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>
@@ -1240,11 +1246,11 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/pipeline.txt"
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 85e5fae720597dac6cad027ccab4fa3d2bf0d636..e23cb25c40a4565997f248c4de71241ef16ca070 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="modelling - Protein Modelling" href="index.html" />
     <link rel="next" title="Modelling Algorithms" href="algorithms.html" />
     <link rel="prev" title="Generating Loops De Novo" href="monte_carlo.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -46,26 +45,26 @@
 <p>Two methods are provided to fully reconstruct sidechains of residues:</p>
 <ul class="simple">
 <li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
 <li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
 and used to reconstruct sidechains of single loops</li>
 </ul>
 <p>Example usage:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">mol</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
+<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><span class="p">,</span> <span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
 
 <span class="c1"># load a protein </span>
 <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
 <span class="c1"># get only amino acids</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">&quot;peptide=true&quot;</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">&quot;peptide=true&quot;</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
 <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s1">&#39;sidechain_test_orig.pdb&#39;</span><span class="p">)</span>
 <span class="c1"># reconstruct sidechains</span>
-<span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+<span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
 <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s1">&#39;sidechain_test_rec.pdb&#39;</span><span class="p">)</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">modelling</span>
+<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>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">modelling</span>
 
 <span class="c1"># load example (has res. numbering starting at 1)</span>
 <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
@@ -75,7 +74,7 @@ and used to reconstruct sidechains of single loops</li>
 <span class="c1"># initialize AllAtom environment and sidechain reconstructor</span>
 <span class="n">env</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">AllAtomEnv</span><span class="p">(</span><span class="n">seqres_str</span><span class="p">)</span>
 <span class="n">env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">prot</span><span class="p">)</span>
-<span class="n">sc_rec</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">SidechainReconstructor</span><span class="p">(</span><span class="n">keep_sidechains</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+<span class="n">sc_rec</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">SidechainReconstructor</span><span class="p">(</span><span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
 <span class="n">sc_rec</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">env</span><span class="p">)</span>
 
 <span class="c1"># reconstruct subset (res. num. 6..10)</span>
@@ -101,7 +100,7 @@ and used to reconstruct sidechains of single loops</li>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structure for sidechain reconstruction. Note, that the sidechain
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structure for sidechain reconstruction. Note, that the sidechain
 reconstruction gets directly applied on the structure itself.</li>
 <li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether complete sidechains in <em>ent</em> (i.e. 
 containing all required atoms) should be kept rigid
@@ -114,8 +113,7 @@ the frame.</li>
 <li><strong>consider_ligands</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether to add ligands (anything in chain
 &#8216;_&#8217;) as static objects.</li>
 <li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code>) &#8211; A rotamer library to extract the rotamers from. The
-default is the <code class="xref py py-meth docutils literal"><span class="pre">Dunbrack</span></code>
-library.</li>
+default is to call <code class="xref py py-meth docutils literal"><span class="pre">&lt;LoadBBDepLib&gt;()</span></code>.</li>
 <li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Only considered when <em>rotamer_model</em>
 is &#8220;frm&#8221;.
 If set to True, the FRM solution undergoes 
@@ -212,7 +210,7 @@ environment before calling this!</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Start of loop.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Start of loop.</li>
 <li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Length of loop.</li>
 <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Chain the loop belongs to.</li>
 <li><strong>start_resnum_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Starts of loops.</li>
@@ -253,9 +251,9 @@ if multiple reconstructors are used (or you must use a distinct <em>env</em>).</
 <li><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) &#8211; Link to this environment.</li>
 <li><strong>use_frm</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; If True, use flexible rotamer model, else rigid.</li>
 <li><strong>use_bbdep_lib</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; If True, use default backbone dependent rot. library
-(<code class="xref py py-meth docutils literal"><span class="pre">Dunbrack</span></code>), else use
+(<code class="xref py py-meth docutils literal"><span class="pre">LoadBBDepLib()</span></code>), else use
 backbone independent one
-(<code class="xref py py-meth docutils literal"><span class="pre">Penultimate</span></code>).</li>
+(<code class="xref py py-meth docutils literal"><span class="pre">LoadLib()</span></code>).</li>
 <li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code>) &#8211; Custom rotamer library to be used.</li>
 </ul>
 </td>
@@ -432,6 +430,9 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
       <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>
@@ -439,11 +440,11 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/modelling/sidechain_reconstruction.txt"
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index c7226c83d6d29c07ee6392a031ad29887d8c9f0f..cdfa24d07cd63593a84b28cff1ae7a355f70aca6 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index ce9c3bed25946e90ca661dc414a86805a914c840..6f7742060998945125c6b0f88727b8cfc622522e 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
     <link rel="up" title="Documentation For Developers" href="developers.html" />
-    <link rel="next" title="Changelog" href="changelog.html" />
+    <link rel="next" title="License" href="license.html" />
     <link rel="prev" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -110,7 +109,7 @@ Generally, we store any data-structure value-by-value as fixed-width types!</p>
 </ul>
 <p>Each serializable class must define a <code class="docutils literal"><span class="pre">Serialize</span></code> function that accepts sinks
 and sources, such as:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="k">template</span> <span class="o">&lt;</span><span class="k">typename</span> <span class="n">DS</span><span class="o">&gt;</span>
+<div class="highlight-cpp"><div class="highlight"><pre><span class="k">template</span> <span class="o">&lt;</span><span class="k">typename</span> <span class="n">DS</span><span class="o">&gt;</span>
 <span class="kt">void</span> <span class="n">Serialize</span><span class="p">(</span><span class="n">DS</span><span class="o">&amp;</span> <span class="n">ds</span><span class="p">)</span> <span class="p">{</span>
   <span class="c1">// serialize element-by-element</span>
 <span class="p">}</span>
@@ -118,7 +117,7 @@ and sources, such as:</p>
 </div>
 <p>Or if this is not possible for an object of type <code class="docutils literal"><span class="pre">T</span></code>, we need to define
 global functions such as:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSource</span><span class="o">&amp;</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span><span class="o">&amp;</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
+<div class="highlight-cpp"><div class="highlight"><pre><span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSource</span><span class="o">&amp;</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span><span class="o">&amp;</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
 <span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSink</span><span class="o">&amp;</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
 </pre></div>
 </div>
@@ -145,7 +144,7 @@ serialize the values manually and convert each element appropriately.</li>
 <h2>Code Example<a class="headerlink" href="#code-example" title="Permalink to this headline">¶</a></h2>
 <p>Here is an example of a class which provides functionality for portable
 and non-portable I/O:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="c1">// includes for this class</span>
+<div class="highlight-cpp"><div class="highlight"><pre><span class="c1">// includes for this class</span>
 <span class="cp">#include</span> <span class="cpf">&lt;boost/shared_ptr.hpp&gt;</span><span class="cp"></span>
 <span class="cp">#include</span> <span class="cpf">&lt;iostream&gt;</span><span class="cp"></span>
 <span class="cp">#include</span> <span class="cpf">&lt;fstream&gt;</span><span class="cp"></span>
@@ -408,9 +407,9 @@ and non-portable I/O:</p>
 </ul>
 </li>
 <li>module <code class="docutils literal"><span class="pre">sidechain</span></code>:<ul>
-<li><code class="file docutils literal"><span class="pre">2010DunbrackLib.dat</span></code>
+<li><code class="file docutils literal"><span class="pre">bb_dep_lib.dat</span></code>
 (<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>)</li>
-<li><code class="file docutils literal"><span class="pre">PenultimateLib.dat</span></code>
+<li><code class="file docutils literal"><span class="pre">lib.dat</span></code>
 (<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>)</li>
 </ul>
 </li>
@@ -450,7 +449,7 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
   <li><a href="index.html">Documentation overview</a><ul>
   <li><a href="developers.html">Documentation For Developers</a><ul>
       <li>Previous: <a href="cmake/index.html" title="previous chapter">ProMod3&#8216;s Share Of CMake</a></li>
-      <li>Next: <a href="changelog.html" title="next chapter">Changelog</a></li>
+      <li>Next: <a href="license.html" title="next chapter">License</a></li>
   </ul></li>
   </ul></li>
 </ul>
@@ -470,6 +469,9 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
       <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>
@@ -477,11 +479,11 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/portableIO.txt"
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 94cc934014dc70ed49d89fbccbc9117b373ad337..fbef0d90c7bcd2f5bca2528facfdc4779bc9e4d3 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
 
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
 
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -124,6 +123,9 @@
       <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>
@@ -131,11 +133,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/references.html b/doc/html/references.html
new file mode 100644
index 0000000000000000000000000000000000000000..30d6dfc76795f056d480a340ca5fb6059969c2aa
--- /dev/null
+++ b/doc/html/references.html
@@ -0,0 +1,223 @@
+<!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>References &mdash; ProMod3 1.2.0 documentation</title>
+    
+    <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '1.2.0',
+        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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
+    <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+    <link rel="next" title="Changelog" href="changelog.html" />
+    <link rel="prev" title="License" href="license.html" />
+   
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head>
+  <body role="document">  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <div class="section" id="references">
+<h1>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h1>
+<table class="docutils citation" frame="void" id="biasini2013" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[biasini2013]</td><td>Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
+Johner N, Schenk AD, Philippsen A and Schwede T (2013).
+OpenStructure: an integrated software framework for
+computational structural biology. Acta Cryst.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="canutescu2003" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[canutescu2003]</td><td>Canutescu AA and Dunbrack RL Jr. (2003).
+Cyclic coordinate descent: A robotics algorithm for protein
+loop closure. Protein Sci.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[canutescu2003b]</td><td>Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
+A graph-theory algorithm for rapid protein side-chain
+prediction. Protein Sci.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="coutsias2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[coutsias2005]</td><td>Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+Resultants and loop closure. International Journal of Quantum
+Chemistry.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="chakravarty1999" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[chakravarty1999]</td><td>Chakravarty S, Varadarajan R (1999).
+Residue depth: a novel parameter for the analysis of
+protein structure and stability. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="davis2006" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[davis2006]</td><td>Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+The backrub motion: how protein backbone shrugs when a sidechain
+dances. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="goldstein1994" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[goldstein1994]</td><td>Goldstein RF (1994).
+Efficient rotamer elimination applied to protein side-chains
+and related spin glasses. Biophys J.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="jones1999" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[Jones1999]</td><td>Jones DT (1999).
+Protein secondary structure prediction based on position-specific
+scoring matrices. J. Mol. Biol.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="kabsch1983" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[kabsch1983]</td><td>Kabsch W, Sander C (1983).
+Dictionary of protein secondary structure: pattern recognition of
+hydrogen-bonded and geometrical features. Biopolymers.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="krivov2009" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[krivov2009]</td><td>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
+Improved prediction of protein side-chain conformations with
+SCWRL4. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="leach1998" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[leach1998]</td><td>Leach AR, Lemon AP (1998).
+Exploring the conformational space of protein side chains using
+dead-end elimination and the A* algorithm. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[shapovalov2011]</td><td>Shapovalov MV and Dunbrack RL Jr. (2011).
+A smoothed backbone-dependent rotamer library for proteins
+derived from adaptive kernel density estimates and
+regressions. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="soding2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[soding2005]</td><td>Söding J (2005).
+Protein homology detection by HMM-HMM comparison.
+Bioinformatics.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="solis2006" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[solis2006]</td><td>Solis AD, Rackovsky S (2006). Improvement of statistical
+potentials and threading score functions using information
+maximization. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="zhou2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[zhou2005]</td><td>Zhou H, Zhou Y (2005).
+Fold Recognition by Combining Sequence Profiles Derived From
+Evolution and From Depth-Dependent Structural Alignment of
+Fragments. Proteins.</td></tr>
+</tbody>
+</table>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+      <li>Previous: <a href="license.html" title="previous chapter">License</a></li>
+      <li>Next: <a href="changelog.html" title="next chapter">Changelog</a></li>
+  </ul></li>
+</ul>
+</div>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="_sources/references.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
+  <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="footer">
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
+      
+      |
+      <a href="_sources/references.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+    
+
+    
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 983fd1a43688c709ba13f6608a27e1cbd61780b1..447f767493c706853fba54c0e0bd935448e28d22 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="scoring - Loop Scoring" href="index.html" />
     <link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
     <link rel="prev" title="Backbone Scorers" href="backbone_scorers.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -320,7 +319,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomInteractionScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -332,7 +331,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.AllAtomInteractionScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -479,7 +478,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPackingScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -491,7 +490,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.AllAtomPackingScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -568,7 +567,7 @@ of residues in the input loop. True by default.</td>
 <dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a>. Calculates a simple
 clash score of all atoms against the environment. There is no need to define
 any parameters here as all interaction energies are fixed (see Eq. (11) in
-<a class="reference internal" href="other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>). By default, the scorer calculates the scores by
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>). By default, the scorer calculates the scores by
 including everything, the stuff set in the environment and the coordinates
 in the input loops. You can change this behaviour with the according
 functions.</p>
@@ -664,6 +663,9 @@ of residues in the input loop. True by default.</td>
       <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>
@@ -671,11 +673,11 @@ of residues in the input loop. True by default.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/scoring/all_atom_scorers.txt"
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index e1b57c32a98e58a6133441cde6027450387db6b9..df2f4d878eca76065a8efa70b267f69cd75f8b58 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="scoring - Loop Scoring" href="index.html" />
     <link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
     <link rel="prev" title="scoring - Loop Scoring" href="index.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -68,8 +67,8 @@ task.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) &#8211; Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) &#8211; Internal SEQRES to be set (single chain or list with one per
 chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
 </tr>
 </tbody>
@@ -106,7 +105,7 @@ structural data was already set, all the existing data gets cleared first.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) &#8211; Structral data to be set as environment. The chains
 in <em>env_structure</em> are expected to be in the same
 order as the SEQRES items provided in constructor.</td>
 </tr>
@@ -130,7 +129,7 @@ positions.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) &#8211; Structural data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Res. number defining the position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) &#8211; Res. number defining the position in the SEQRES.</li>
 <li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index of chain the structural data belongs to.</li>
 </ul>
 </td>
@@ -279,7 +278,7 @@ providing lists of integers.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
 </tr>
 </tbody>
 </table>
@@ -328,9 +327,9 @@ providing lists of integers.</p>
 <em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ConstraintFunction</code><span class="sig-paren">(</span><em>min_dist</em>, <em>max_dist</em>, <em>values</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ConstraintFunction" title="Permalink to this definition">¶</a></dt>
 <dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>.
 Defines a constraint function. The score for a distance between <em>min_dist</em> and
-<em>max_dist</em> is determined by liner interpolation assuming the first and last
-value exactly lying on <em>min_dist</em> ang <em>max_dist</em>. For distances outside the
-range defined by <em>min_dist</em> and <em>max_dist</em>, the score is 0.0.</p>
+<em>max_dist</em> is determined by linear interpolation assuming the first and last
+value exactly lying on <em>min_dist</em> and <em>max_dist</em>. For distances outside the
+range defined by <em>min_dist</em> and <em>max_dist</em>, the returned score is 0.0.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -343,10 +342,7 @@ between <em>min_dist</em> and <em>max_dist</em></li>
 </ul>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Index of added constraint definition</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>min_dist</em> &gt;= <em>max_dist</em> or when
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>min_dist</em> &gt;= <em>max_dist</em> or when
 <em>min_dist</em> or <em>max_dist</em> are negative or when <em>values</em> contains no
 elements</p>
 </td>
@@ -360,7 +356,7 @@ elements</p>
 <em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ContactFunction</code><span class="sig-paren">(</span><em>max_dist</em>, <em>score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ContactFunction" title="Permalink to this definition">¶</a></dt>
 <dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>.
 Defines a simple contact function. The score value is <em>score</em> if
-distance &lt; <em>max_dist</em> and 0 otherwise.</p>
+distance &lt; <em>max_dist</em> and 0.0 otherwise.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -389,7 +385,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The sequence with which all added structures must match</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) &#8211; The sequence with which all added structures must match</li>
 <li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunctionType</span></code></a>) &#8211; Whether you want to assess pairwise distances between CA
 or CB atoms</li>
 </ul>
@@ -404,7 +400,7 @@ or CB atoms</li>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) &#8211; Alignment, where first sequence represent the initial
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) &#8211; Alignment, where first sequence represent the initial
 SEQRES and the second sequence the actual structural
 info. The second sequence must have a view attached.</td>
 </tr>
@@ -503,6 +499,9 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
       <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>
@@ -510,11 +509,11 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/scoring/backbone_score_env.txt"
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 71276424ad8d5762fa2f4f87b16a5e46d6c22fa1..06c5f4a4d0e2a2811f43df1b850c52ce292e95ac 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="scoring - Loop Scoring" href="index.html" />
     <link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
     <link rel="prev" title="Backbone Score Environment" href="backbone_score_env.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -344,7 +343,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">CBPackingScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -356,7 +355,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.CBPackingScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -380,7 +379,7 @@ called for every type of amino acids and for every <em>count</em> &lt;= <em>max_
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for which to set energy.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for which to set energy.</li>
 <li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of surrounding CB positions for which to set energy.</li>
 <li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Energy to set for those parameters.</li>
 </ul>
@@ -442,9 +441,9 @@ of amino acids.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Radius in which other cbeta atoms are counted.</li>
+<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Radius in which other cbeta atoms are considered.</li>
 <li><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Number of equally sized bins to discretize distances (range
-of [0,*cutoff*]).</li>
+of [0, <em>cutoff</em>]).</li>
 <li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Minimal separation in sequence two cbeta atoms must have to
 be considered.</li>
 </ul>
@@ -475,7 +474,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal"><span class="pre">CBetaScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -487,7 +486,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.CBetaScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -514,8 +513,8 @@ SetEnergy(aa2, aa1, bin, energy).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for second interaction partner.</li>
 <li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the interaction distance.</li>
 <li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Energy to set for those parameters.</li>
 </ul>
@@ -651,7 +650,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal"><span class="pre">ReducedScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -663,7 +662,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.ReducedScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -694,8 +693,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; Amino acid for second interaction partner.</li>
 <li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the interaction distance.</li>
 <li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the alpha angle.</li>
 <li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Discrete bin describing the beta angle.</li>
@@ -780,7 +779,7 @@ of residues to be scored. True by default.</td>
 <dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Calculates a simple
 clash score of a loop itself and with the set environment. There is no need to
 define any parameters here as all interaction energies are fixed (see Eq. (11)
-in <a class="reference internal" href="other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>).</p>
+in <a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>).</p>
 <dl class="method">
 <dt id="promod3.scoring.ClashScorer.DoInternalScores">
 <code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
@@ -899,7 +898,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal"><span class="pre">HBondScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -911,7 +910,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.HBondScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -1054,7 +1053,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal"><span class="pre">SSAgreementScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -1066,7 +1065,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.SSAgreementScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -1187,7 +1186,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal"><span class="pre">TorsionScorer</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -1199,7 +1198,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.scoring.TorsionScorer.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -1380,6 +1379,9 @@ of residues to be scored. True by default.</td>
       <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>
@@ -1387,11 +1389,11 @@ of residues to be scored. True by default.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/scoring/backbone_scorers.txt"
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index e733603063ec5484bad703f5de8006b1f24d4029..2d032be3dae6b1e7f45fd5409a79eb07aa9b1c84 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Users" href="../users.html" />
     <link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
     <link rel="prev" title="Subrotamer Optimization" href="../sidechain/subrotamer_optimizer.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -44,11 +43,15 @@
   <div class="section" id="module-promod3.scoring">
 <span id="scoring-loop-scoring"></span><h1><a class="reference internal" href="#module-promod3.scoring" title="promod3.scoring: Loop Scoring"><code class="xref py py-mod docutils literal"><span class="pre">scoring</span></code></a> - Loop Scoring<a class="headerlink" href="#module-promod3.scoring" title="Permalink to this headline">¶</a></h1>
 <p>Tools and algorithms to score loops. The scoring system is split between an
-environment which contains model-specific data and scorers which evaluate loops.</p>
+environment and scorers.
+Several scorers can be attached to the same environment containing the
+actual structural data of the current modelling problem.
+The environment is updated as the modelling proceeds and manages efficient
+spatial lookups to be used by the attached scorers.</p>
 <p>In this example, we load a structure, setup a score environment, link a few
 scorers to it and finally score some loops:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span>
+<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><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span>
 
 <span class="c1"># load data</span>
 <span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">&quot;data/1CRN.pdb&quot;</span><span class="p">)</span>
@@ -67,8 +70,8 @@ scorers to it and finally score some loops:</p>
 <span class="c1"># calculate scores for 10 residues starting at residue number 23.</span>
 <span class="c1"># all required structural information comes from the environment</span>
 <span class="c1"># that can evolve as the modelling proceeds.</span>
-<span class="nb">print</span> <span class="s2">&quot;Clash-Score&quot;</span><span class="p">,</span> <span class="n">clash_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="mi">23</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
-<span class="nb">print</span> <span class="s2">&quot;CBeta-Score&quot;</span><span class="p">,</span> <span class="n">cbeta_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="mi">23</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
+<span class="k">print</span> <span class="s2">&quot;Clash-Score&quot;</span><span class="p">,</span> <span class="n">clash_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="mi">23</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
+<span class="k">print</span> <span class="s2">&quot;CBeta-Score&quot;</span><span class="p">,</span> <span class="n">cbeta_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="mi">23</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
 </pre></div>
 </div>
 <p>Contents:</p>
@@ -140,6 +143,9 @@ scorers to it and finally score some loops:</p>
       <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>
@@ -147,11 +153,11 @@ scorers to it and finally score some loops:</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/scoring/index.txt"
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 998c0c6c19f3cec55ad955d5c844295d786d62b2..11607329cda51081dbb20debfec1fbce06a29a19 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="scoring - Loop Scoring" href="index.html" />
     <link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
     <link rel="prev" title="All Atom Scorers" href="all_atom_scorers.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -49,7 +48,7 @@
 <dt id="promod3.scoring.SCWRL3PairwiseScore">
 <code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3PairwiseScore</code><span class="sig-paren">(</span><em>d</em>, <em>Rij</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3PairwiseScore" title="Permalink to this definition">¶</a></dt>
 <dd><p>Pairwise score from the SCWRL3 sidechain construction algorithm
-<a class="reference internal" href="#canutescu2003b" id="id1">[canutescu2003b]</a>.</p>
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -82,7 +81,7 @@ Suggestions from the paper:</p>
 <dt id="promod3.scoring.SCWRL3DisulfidScore">
 <code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3DisulfidScore</code><span class="sig-paren">(</span><em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>sg_pos_one                              ca_pos_two</em>, <em>cb_pos_two</em>, <em>sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3DisulfidScore" title="Permalink to this definition">¶</a></dt>
 <dd><p>Implements the empirically derived disulfid score from the SCWRL3 sidechain
-construction algorithm <a class="reference internal" href="#canutescu2003b" id="id2">[canutescu2003b]</a>.</p>
+construction algorithm <a class="reference internal" href="../references.html#canutescu2003b" id="id2">[canutescu2003b]</a>.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -107,12 +106,6 @@ construction algorithm <a class="reference internal" href="#canutescu2003b" id="
 </table>
 </dd></dl>
 
-<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label">[canutescu2003b]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>)</em> Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).</td></tr>
-</tbody>
-</table>
 </div>
 </div>
 
@@ -157,6 +150,9 @@ construction algorithm <a class="reference internal" href="#canutescu2003b" id="
       <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>
@@ -164,11 +160,11 @@ construction algorithm <a class="reference internal" href="#canutescu2003b" id="
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/scoring/other_scoring_functions.txt"
diff --git a/doc/html/search.html b/doc/html/search.html
index 175b5dbecda4fd05bc276408aaeabcf79e257d85..bf365f21f11509f482f4288999cb20220e03f5dc 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -23,6 +23,7 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <script type="text/javascript" src="_static/searchtools.js"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
   <script type="text/javascript">
@@ -32,14 +33,12 @@
   <script type="text/javascript" id="searchindexloader"></script>
   
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -86,11 +85,11 @@
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
     </div>
 
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 0c62df2650b19609ccc5d2fdf8536279e9693cc2..66ae0659d9b879a609f926861d5176908092c1b2 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
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ver:[16,34],everi:[0,1,8,10,13,21,22,26,27,28,31,32,34,35,36,39,40,41,44,46,49,50,52,53],everyth:[1,2,3,7,8],evolut:38,evolv:42,exact:[0,7,10,13,37],exactli:[2,10,26,28,31,35,40,44,50,51],exampl:[0,1,2,8,11,13,16,17,18,20,21,23,25,26,27,28,30],example_reconstruct:47,exce:[39,41],exceed:[26,29],except:[0,3,13,20,26,29,34,35,50],exclud:[8,20,26],exclus:[1,8,20,25],exec:7,execut:0,exercis:20,exisit:17,exist:[0,1,2,4,8,10,11,13,14,16,21,22,26,31,32,33,34,35,37,39,40,41,48,49,51,52],exit:[0,1,11,13],exit_cod:1,exit_statu:11,exot:8,exp:34,expect:[1,7,21,25,26,35,36,40,44,53],expens:26,experiment:35,explain:[1,8],explan:8,explicit:2,explicitli:20,explor:38,exponenti:34,exponentialcool:34,expos:26,express:[20,44],ext:11,extend:[1,4,8,16,17,24,26,28],extendatcterm:29,extendatnterm:29,extended_search:[31,35],extens:[0,3,11,13,29,35],extension_penalti:29,extent:26,extern:[3,4,5,7,8,34],extra:[2,3,8,16,22,37,48],extra_bin:26,extra_force_field:35,extract:[8,9,21,22,23,25,26,27,28,30,31,32,34,35,36,39,40,41,44,50],extractbackbon:21,extractloopposit:25,extractstatist:27,extrem:22,f_i:26,f_idx:40,facilit:28,factor:[10,25,34,49],fail:[0,1,8,11,14,22,31,32,35],failur:[0,8,11,13,20,52],fall:32,fallback:52,fals:[1,8,10,11,13,22,25,26,29,31,34,35,36,44,47,49,50],far:[31,35],fast:[9,18,19,21,25,26,27,37,39,40,41,52],fasta:[0,13,30,35],faster:[10,25,26,32,33,40],fastest:[32,35],favor:33,favourit:1,fed:[4,16],fedora:8,fee:20,feed:[4,21,31],feel:[8,16],fellow:8,fetch:16,few:[2,8,16,25,37,42],ff_aa:25,ff_aa_on:25,ff_aa_two:25,ff_ala:25,ff_arg:25,ff_asn:25,ff_asp:25,ff_cy:25,ff_cys2:25,ff_gln:25,ff_glu:25,ff_gly:25,ff_hisd:25,ff_hise:25,ff_ile:25,ff_leu:25,ff_lookup:[25,32,35],ff_lookup_charmm:37,ff_ly:25,ff_met:25,ff_phe:25,ff_pro:25,ff_ser:25,ff_thr:25,ff_trp:25,ff_tyr:25,ff_val:25,ff_xxx:25,field:[20,35,37,52],fifti:20,figur:16,file:[0,1,2,3,4,5,8],filecheck:16,fileexist:11,fileextens:11,filegzip:11,filenam:[0,8,11,13,25,26,27,28,37,39,41,48,52],filenotfound:33,fill:[4,7,8,13,16,23,26,29,30,31,33,35],fillfromdatabas:[31,35],fillfrommontecarlosampl:[31,35],fillloopsbydatabas:35,fillloopsbymontecarlo:35,filo:40,filtercandid:33,filtercandidateswithsc:33,final_model:[30,35],find:[4,7,8,10,16,21,23],findchain:42,findeigen3:20,findwithin:8,fine:8,finish:53,fire:[1,7],first:[0,1,8,10,13,16,18,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,52],fit:[16,20,22,26,30,31],fix:[3,8,11,16,25,32,36,37,39,41],fix_cterm:32,fix_nterm:32,fix_surrounding_hydrogen:25,flag1:4,flag2:4,flag:[0,2,4,8,10,11,22,26,35,36,49,50],flanking_rot_angle_on:22,flanking_rot_angle_two:22,fletch:[26,47],fletcher:35,flexibl:[0,19,36,44,47,49,50,53],flip:52,flood:26,flush:[1,16],fold:38,folder:[2,4,8,16,18,37],follow:[0,1,2,4,5,8,10,11,16,18,20,22,23,25,26,28,29,30,31,35,36,37,39,41,47,49,50,51,52],fontsiz:27,forbidden:8,forc:[25,32,35],force_const:[25,32],forcefield:23,forcefieldaminoacid:25,forcefieldbondinfo:25,forcefieldconnect:25,forcefieldharmonicangleinfo:25,forcefieldharmonicimproperinfo:25,forcefieldljpairinfo:25,forcefieldlookup:[25,32,35,37],forcefieldperiodicdihedralinfo:25,forcefieldureybradleyangleinfo:25,forg:16,forget:[1,8],form:[14,20,24,25,26,30,35,40,52],formal:[31,32,49,52],format:[0,5,13,20,26,48],formula:33,forward:16,found:[1,4,8,11,13,16,21,23,26,28,31,32,33,34,35,36,44,46,52],foundat:1,four:[9,34],fraction:[26,28,32,34],frag_db:[23,26,31,37],frag_info:26,frag_length:[23,26,28],frag_map:26,frag_po:[23,26,28],frag_residu:[23,26],frag_seq:[23,26],frag_siz:26,fragdb:[23,24,26,31,35,37],fragger:[23,26,28,34,35],fragger_handl:35,fragger_map:26,fraggerhandl:[26,28,35],fraggermap:[26,28],fragment:[3,9,22,23,24],fragment_db:35,fragment_handl:28,fragment_info:26,fragment_length:[26,28],fragmentinfo:[26,31],fragments_per_posit:28,fragmentsampl:34,frame:[3,16,35,36],frame_energi:49,frame_residu:[45,47],frameresidu:[45,49,50],framework:[8,19,38],free:[8,20,51,52],frequenc:[26,34],frm:36,frmrotam:[44,49,53],frmrotamergroup:[44,46,49,50],from:[0,1,2,3,4,5,6,7,8,9,10,11,13,16,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42],fromhhm:26,fromhoriz:26,fromresidu:52,front:[1,11,16],fstream:37,fudg:25,fulfil:[26,52],full:[0,1,8,10,21,25,26,29,30,31,34,36,47,49],full_seq:[29,31],fullgapextend:[29,35],fulli:[8,16,21,22,26,29,30,36],function_typ:40,functions_specific_to_your_act:8,fundament:37,funni:[2,8],further:[10,28,29,35,36,37],furthermor:37,futur:[25,26],gamma:[40,41,44],gamma_bin:41,gap:[0,3,9,18,24,25],gapextend:[29,35],gapfre:26,gapless:[0,13],gather:[4,12,16,26,28,47,49,52],gauc:52,gauch:52,gauche_minu:52,gauche_plu:52,gciiipgatcpgdyan:[31,35],gener:[1,2,3,5,8,10,13,14,16,18,19,20,23,24],generatedenovotrajectori:28,generatestructureprofil:26,geom:[21,22,25,26,28,32,35,44,49],geometr:[9,23],geoom:43,get:[0,1,2,7,8,16],getaa:[21,22,25],getaaa:21,getaah:21,getactivesubrotam:49,getallatomposit:[21,32,36],getallatomscoringkei:31,getallatomweight:31,getanchoratomindex:21,getangl:47,getangularbins:26,getatomcount:8,getatomnam:21,getatomna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Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3&#8216;s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils 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Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43],acid:[21,25,27],action:[0,1,4,5,7,8],actiontestcas:1,algorithm:28,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,argument:13,atom:[21,32,39],backbon:[32,40,41,52],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,7,35,49],can:51,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:52,construct:[40,50],constructor:50,contain:6,contribut:8,conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,52],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:52,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:1,exisit:37,extend:29,featur:[8,26],file:[11,37],find:26,fit:32,forcefield:25,fragment:26,frame:[45,50],from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,51],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,51],imag:[5,7],instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,52],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,must:1,non:52,novo:[28,34],object:[24,34,45],optim:53,ost:[5,7,25],other:43,output:1,own:8,pairwis:40,pairwisescor:41,pars:13,parser:13,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,relax:32,releas:3,repres:22,residu:50,rigid:28,ring:33,rotam:[46,48,49,50,52],rotamerid:51,run:[1,2,5,7,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43],scorer:[8,34,39,41],script:[1,5,7],scwrl3:43,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,11],sidechain:[0,36,47],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:53,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:52,unit:[1,4,8],user:54,write:8,your:8}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 3724f552e9c88343293899410277feb0d2ee412e..0d6a6e1c6f943965ec6263627010d26b10abae60 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
     <link rel="prev" title="Rotamer Graph" href="graph.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -49,7 +48,7 @@ the sulfur atoms. It is possible to improve performance in sidechain
 reconstruction regarding cysteins when finding and separately handle
 disulfid bonds. The scoring module implements an empirically derived disulfid
 score (<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>) as defined in
-<a class="reference internal" href="../scoring/other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>. The paper proposes two rotamers to be in a disulfid
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>. The paper proposes two rotamers to be in a disulfid
 bonded state, if the resulting disulfid score plus the self energies of the
 involved rotamers is below 45. If there are several cysteines close together,
 this problem gets another layer of complexity. One has to assure, that
@@ -76,10 +75,10 @@ rotamers to the result of the geometric expression.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) &#8211; First rotamer</li>
 <li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) &#8211; Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CA position of first rotamer</li>
-<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CB position of first rotamer</li>
-<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CA position of second rotamer</li>
-<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CB position of second rotamer</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; CB position of second rotamer</li>
 </ul>
 </td>
 </tr>
@@ -112,8 +111,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>rotamer_groups</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
 <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) &#8211; Every group represents a cysteine</li>
-<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The CA positions of the according rotamers</li>
-<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The CB positions of the according rotamers</li>
+<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; The CB positions of the according rotamers</li>
 <li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; The score two rotamers must have to be considered
 as a disulfid bond</li>
 <li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; If set to true and the input consists of flexible
@@ -172,6 +171,9 @@ describe the optimal rotamers in the according rotamer groups.</p>
       <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>
@@ -179,11 +181,11 @@ describe the optimal rotamers in the according rotamer groups.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
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-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
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+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/disulfid.txt"
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 9230a415148eeae3d628663743913f9c46ab6705..a2b34846c8fd7f464bf38e8cabc11fff35cb885d 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
     <link rel="prev" title="Rotamers" href="rotamer.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -161,6 +160,9 @@ can be passed to rotamer groups for calculating frame energies.</p>
       <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>
@@ -168,11 +170,11 @@ can be passed to rotamer groups for calculating frame energies.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/frame.txt"
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index e547f6f72ad4a595a7f20713cf3469da52324898..e90aa3a9efa7f8c90d04cdd927346ea590d939ff 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
     <link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -46,7 +45,7 @@
 <p>Once having a frame representing the rigid parts, the internal energies in
 rotamer groups can be calculated. To come to a final solution of the sidechain
 modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements a
+overall solution has to be found. ProMod3 implements a
 <a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.GraphMinimizer</span></code></a> that allows to find solutions using
 tree decomposition, A* and Monte Carlo algorithms.</p>
 <dl class="class">
@@ -112,6 +111,9 @@ conformations for every amino acid position.</td>
       <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>
@@ -119,11 +121,11 @@ conformations for every amino acid position.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/graph.txt"
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 3af49da0fb86f519b9e07bbc4fd4a050449415a8..bbe62850008062be04146f33401e15206584db40 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="Documentation For Users" href="../users.html" />
     <link rel="next" title="RotamerID" href="rotamer_id.html" />
     <link rel="prev" title="Modelling Algorithms" href="../modelling/algorithms.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -44,28 +43,28 @@
   <div class="section" id="module-promod3.sidechain">
 <span id="sidechain-sidechain-modelling"></span><h1><a class="reference internal" href="#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> - Sidechain Modelling<a class="headerlink" href="#module-promod3.sidechain" title="Permalink to this headline">¶</a></h1>
 <p>Tools and algorithms to model sidechains given backbone coordinates. The full
-module is heavily based on SCWRL4 <a class="reference internal" href="#krivov2009" id="id1">[krivov2009]</a> . The according paper describes
+module is heavily based on SCWRL4 <a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a> . The according paper describes
 the modelling of sidechains using two different rotamer models. A rigid model,
-as well as a flexible model. Both models are implemented in PROMOD3 and can be
+as well as a flexible model. Both models are implemented in ProMod3 and can be
 applied in flexible ways.</p>
 <p>The following code fragment shows an example of a basic sidechain reconstruction
 algorithm using the functionality in the module. Note, that this code will crash
 as soon as you have structures containing all the weirdness the PDB throws at
 us. In this case, you should use the full fletched sidechain reconstruction
 pipelines available in the modelling module.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">sidechain</span>
+<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><span class="p">,</span><span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">sidechain</span>
 
 <span class="c1"># load a protein</span>
 <span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">&#39;data/1CRN.pdb&#39;</span><span class="p">)</span>
 <span class="c1"># load rotamer library</span>
-<span class="n">library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
+<span class="n">library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadBBDepLib</span><span class="p">()</span>
 <span class="c1"># we need a rotamer constructor to create any rotamers or </span>
 <span class="c1"># frame residues </span>
-<span class="n">rot_constructor</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">SCWRLRotamerConstructor</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
+<span class="n">rot_constructor</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">SCWRLRotamerConstructor</span><span class="p">(</span><span class="bp">False</span><span class="p">)</span>
 
 <span class="c1"># create new entity from protein only containing the amino acids</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">&quot;peptide=true&quot;</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">&quot;peptide=true&quot;</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
 
 <span class="c1"># gather some data, the rotamer ids and backbone torsion angles</span>
 <span class="n">torsion_angles</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
@@ -111,6 +110,9 @@ pipelines available in the modelling module.</p>
                     <span class="n">r</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">i</span><span class="p">,</span> <span class="n">library</span><span class="p">,</span>
                     <span class="n">torsion_angles</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">torsion_angles</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span>
 
+    <span class="c1"># calculate pairwise energies towards the rigid frame</span>
+    <span class="c1"># the values will be stored and used by the solving algorithm</span>
+    <span class="c1"># later on when considering self energies</span>
     <span class="n">rot_group</span><span class="o">.</span><span class="n">SetFrameEnergy</span><span class="p">(</span><span class="n">frame</span><span class="p">)</span>
     <span class="c1"># remove super unlikely rotamer in rotamer group </span>
     <span class="c1"># e.g. those who clash with the frame</span>
@@ -157,6 +159,7 @@ pipelines available in the modelling module.</p>
 <li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-library-entry-type">The Library Entry Type</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#rotamer-configurations">Rotamer Configurations</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="rotamer_constructor.html">Rotamer Constructor</a><ul>
@@ -169,12 +172,6 @@ pipelines available in the modelling module.</p>
 <li class="toctree-l1"><a class="reference internal" href="subrotamer_optimizer.html">Subrotamer Optimization</a></li>
 </ul>
 </div>
-<table class="docutils citation" frame="void" id="krivov2009" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[krivov2009]</a></td><td>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.</td></tr>
-</tbody>
-</table>
 </div>
 
 
@@ -208,6 +205,9 @@ pipelines available in the modelling module.</p>
       <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>
@@ -215,11 +215,11 @@ pipelines available in the modelling module.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/index.txt"
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index cca071873f529654b50e681922af16e723f72672..4abbd8435afcdfdb0f52272470620d7d1b919d56 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
     <link rel="prev" title="Disulfid Bond Evaluation" href="disulfid.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -43,24 +42,26 @@
             
   <div class="section" id="loading-rotamer-libraries">
 <h1>Loading Rotamer Libraries<a class="headerlink" href="#loading-rotamer-libraries" title="Permalink to this headline">¶</a></h1>
-<p>Since the PROMOD3 sidechain modelling algorithms are mainly designed after the
-work of the Dunbrack lab <a class="reference internal" href="index.html#krivov2009" id="id1">[krivov2009]</a> , their backbone dependent rotamer
-library is probably the way to go. There exists a binary version of their
-2010 libary <a class="reference internal" href="#shapovalov2011" id="id2">[shapovalov2011]</a> , that can
-directly be loaded. As an alternative, there is also a binary file containing
-the backbone independent Penultimate library <a class="reference internal" href="#lovell2000" id="id3">[lovell2000]</a> .</p>
+<p>There are several rotamer libraries that can be used in ProMod3. ProMod3
+is optimized for the use with backbone dependent rotamer libraries such
+as the 2010 library provided by the Dunbrack lab <a class="reference internal" href="../references.html#shapovalov2011" id="id1">[shapovalov2011]</a>.
+You can request a licence <a class="reference external" href="http://dunbrack.fccc.edu/bbdep2010/">here</a>
+and generate such a library as described in
+extras/data_generation/rotamer_library/README. Alternatively, ProMod3
+provides its own backbone dependent or backbone independent libraries
+that can be loaded with <a class="reference internal" href="#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal"><span class="pre">LoadBBDepLib()</span></code></a> / <a class="reference internal" href="#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal"><span class="pre">LoadLib()</span></code></a>.</p>
 <dl class="method">
-<dt id="promod3.sidechain.LoadDunbrackLib">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadDunbrackLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadDunbrackLib" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads the 2010 backbone dependent rotamer library from the dunbrack lab.
-The library has been generated using the ReadDunbrackFile function
-using the file with smoothing factor 5 and nonrotameric dihedrals
-sampled in 20 degree steps.</p>
+<dt id="promod3.sidechain.LoadBBDepLib">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadBBDepLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadBBDepLib" title="Permalink to this definition">¶</a></dt>
+<dd><p>A backbone dependent rotamer library shipped with ProMod3. You can find
+details on how it is created in extras/data_generation/rotamer_library/README.
+All scripts to build it are in the same directory as the README file and
+build the basis for custom versions.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested library</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested Library</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a></td>
 </tr>
@@ -69,12 +70,12 @@ sampled in 20 degree steps.</p>
 </dd></dl>
 
 <dl class="method">
-<dt id="promod3.sidechain.LoadPenultimateLib">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadPenultimateLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadPenultimateLib" title="Permalink to this definition">¶</a></dt>
-<dd><p>Loads the backbone independent Penultimate library. The values for the dihedral
-angles are directly extracted from the publication without considering the
-probabilities specific for helices/sheets. Due to no assigned standard
-deviations, the flexible rotamer model won&#8217;t produce meaningful results.</p>
+<dt id="promod3.sidechain.LoadLib">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadLib" title="Permalink to this definition">¶</a></dt>
+<dd><p>A backbone independent rotamer library shipped with ProMod3. You can find
+details on how it is created in extras/data_generation/rotamer_library/README.
+All scripts to build it are in the same directory as the README file and
+build the basis for custom versions.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -92,8 +93,9 @@ deviations, the flexible rotamer model won&#8217;t produce meaningful results.</
 <code class="descclassname">promod3.sidechain.</code><code class="descname">ReadDunbrackFile</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ReadDunbrackFile" title="Permalink to this definition">¶</a></dt>
 <dd><p>Reads a file as it is provided when you get a licence for the 2010 library of
 the Dunbrack lab. It can only read the classic version, where all rotamers
-are in a single file. Specific distributions of nonrotameric sidechains
-cannot be read.</p>
+are in a single file. Specific distributions of non-rotameric sidechains
+cannot be read. You can find an example described in
+extras/data_generation/rotamer_library/README</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -113,18 +115,6 @@ incomplete if the last problem gets triggered.</td>
 </table>
 </dd></dl>
 
-<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[shapovalov2011]</a></td><td>Shapovalov MV and Dunbrack RL Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="lovell2000" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id3">[lovell2000]</a></td><td>Lovell SC, Word JM, Richardson JS, Richardson DC (2000). The penultimate rotamer library. Proteins.</td></tr>
-</tbody>
-</table>
 </div>
 
 
@@ -160,6 +150,9 @@ incomplete if the last problem gets triggered.</td>
       <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>
@@ -167,11 +160,11 @@ incomplete if the last problem gets triggered.</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/loading.txt"
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 582ce7f7647665d09d4bb7ee052bdda578fd494e..77b9802297e58cf49f50a3a6baaf0ab31411d9f1 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Frame" href="frame.html" />
     <link rel="prev" title="RotamerID" href="rotamer_id.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -47,7 +46,7 @@
 <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects. There exist two types. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> and
 <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>.
 To gather all possible rotamers for one particular sidechain position,
-PROMOD3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.
+ProMod3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.
 Pairwise interactions between particles give raise to pairwise energies between
 rotamers. Nevertheless, the energy calculation itself happens on the level
 of RotamerGroups and is mostly hidden away in the construction of the
@@ -86,11 +85,11 @@ has to be defined at initialization.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>type</strong> (<a class="reference internal" href="#promod3.sidechain.SidechainParticle" title="promod3.sidechain.SidechainParticle"><code class="xref py py-class docutils literal"><span class="pre">SidechainParticle</span></code></a>) &#8211; Type of particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Positions of particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Positions of particle</li>
 <li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Charge of particle, will be used in case H-Bonds</li>
 <li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; Name of particle. This name will be given to an actual
-<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> if a rotamer gets applied
-to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> if a rotamer gets applied
+to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a></li>
 </ul>
 </td>
 </tr>
@@ -198,7 +197,7 @@ to a <a class="reference external" href="https://www.openstructure.org/docs/dev/
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>lone_pair</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Lone pair direction</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>lone_pair</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Lone pair direction</td>
 </tr>
 </tbody>
 </table>
@@ -213,7 +212,7 @@ hydrogen, this would be the direction of backbone-N to backbone-H.</p>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Polar direction of particle</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) &#8211; Polar direction of particle</td>
 </tr>
 </tbody>
 </table>
@@ -290,7 +289,7 @@ in this process.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
 <strong>res</strong></li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; New name of <strong>res</strong>. Nothing happens in case of the
@@ -485,7 +484,7 @@ belongs to.</p>
 <em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>T</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer" title="Permalink to this definition">¶</a></dt>
 <dd><p>The FRMRotamer represents a rotamer of the so called flexible rotamer model,
 where one rotamer gets represented by several subrotamers.
-The idea is, that all particles of all subrotamers are given at
+The idea is that all particles of all subrotamers are given at
 initialization. Subrotamers are then defined by providing lists of indices.
 One particle can be part of several subrotamers.</p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -566,7 +565,7 @@ No atoms are removed from <strong>res</strong> in this process.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
 the sidechain</li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; New name of residue. Nothing happens in case of the
@@ -966,7 +965,7 @@ particles of the same residue.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
 the sidechain</li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; New name of residue. Nothing happens in case of the
@@ -1100,7 +1099,7 @@ particles of the same residue.</li>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue to be reconstructed</li>
 <li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Flag, whether polar hydrogens should be added to
 the sidechain</li>
 <li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) &#8211; New name of residue. Nothing happens in case of the
@@ -1217,6 +1216,9 @@ rotamers with <em>self_energy</em> &gt; <em>l_e</em> + <em>thresh</em></p>
       <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>
@@ -1224,11 +1226,11 @@ rotamers with <em>self_energy</em> &gt; <em>l_e</em> + <em>thresh</em></p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/rotamer.txt"
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 0a026c732216121edf1f9e241a6df6442596da23..67893a182db3db05db887881f35828857ffa7036 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Rotamer Graph" href="graph.html" />
     <link rel="prev" title="Rotamer Library" href="rotamer_lib.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -44,7 +43,7 @@
   <div class="section" id="rotamer-constructor">
 <h1>Rotamer Constructor<a class="headerlink" href="#rotamer-constructor" title="Permalink to this headline">¶</a></h1>
 <p>Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by PROMOD3</p>
+functionality provided by ProMod3</p>
 <div class="section" id="constructing-rotamers-and-frame-residues">
 <h2>Constructing Rotamers and Frame Residues<a class="headerlink" href="#constructing-rotamers-and-frame-residues" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
@@ -107,7 +106,7 @@ any rotamers for ALA and GLY.</td>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; To extract the required backbone atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; To extract the required backbone atoms</li>
 <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) &#8211; To extract the required backbone atoms</li>
 <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index of residue in <strong>all_atom_pos</strong> from which to
 extract the required backbone atoms</li>
@@ -167,7 +166,7 @@ why the phi angle of the residue is required as an input.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which to extract the backbone positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which to extract the backbone positions</li>
 <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) &#8211; To extract the backbone positions</li>
 <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index of residue in <strong>all_atom_pos</strong> from which to
 extract the backbone positions</li>
@@ -213,7 +212,7 @@ particles for all polar hydrogens.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which to extract the sidechain positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which to extract the sidechain positions</li>
 <li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) &#8211; To extract the sidechain positions</li>
 <li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index of residue in <strong>all_atom_pos</strong> from which to
 extract the sidechain positions</li>
@@ -237,7 +236,7 @@ atom positions are set in <strong>all_atom_pos</strong>.</p>
 <dl class="method">
 <dt id="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue">
 <code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
 This can be useful to mark a region occupied by a ligand. Note, that
 there won&#8217;t be any parametrization of hbonds in this function. All atoms
 of the residue will be represented as carbons and hydrogens are skipped.</p>
@@ -246,7 +245,7 @@ of the residue will be represented as carbons and hydrogens are skipped.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which all atoms will be taken to
 construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
 <li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
 </ul>
@@ -262,7 +261,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
 <dl class="method">
 <dt id="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidueHeuristic">
 <code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
 a heuristic treatment of the atoms based on the passed compounds library.
 This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal"><span class="pre">ConstructFrameResidue()</span></code></a>,
 which will be called by this function if the residue is not known by the given
@@ -280,10 +279,10 @@ as in the <a class="reference internal" href="rotamer.html#promod3.sidechain.Sid
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Residue from which all atoms will be taken to
 construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
 <li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
-<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) &#8211; OST compound library to use</li>
+<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) &#8211; OST compound library to use</li>
 </ul>
 </td>
 </tr>
@@ -361,6 +360,9 @@ to be assigned</td>
       <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>
@@ -368,11 +370,11 @@ to be assigned</td>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/rotamer_constructor.txt"
diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
index e324b292b422c8a57350ef8cfba159adabf832f7..8cfa78a50bfb70c6926157a9fbb92ed83360388a 100644
--- a/doc/html/sidechain/rotamer_id.html
+++ b/doc/html/sidechain/rotamer_id.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Rotamers" href="rotamer.html" />
     <link rel="prev" title="sidechain - Sidechain Modelling" href="index.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -93,7 +92,7 @@ or as <code class="docutils literal"><span class="pre">promod3.sidechain.Rotamer
 <div class="section" id="how-can-i-get-an-id">
 <h2>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h2>
 <p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
 or from amino acid three letter codes.</p>
 <dl class="method">
 <dt id="promod3.sidechain.TLCToRotID">
@@ -118,12 +117,12 @@ exactly the naming convention defined above.</p>
 <dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
 to generate special IDs this way
 (e.g. HSD, HSE or the special prolines/cysteins) since they&#8217;re simply not
-defined in <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+defined in <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; AA enum of amino acid</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) &#8211; AA enum of amino acid</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
 </tr>
@@ -176,6 +175,9 @@ defined in <a class="reference external" href="https://www.openstructure.org/doc
       <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>
@@ -183,11 +185,11 @@ defined in <a class="reference external" href="https://www.openstructure.org/doc
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/rotamer_id.txt"
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 7bfcf345dae719027bd12f4096db2da54f3ca84b..28ed4bbb91c6c9e28928deb2acd8ea6022365b30 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
     <link rel="prev" title="Frame" href="frame.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -48,7 +47,7 @@ sidechain can completely be described in terms of dihedral angles. Preferred
 combinations of such dihedral angles are a result of steric properties and
 can be gathered in rotamer libraries. Different libraries exist in the field
 and their main difference is, whether the provided sidechain conformations
-are dependent on their backbone or not. PROMOD3 provides you with a
+are dependent on their backbone or not. ProMod3 provides you with a
 <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a> organizing rotamers for the different aminoacids
 in equidistant phi/psi bins, as well as a simple <a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>.
 Both libraries are containers for <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> and are optimized
@@ -82,7 +81,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -94,7 +93,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.sidechain.RotamerLib.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -202,7 +201,7 @@ less machine-dependent).</p>
 <tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a></td>
 </tr>
 <tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
 </tr>
 </tbody>
 </table>
@@ -214,7 +213,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
 <dt id="promod3.sidechain.BBDepRotamerLib.SavePortable">
 <code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
 <dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
 for details.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -262,10 +261,12 @@ is given or when the library is already static.</p>
 added to the library or can be interpolated.
 In the first option, <em>phi</em> and <em>psi</em> simply get transformed to the
 according bin using following formalism: bin = round((angle + pi)/bin_size).
-In case of interpolation, the chi angles and the according standard
-deviations of the rotamers get bilinearly interpolated using the
-corresponding rotamers with same configuration from the neighbouring bins.
-This behaviour can be controlled with the SetInterpolate function.
+In case of interpolation, the chi angles of rotameric dihedral angles and the
+according standard deviations of the rotamers get bilinearly interpolated
+using the corresponding rotamers with same configuration from the
+neighbouring bins. No interplation is applied to non-rotameric dihedral
+angles (chi2 in ASP, ASN, HIS, PHE, TRP, TYR; chi3 in GLU, GLN).
+This behaviour can be controlled with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="promod3.sidechain.BBDepRotamerLib.SetInterpolate"><code class="xref py py-meth docutils literal"><span class="pre">SetInterpolate()</span></code></a>.
 The query function follows following strategies in case of
 special <em>id</em> requests.</p>
 <ul class="simple">
@@ -330,7 +331,8 @@ not fulfilled</td>
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Controls behaviour when QueryLib function gets called</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) &#8211; Controls behaviour when <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="promod3.sidechain.BBDepRotamerLib.QueryLib"><code class="xref py py-meth docutils literal"><span class="pre">QueryLib()</span></code></a>
+gets called</td>
 </tr>
 </tbody>
 </table>
@@ -433,14 +435,14 @@ functionalities.</p>
 <em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
 <dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
 The function tries to automatically identify the <a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> based
-on the residue name. The probability gets set to zero and the standard
-deviations to 0. All not required chi angles with their corresponding
-standard deviations are NaN.</p>
+on the residue name. The probability and standard deviations are set to 0.0,
+all not required chi angles with their corresponding  standard deviations to
+NaN.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Source of dihedral angles</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Source of dihedral angles</td>
 </tr>
 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></td>
 </tr>
@@ -464,7 +466,7 @@ are NaN.</p>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Source of dihedral angles</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.8.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) &#8211; Source of dihedral angles</li>
 <li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) &#8211; The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></li>
 </ul>
 </td>
@@ -596,6 +598,72 @@ considered similar</li>
 
 </dd></dl>
 
+</div>
+<div class="section" id="rotamer-configurations">
+<h2>Rotamer Configurations<a class="headerlink" href="#rotamer-configurations" title="Permalink to this headline">¶</a></h2>
+<p>In rotamers, one distinguishes between rotameric and non-rotameric sidechain
+dihedral angles. The rotameric ones are around SP3-SP3 hybridized bonds and
+typically have three distinct configurations (trans, gauche-, gauche+).
+The non-rotameric ones behave differently. ProMod3 offers some functionality
+to estimate those configurations.</p>
+<dl class="class">
+<dt id="promod3.sidechain.DihedralConfiguration">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">DihedralConfiguration</code><a class="headerlink" href="#promod3.sidechain.DihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<dd><p>Enumerates the possible sidechain dihedral configurations</p>
+<table class="hlist"><tr><td><ul class="simple">
+<li>TRANS - Trans configuration (120 &lt; angle &lt; -120)</li>
+<li>GAUCHE_PLUS - Gauche+ configuration (0 &lt; angle &lt; 120)</li>
+<li>GAUCHE_MINUS - Gauce- configuration (-120 &lt; angle &lt; 0)</li>
+<li>NON_ROTAMERIC - Dihedral without SP3-SP3 bond</li>
+<li>INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist...)</li>
+</ul>
+</td></tr></table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetRotamericConfiguration">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetRotamericConfiguration</code><span class="sig-paren">(</span><em>angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetRotamericConfiguration" title="Permalink to this definition">¶</a></dt>
+<dd><p>Evaluates the <em>angle</em> according to the ranges specified for
+<a class="reference internal" href="#promod3.sidechain.DihedralConfiguration" title="promod3.sidechain.DihedralConfiguration"><code class="xref py py-class docutils literal"><span class="pre">DihedralConfiguration</span></code></a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) &#8211; Angle to be evaluated</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
+INVALID if <em>angle</em> is NaN.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.GetDihedralConfiguration">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetDihedralConfiguration</code><span class="sig-paren">(</span><em>entry</em>, <em>id</em>, <em>dihedral_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetDihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<dd><p>Estimates configuration of a sidechain dihedral angle in a specific
+<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> with the knowledge of its identity. This allows
+to also return NON_ROTAMERIC (e.g. chi2 for ASN).</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>entry</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>) &#8211; Sidechain dihedral angle comes from here</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) &#8211; Identity of rotamer</li>
+<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) &#8211; Specifies angle (0 =&gt; chi1, ..., 3 =&gt; chi4)</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Result of <a class="reference internal" href="#promod3.sidechain.GetRotamericConfiguration" title="promod3.sidechain.GetRotamericConfiguration"><code class="xref py py-meth docutils literal"><span class="pre">GetRotamericConfiguration()</span></code></a> if specified
+angle is Rotameric, NON_ROTAMERIC if specified angle is
+valid and non rotameric, INVALID otherwise.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 </div>
 </div>
 
@@ -611,6 +679,7 @@ considered similar</li>
 <li><a class="reference internal" href="#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
 <li><a class="reference internal" href="#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
 <li><a class="reference internal" href="#the-library-entry-type">The Library Entry Type</a></li>
+<li><a class="reference internal" href="#rotamer-configurations">Rotamer Configurations</a></li>
 </ul>
 </li>
 </ul>
@@ -642,6 +711,9 @@ considered similar</li>
       <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>
@@ -649,11 +721,11 @@ considered similar</li>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/rotamer_lib.txt"
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 569714780b9983a1a1ad56afc95d30978e7b9a21..91795b7e1903aa1926ced0d62de3f728204ad7f8 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -23,18 +23,17 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
     <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
     <link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
     <link rel="prev" title="Loading Rotamer Libraries" href="loading.html" />
    
-  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -118,6 +117,9 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
       <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>
@@ -125,11 +127,11 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="../_sources/sidechain/subrotamer_optimizer.txt"
diff --git a/doc/html/users.html b/doc/html/users.html
index cbda6deb9b452b831f78abc83db49bf749632748..2de97d203698d4e6fff984d32b18d5639fc0a698 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -23,17 +23,16 @@
     <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>
+    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
     <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
     <link rel="next" title="Getting Started" href="gettingstarted.html" />
-    <link rel="prev" title="Welcome To ProMod3’s Documentation!" href="index.html" />
+    <link rel="prev" title="ProMod3" href="index.html" />
    
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
   
   <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
 
   </head>
-  <body role="document">
-  
+  <body role="document">  
 
     <div class="document">
       <div class="documentwrapper">
@@ -54,6 +53,7 @@ scripts using the functionality of this library.</p>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="actions/index.html#building-models">Building models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="actions/index.html#sidechain-modelling">Sidechain Modelling</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="buildsystem.html">Building ProMod3</a><ul>
@@ -63,6 +63,11 @@ scripts using the functionality of this library.</p>
 <li class="toctree-l2"><a class="reference internal" href="buildsystem.html#installing-project">Installing ProMod3</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="container/docker.html">Docker</a></li>
+<li class="toctree-l2"><a class="reference internal" href="container/singularity.html">Singularity</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="modelling/index.html"><code class="docutils literal"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="modelling/pipeline.html">Modelling Pipeline</a></li>
 <li class="toctree-l2"><a class="reference internal" href="modelling/model_checking.html">Model Checking</a></li>
@@ -124,7 +129,7 @@ scripts using the functionality of this library.</p>
 <h3>Related Topics</h3>
 <ul>
   <li><a href="index.html">Documentation overview</a><ul>
-      <li>Previous: <a href="index.html" title="previous chapter">Welcome To ProMod3&#8217;s Documentation!</a></li>
+      <li>Previous: <a href="index.html" title="previous chapter">ProMod3</a></li>
       <li>Next: <a href="gettingstarted.html" title="next chapter">Getting Started</a></li>
   </ul></li>
 </ul>
@@ -144,6 +149,9 @@ scripts using the functionality of this library.</p>
       <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>
@@ -151,11 +159,11 @@ scripts using the functionality of this library.</p>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2018, ProMod3 authors.
+      &copy;2013-2018, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
       
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.6</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
       
       |
       <a href="_sources/users.txt"