diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 5b24bb3c5d13289075f1aae105755f787c82cdb2..9076ce69feb128c2b7aae64c72ee098875fb0d7f 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -85,7 +85,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index 6b6f952c996a86b27904f39e45f915e5c2c20918..394659cdabb2071bad5e6ce39c086b7db923dcde 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -52,6 +52,11 @@
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">ost</span>
+
+<span class="k">def</span> <span class="nf">_MsgErrorAndExit</span><span class="p">(</span><span class="n">msg</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">):</span>
+    <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+    <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
 
 <div class="viewcode-block" id="FileExists"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExists">[docs]</a><span class="k">def</span> <span class="nf">FileExists</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="nb">file</span><span class="p">):</span>
   <span class="sd">&#39;&#39;&#39;</span>
@@ -73,8 +78,8 @@
 <span class="sd">            missing.</span>
 <span class="sd">  &#39;&#39;&#39;</span>
   <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="nb">file</span><span class="p">):</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">))</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
+    <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">),</span>
+                     <span class="n">exit_status</span><span class="p">)</span>
 </div>
 <div class="viewcode-block" id="FileExtension"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExtension">[docs]</a><span class="k">def</span> <span class="nf">FileExtension</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">extensions</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
   <span class="sd">&#39;&#39;&#39;</span>
@@ -118,16 +123,16 @@
     <span class="n">filename</span><span class="p">,</span> <span class="n">fileext</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">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">gz</span><span class="p">:</span>
       <span class="n">extension_string</span> <span class="o">=</span> <span class="s">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
-      <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span>
-                       <span class="o">+</span><span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">)</span>
-      <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
+      <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
+                       <span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+                       <span class="n">exit_status</span><span class="p">)</span>
   <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="s">&#39;&#39;</span><span class="p">:</span>
     <span class="n">extension_string</span> <span class="o">=</span> <span class="s">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
       <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">&#39;, &#39;</span> <span class="o">+</span> <span class="s">&#39;.gz, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">&#39;.gz&#39;</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span>
-                     <span class="o">+</span><span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">)</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
+      <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
+                       <span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+                       <span class="n">exit_status</span><span class="p">)</span>
   <span class="n">fileext</span> <span class="o">=</span> <span class="n">fileext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
   <span class="k">for</span> <span class="n">ext</span> <span class="ow">in</span> <span class="n">extensions</span><span class="p">:</span>
     <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="n">ext</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span>
@@ -138,9 +143,9 @@
   <span class="n">extension_string</span> <span class="o">=</span> <span class="s">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
   <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
     <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">&#39;, &#39;</span> <span class="o">+</span> <span class="s">&#39;.gz, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">&#39;.gz&#39;</span>
-  <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span>
-                   <span class="o">+</span><span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">)</span>
-  <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
+  <span class="n">_MsgErrorAndExit</span><span class="p">(</span><span class="s">&#39;</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. &#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
+                   <span class="s">&#39;Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&#39;</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+                   <span class="n">exit_status</span><span class="p">)</span>
 </div>
 <span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span>
   <span class="s">&#39;FileExists&#39;</span><span class="p">,</span>
@@ -188,7 +193,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index df9d374eef9b2ff7036fa06e5fc6955fe4dadfe3..810c78112b3f77da7bcf152815379b9db1a022a2 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -46,6 +46,15 @@ Here is a list of more options used within |project|:
 * ``DISABLE_LINKCHECK`` Don't test links from documentation on ``make check``
   (implicit by ``DISABLE_DOCUMENTATION``)
 
+Since we use |ost_s| in the background, some of its options for |cmake| are
+also relevant, here. Basically they need to be set to exactly the same value.
+Even if |project| builds with different settings, it may start producing funny
+results at an unexpected point. If you do not know the values, grep the option
+in the :file:`CMakeCache.txt` of |ost_s|:
+
+* ``OPTIMIZE``
+* ``OST_DOUBLE_PRECISION``
+
 Instead of calling |cmake| by yourself, there is the :file:`conf-scripts`
 directory, providing smallish scripts to invoke |cmake| the right way for
 various systems. Usually those scripts just need the |ost_s| and |qmean| paths
@@ -97,4 +106,4 @@ special targets:
 .. _eigen3: http://eigen.tuxfamily.org/
 
 ..  LocalWords:  cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html
-..  LocalWords:  doctest linkcheck qmean DQMEAN eigen
+..  LocalWords:  doctest linkcheck qmean DQMEAN eigen CMakeCache
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 4c6e894a2934d7d11c1fdf876ec5af1d534265e3..cba83fe74690987db5c4af4a7b92558edad9f2a8 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -98,6 +98,15 @@ directory. Don&#8217;t forget to put a <tt class="docutils literal"><span class=
 <li><tt class="docutils literal"><span class="pre">DISABLE_LINKCHECK</span></tt> Don&#8217;t test links from documentation on <tt class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></tt>
 (implicit by <tt class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></tt>)</li>
 </ul>
+<p>Since we use OST in the background, some of its options for CMake are
+also relevant, here. Basically they need to be set to exactly the same value.
+Even if ProMod3 builds with different settings, it may start producing funny
+results at an unexpected point. If you do not know the values, grep the option
+in the <tt class="file docutils literal"><span class="pre">CMakeCache.txt</span></tt> of OST:</p>
+<ul class="simple">
+<li><tt class="docutils literal"><span class="pre">OPTIMIZE</span></tt></li>
+<li><tt class="docutils literal"><span class="pre">OST_DOUBLE_PRECISION</span></tt></li>
+</ul>
 <p>Instead of calling CMake by yourself, there is the <tt class="file docutils literal"><span class="pre">conf-scripts</span></tt>
 directory, providing smallish scripts to invoke CMake the right way for
 various systems. Usually those scripts just need the OST and QMEAN paths
@@ -201,7 +210,7 @@ builder</li>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index b130401c078e6a83787778ff52d62b20098cb933..57c85fd1c70c30a252b01e7c5620f121c8baf32f 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -127,7 +127,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 11:54, 2014.
+      Last updated on Aug 11 08:42, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 1564617236456abd2e4b705547b7b25d0004cc77..8536f4005ac653e9b187b97a56e628ebcc72358b 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -745,7 +745,7 @@ contributions to web pages using ProMod3.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 08:42, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index 2f9b0bd2d9b69e34ed0ee1212a7b8e1fd02b3c05..e80793532552237fdd579d78bb729b827773f50a 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -217,7 +217,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 11:54, 2014.
+      Last updated on Aug 11 09:05, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 61373e9a0a2ee7f2d119ae22e2446402dc710892..a8b9ea0cd93108e8a012038a69235547ddc400fc 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -123,7 +123,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 11:54, 2014.
+      Last updated on Aug 11 09:05, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 4198ed7194c60bff02f162ad9d59db9f411013b6..f49d52d8b98f603b12c92c7bf5171e651a932f9a 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -140,7 +140,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 338067fcc562c174b490fd36d57440e9b43f64a5..68a5a6873bb534e2d6371308017069ba1babdd93 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -334,7 +334,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/index.html b/doc/html/index.html
index 9f457b6468d31f1edaa042527323be92ee1a68b4..649999215a61daa34622b56838e788732ae6f5d2 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -134,7 +134,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/meld/index.html b/doc/html/meld/index.html
index 11f75c69a756dc5d4317143c7db987254fd3abcf..a10156c1ee4a4967925c980dff2270fbba6586e0 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/meld/index.html
@@ -127,7 +127,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 11:54, 2014.
+      Last updated on Aug 11 08:42, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/meld/loop.html b/doc/html/meld/loop.html
index 4c96dedd051543932f4bbe16cebb17748f4204a3..51e549ed148c1f1ba655395e7f0be762cd3c481b 100644
--- a/doc/html/meld/loop.html
+++ b/doc/html/meld/loop.html
@@ -338,7 +338,7 @@ extension of the gap.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 11:54, 2014.
+      Last updated on Aug 11 08:42, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/meld/rawmodel.html b/doc/html/meld/rawmodel.html
index 6ce3448981d235303154f7350e1125d6f1ea0196..0b2978a85e351afa5864115101d1a59796ba3415 100644
--- a/doc/html/meld/rawmodel.html
+++ b/doc/html/meld/rawmodel.html
@@ -221,7 +221,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 11:54, 2014.
+      Last updated on Aug 11 08:42, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index fa69201d044980768da879cf410081d7f709e4d1..12044229f7d8f4641a521777fef1c1f27935d098 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 543390b6446f33313b8a9c7bbda3d32dbc1f5a1f..78656b0c9be81fdfa1dd7f3300dbfe5ffa8d2414 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/search.html b/doc/html/search.html
index beab970fcf713ba870ed4b8cae113a2f37f267e9..dfa8cb3d63eb66f1d70694ba03bd4b5cf5b7fd36 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 14:22, 2014.
+      Last updated on Aug 11 10:54, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index b52058020aa72497284d3e6fc3154b1172f2b72a..1cf83e971a12f9bea4ed018503b22d583cc26ed8 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:42,terms:{aln:6,all:[8,0,1,5,6],code:[8,0,5],forget:[8,5],chain:[8,6],messi:8,skip:8,forbidden:8,sidechains_unit_test:8,ost:[0,1,2,3,4,5,6,7,8,9,10],disable_document:[8,5],prefix:[8,0],concept:8,per:[8,7],abil:8,follow:[8,6],middl:8,structuralgap:1,readabl:8,init:8,program:7,under:8,introduc:8,sourc:[8,0,5],everi:[8,6],string:0,fals:[8,0,1,6],internet:8,candid:1,worst:8,failur:[8,0],veri:[8,0],affect:8,runnabl:8,tri:6,four:1,magic:8,level:[8,5],did:8,list:[8,0,1,5,6],assertequ:8,item:[8,6],fileextens:0,servic:8,dir:8,malici:8,promod_gcc_45:8,your_modul:8,direct:8,past:8,second:6,design:0,pass:8,download:5,acid:6,even:8,index:[8,4],what:[8,0,5],hide:8,sub:8,resembl:8,sum:1,calcul:1,find:8,current:8,delet:6,version:[8,5],"new":[8,1,6],boost:[0,1,2,3,4,5,6,7,8,9,10],method:1,meld:3,subtre:8,submodule1:8,honour:1,gener:8,never:8,here:[8,0,5,6],sphinx:[0,1,2,3,4,5,6,7,8,9,10],save:8,lib_stage_path:8,let:8,set_directory_properti:8,path:[8,0,5],along:8,modifi:[8,6,3],implicit:5,valu:0,wait:8,headlin:8,search:[8,4,5],produc:5,executable_output_path:8,setup_boost:8,promod3_version_minor:8,doctest:[8,5],within:[8,5],action:8,implement:8,stage_dir:8,honor:6,chanc:8,argpars:0,spawn:8,via:8,extra:8,activ:8,modul:3,submodul:8,put:[8,0,5],unix:8,api:9,instal:[8,5],total:1,unit:[],highli:5,fed:8,from:[0,1,3,5,6,8,9],describ:0,would:[8,5],regist:8,two:8,next:8,everybodi:8,few:[8,5,1,6],live:8,call:[8,5],recommend:5,loadalign:6,checkout:8,tell:[8,0],tightli:8,more:[8,5,6],sort:1,chapter:8,peopl:8,relat:8,notic:8,warn:8,flag:[8,0],include_directori:8,particular:8,known:0,actual:[8,1],hold:[1,6],cach:[8,5],must:8,py_run:8,hous:8,setup:[8,3],work:[8,5],histori:8,remain:6,paragraph:8,can:[8,0,5,6],torsion_scor:1,purpos:8,root:8,fetch:[8,0],def:8,control:8,give:8,process:8,add_argu:0,indic:0,topic:8,candit:1,want:[8,5],phrase:8,backbonelist:1,hydrogen:6,packing_scor:1,alwai:8,gcc:8,cours:8,end:[8,0,1,5],thing:[8,5],rather:8,comfort:0,sever:[8,5],verifi:0,config:8,updat:8,python_vers:8,product:8,entityhandl:[1,6],rebas:8,mess:8,clone:8,after:[8,5],usabl:8,sortbyscor:1,befor:8,wrong:5,attent:8,mai:[8,6],multipl:8,data:8,grow:6,man:[8,5],"short":8,practic:8,ost_doc_url:8,sit:8,correspond:[8,1],stash:8,exclud:8,alias:8,"switch":8,maintain:8,environ:8,allow:8,exclus:8,order:1,origin:8,promod3_version_major:8,help:[8,5],over:[8,5,6],insight:8,becaus:[8,5],report:[8,6],through:8,same:[5,1],gitignor:8,still:8,pointer:5,entiti:[8,1],perfect:8,output_vari:8,binari:8,fix:[8,0],selenium:6,structuralgaplist:6,carri:[8,0],drawback:8,onc:8,python_doc_url:8,therefor:8,easier:1,linkcheck:[8,5],them:8,good:8,"return":[0,1,6],thei:[8,1],python:[0,1,2,3,4,5,6,7,8,9,10],dai:0,exot:8,"break":8,framework:8,conquer:8,clash_bb_scor:1,instead:[8,0,5],front:[8,0,5],now:[8,6],align:6,minimalist:6,cmake_cxx_flags_releas:8,libexec_stage_path:8,name:[8,0],rmsd:1,anyth:[8,5],separ:8,easili:8,achiev:8,each:8,debug:8,found:8,went:8,complet:[8,6],side:8,mean:[8,0,5],compil:8,everyth:8,monolith:8,parwis:6,cmake_module_path:8,test_sidechain:8,idea:[8,3],realli:[8,0,5],runtest:8,"static":8,"2b1":5,our:8,special:[8,5],out:[8,5],variabl:[8,5],shown:8,goe:[8,5],promod3_unittest:8,crucial:8,content:[8,4,10],reader:8,print:[5,6],got:5,exec_program:8,dive:8,integr:8,runtimeerror:[1,6],differ:[8,5],free:8,standard:[],test_someth:8,reason:8,base:[0,6],ask:8,org:8,basi:8,could:[8,6],insert:[1,6],keep:8,turn:[8,0],clash_sc_scor:1,place:8,think:8,first:[8,3],oper:8,softwar:8,major:8,suffix:0,obviou:8,prevent:8,feel:8,sidechains_pymod:8,number:[1,6],yourself:[8,5],restrict:8,date:8,alreadi:8,done:8,least:[8,5],blank:8,stabl:8,miss:[0,1,6],exit_statu:0,given:[0,1],script:[8,0,5],top:[8,5],perfectli:8,mkdir:8,system:[8,5,3],messag:[8,0],stack:8,attach:6,stori:8,master:8,too:8,termin:0,scheme:8,"final":[8,6],store:[8,1,6],includ:[8,0,3],shell:[5,0],option:[8,0,5],tool:0,copi:[8,6],restrict_chain:6,openstructur:[0,1,2,3,4,5,6,7,8,9,10],part:8,pars:0,boost_include_dir:8,mostli:8,rst:8,off:[8,6],than:8,kind:8,target:[8,5],whenev:8,provid:[8,5],seamlessli:8,tree:8,unrecognis:0,project:8,nevertheless:8,reus:6,str:[0,6],were:8,posit:[0,1],toward:8,initi:3,builder:5,python_binari:8,sometim:8,mind:8,argument:[],packag:8,manner:8,have:[8,5,1,6],"__main__":8,need:[8,0,5],fasta:6,tidi:8,cmake_current_source_dir:8,optimis:8,rmsdto:1,imagin:8,probabl:[8,5],built:8,advic:8,inform:6,diverg:8,self:8,dedic:[8,5],lost:8,also:[8,0,5,6],exampl:[8,5,6],take:[8,6],which:[8,5,6,7],thoroughli:8,noth:8,singl:[8,6],"_opt":8,sure:8,distribut:8,clash:1,track:0,forg:8,compress:0,wno:8,most:[8,0,6],hotfix:8,"class":[],charg:8,renam:3,bug:8,url:8,doc:[8,5],later:8,cover:[8,0,7],doe:[8,0,6],ext:0,declar:8,clean:[8,5],latest:5,review:8,came:8,cmakelist:[8,5],show:8,dbg:8,attachview:6,bring:8,permiss:8,cmake_support:8,fine:8,anywai:8,eigen:5,involv:8,access:1,onli:[8,0,6],locat:5,explain:8,configur:[8,5],solut:8,figur:8,should:[8,0],header_stage_path:8,suppos:[8,1],templat:6,folder:8,move:8,hit:8,unus:8,variou:5,get:[8,5],watch:8,cannot:8,loadpdb:6,increas:1,toolbox:8,requir:[8,5,1],setup_compiler_flag:8,add_changelog_to_doc:8,enabl:0,coord:1,"default":[8,5],common:[8,0],contain:[8,0,5,6,9],python_root:5,where:8,remov:5,view:8,set:[8,0,1,5,6],seq:8,allatom_scor:1,frame:8,abort:8,ost_include_dir:8,see:8,temporarili:8,result:6,arg:8,testcas:8,reserv:0,sport:8,subject:8,awar:8,statu:8,detect:0,extend:8,someth:8,version_great:8,enumer:8,label:8,state:[8,5],score:1,subdir:8,simplest:8,"import":[8,0,5,6],awai:8,paramet:[0,1,6],approach:8,attribut:8,accord:8,parent:6,sole:8,cmake_cxx_compiler_vers:8,test_your_modul:8,recent:8,solv:8,come:[8,0],addit:[8,0],fail:[8,1],extens:[0,1],howev:1,disable_doctest:[8,5],promod3_version_patch:8,tutori:8,grain:8,fno:8,modif:6,whole:[8,6],pdb:[0,6],comment:8,sidechains_rst:8,"1ake":6,point:[8,5,1],cxx:8,overview:8,unittest:8,argumentpars:0,pop:8,walk:8,residu:[1,6],header:[8,5],featur:8,littl:8,test_submodule1:8,assum:8,torsion:1,quit:8,template_structur:6,creat:[8,5],coupl:8,rebuild:[8,5],three:8,been:8,sinc:[8,0],compon:8,trigger:8,besid:5,treat:[8,6],basic:[8,5,6],txt:[8,5],ost_root:[8,5],popul:[8,5],seq_alg:8,tini:8,quickli:8,life:[8,1],convert:6,ani:8,coordin:[],togeth:8,els:8,fileexist:0,educ:8,those:[8,5],"case":8,cmake_c_compiler_vers:8,uncertain:8,look:[8,0],raw:9,testfileexistsfals:8,straight:8,properti:8,commerci:8,formatt:8,invok:[8,5],boost_root:5,abov:8,error:0,dost_root:[8,5],loop:9,pack:1,methionin:6,bin:8,smng:3,helper:1,readi:5,sidechain:[8,1,6],henc:8,non:8,itself:8,clutter:8,conf:[8,5],protein:[9,6],calpha_onli:6,"__init__":8,reviv:8,develop:[],fedora:8,etc:8,suggest:8,belong:8,savepdb:6,files_to_be_remov:8,"while":[8,0],member:[8,6],fragment:1,complex:8,advis:8,admir:8,document:3,conflict:8,higher:5,http:8,optim:8,bienchen:8,make_directori:8,hand:5,driven:8,moment:8,rais:[1,6],disable_linkcheck:[8,5],user:[],extern:8,respons:8,tradition:0,expand:8,codetest:8,task:8,conop:8,pymod:8,find_packag:8,macro:8,markup:8,well:[8,5,1,6],without:[8,0,6],command:[],branchnam:8,thi:[0,1,5,6,7,8,9],endif:8,gzip:0,model:7,academ:8,spend:8,piec:8,usual:[8,5],add_doc_sourc:8,clash_scor:1,just:[8,5],entri:8,elabor:8,reduced_scor:1,obtain:6,rest:[0,1,2,3,4,5,6,7,8,9,10],touch:8,web:[8,5],loopcandid:1,restructuredtext:[0,1,2,3,4,5,6,7,8,9,10],makefil:[8,5],except:8,param:1,add:[8,1],densiti:1,input:0,subsequ:6,match:[8,6],opt:0,around:8,format:8,handl:6,specimen:0,term:8,source2:8,source1:8,mol:8,bit:[8,5],you:[8,0,5],mod:8,eigen3_include_dir:5,loss:8,like:[8,5,6],success:[0,1],incred:6,manual:[8,5],html:[8,5,3],test_:8,test_awesome_featur:8,"boolean":0,either:[8,6],output:[8,0],hook:8,page:[8,4,5],www:8,right:[8,5],often:[8,0],acknowledg:8,some:[8,0],begin:8,resolv:8,intern:8,proper:8,librari:8,qmean:[8,5],thu:0,smallish:[8,5],lead:0,avoid:8,definit:8,subclass:8,exit:0,select:6,recognis:8,devot:7,condit:8,amino:6,core:0,plu:8,cmake_source_dir:8,backbon:[1,6],step:8,promot:8,repositori:[8,3],"__name__":8,add_subdirectori:8,intervent:8,mmcif:0,stage:[],trustworthi:8,src:8,about:[8,6],rare:8,materi:8,manag:8,coars:8,commit:8,mol_alg:8,disabl:8,qmean_root:[8,5],real:8,"float":1,automat:[8,0],due:[1,6],promod3_version_str:8,empti:8,cmake_cxx_flag:8,strip:6,announc:8,merg:8,git:3,log:8,wai:[8,5],pictur:8,qmean_include_dir:8,support:[8,0],renumb:6,custom:8,avail:[8,5],strict:8,sortbycorrel:1,much:[8,6],interfac:8,author:8,lot:[8,0],suit:8,forward:8,stai:8,parse_arg:0,unfortun:8,"function":0,headach:8,enough:8,tupl:0,buildrawmodel:6,somethingtest:8,back:8,link:[8,5],atom:[1,6],don:[8,5],line:[],inlin:8,"true":[8,0,1,6],setup_stag:8,pull:[8,5],tripl:0,immedi:8,consist:8,possibl:[8,6],whether:0,type:[0,1,6],insertinto:1,displai:0,below:8,otherwis:8,problem:8,similar:5,testutil:8,gather:[8,7],evalu:8,"int":0,certain:5,utilis:[8,0],fellow:8,incomplet:6,exist:[8,0,1],file:[],dqmean_root:[8,5],deuterium:6,check:[8,0,5],fill:8,echo:8,again:[8,5],calpha:6,when:[8,6],detail:[8,6],other:[8,5,6],bool:[0,1],seem:8,test:[],cmake_compiler_is_gnucxx:8,phosphoserin:6,nice:8,correl:1,bb_list:1,toentiti:1,additional_make_clean_fil:8,determin:0,rawmodelingresult:6,sequenc:[9,1,6],cmake_build_typ:8,cmake_minimum_requir:8,briefli:8,consid:8,gap:[1,6],homolog:7,doptim:8,fatal_error:8,legal:8,reduc:1,peptid:[1,6],algorithm:6,project_binary_dir:8,directori:[],descript:8,pseudo:6,rule:8,ignor:6,time:[8,6],push:8},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:attribute","4":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","class","Python class"]},filenames:["core/argcheck","meld/loop","users","changelog","index","buildsystem","meld/rawmodel","core/index","contributing","meld/index","developers"],titles:["<tt class=\"docutils literal\"><span class=\"pre\">argcheck</span></tt> - Standard tests for command line arguments","Loop Modeling","Documentation For Users","Changelog","Welcome to ProMod3&#8217;s documentation!","Building ProMod3","Raw Coordinate Modeling","<tt class=\"docutils literal\"><span class=\"pre\">core</span></tt> - ProMod3 core functionality","Contributing","<tt class=\"docutils literal\"><span class=\"pre\">meld</span></tt> - Coordinate modeling","Documentation For Developes"],objects:{"promod3.core.argcheck":{FileExtension:[0,1,1,""],FileExists:[0,1,1,""]},"sm.meld.LoopCandidate":{correl:[1,3,1,""],clash_score:[1,3,1,""],allatom_score:[1,3,1,""],score:[1,3,1,""],reduced_score:[1,3,1,""],torsion_score:[1,3,1,""],InsertInto:[1,2,1,""],gap:[1,3,1,""],clash_sc_score:[1,3,1,""],ToEntity:[1,2,1,""],clash_bb_score:[1,3,1,""],coords:[1,3,1,""],packing_score:[1,3,1,""],RmsdTo:[1,2,1,""]},"sm.meld":{LoopCandidate:[1,4,1,""],LoopCandidates:[1,4,1,""],BuildRawModel:[6,1,1,""],RawModelingResult:[6,4,1,""]},"sm.meld.RawModelingResult":{model:[6,3,1,""],gaps:[6,3,1,""]},"sm.meld.LoopCandidates":{SortByScore:[1,2,1,""],model:[1,3,1,""],SortByCorrel:[1,2,1,""],Add:[1,2,1,""]},promod3:{core:[7,0,1,""],meld:[9,0,1,""]}},titleterms:{pre:[0,7,9],own:8,modul:8,argument:0,indic:4,raw:6,api:[1,6],file:0,tabl:4,run:5,your:8,unit:8,git:8,develop:10,welcom:4,how:8,parti:8,make:5,write:8,start:8,build:5,branch:8,test:[8,0],document:[8,4,10,2],promod3:[5,4,7],meld:9,"function":7,core:7,liter:[0,7,9],argcheck:0,contribut:8,chang:3,standard:0,coordin:[9,6],user:2,releas:3,cmake:[8,5],line:0,"class":[0,7,9],stage:8,third:8,changelog:3,directori:8,docutil:[0,7,9],introduct:[0,6],structur:8,issu:8,command:0,span:[0,7,9],model:[9,1,6],licens:8,loop:1,depend:5}})
\ No newline at end of file
+Search.setIndex({envversion:42,terms:{aln:6,all:[8,0,1,4,6],code:[8,0,4],forget:[8,4],chain:[8,6],messi:8,skip:8,forbidden:8,sidechains_unit_test:8,ost:[0,1,2,3,4,5,6,7,8,9,10],disable_document:[8,4],prefix:[8,0],concept:8,subclass:8,abil:8,follow:[8,6],middl:8,structuralgap:1,readabl:8,init:8,program:7,under:8,introduc:8,sourc:[8,0,4],everi:[8,6],string:0,fals:[8,0,1,6],internet:8,candid:1,worst:8,failur:[8,0],veri:[8,0],affect:8,runnabl:8,tri:6,four:1,magic:8,level:[8,4],did:8,list:[8,0,1,4,6],assertequ:8,item:[8,6],fileextens:0,smallish:[8,4],align:6,dir:8,malici:8,promod_gcc_45:8,your_modul:8,direct:8,past:8,second:6,design:0,pass:8,download:4,acid:6,even:[8,4],index:[8,3],what:[8,0,4],hide:8,sub:8,resembl:8,sum:1,invok:[8,4],anywai:8,current:8,delet:6,version:[8,4],"new":[8,1,6],boost:[0,1,2,3,4,5,6,7,8,9,10],method:1,meld:[8,5],subtre:8,submodule1:8,honour:1,gener:8,never:8,here:[8,0,4,6],lib_stage_path:8,let:8,set_directory_properti:8,path:[8,0,4],along:8,modifi:[8,6,5],implicit:4,valu:[4,0],wait:8,test_someth:8,search:[8,3,4],executable_output_path:8,setup_boost:8,promod3_version_minor:8,doctest:[8,4],action:8,implement:8,pack:1,honor:6,chanc:8,methionin:6,via:8,extra:8,solut:8,modul:5,submodul:8,ask:8,unix:8,api:[8,9],instal:[8,4],total:1,unit:[],highli:4,fed:8,from:[0,1,5,4,6,8,9],describ:0,would:[8,4],regist:8,two:8,next:8,everybodi:8,few:[8,4,1,6],live:8,call:[8,4],recommend:4,loadalign:6,checkout:8,tell:[8,0],tightli:8,more:[8,4,6],sort:1,trustworthi:8,peopl:8,relat:8,notic:8,warn:8,flag:[8,0],include_directori:8,particular:8,known:0,rare:8,hold:[1,6],cach:[8,4],must:8,ost_double_precis:4,py_run:8,hous:8,setup:[8,5],work:[8,4],histori:8,remain:6,paragraph:8,can:[8,0,4,6],torsion_scor:1,purpos:8,root:8,fetch:[8,0],def:8,control:8,give:8,process:8,add_argu:0,indic:[],topic:8,abort:8,want:[8,4],phrase:8,backbonelist:1,hydrogen:6,packing_scor:1,alwai:8,gcc:8,cours:8,end:[8,0,1,4],thing:[8,4],rather:8,peptid:[1,6],comfort:0,calpha_onli:6,"__init__":8,opt:0,instead:[8,0,4],config:8,updat:8,python_vers:8,product:8,entityhandl:[1,6],rebas:8,mess:8,dive:8,after:[8,4],usabl:8,sortbyscor:1,befor:8,wrong:4,attent:8,date:8,multipl:8,data:8,grow:6,man:[8,4],subsequ:6,"short":8,practic:8,mol_alg:8,sit:8,correspond:[8,1],stash:8,exclud:8,alias:8,"switch":8,maintain:8,environ:8,allow:8,exclus:8,order:1,origin:8,promod3_version_major:8,eigen:4,over:[8,4,6],insight:8,becaus:[8,4],increas:1,through:8,files_to_be_remov:8,gitignor:8,still:8,pointer:4,entiti:[8,1],perfect:8,output_vari:8,funni:4,fix:[8,0],selenium:6,structuralgaplist:6,relev:4,carri:[8,0],complex:8,onc:8,python_doc_url:8,therefor:8,easier:1,linkcheck:[8,4],them:8,good:8,"return":[0,1,6],thei:[8,4,1],python:[0,1,2,3,4,5,6,7,8,9,10],dai:0,exot:8,"break":8,framework:8,conquer:8,clash_bb_scor:1,verifi:0,front:[8,0,4],now:[8,6],minimalist:6,cmake_cxx_flags_releas:8,libexec_stage_path:8,name:[8,0],rmsd:1,anyth:[8,4],separ:8,easili:8,achiev:8,each:8,debug:8,found:8,went:8,higher:4,side:8,mean:[8,0,4],compil:8,monolith:8,parwis:6,strip:6,idea:[8,5],realli:[8,0,4],runtest:8,"static":8,coord:1,our:8,special:[8,4],out:[8,4],variabl:[8,4],shown:8,goe:[8,4],promod3_unittest:8,crucial:8,content:[8,3,10],reader:8,print:[4,6],got:4,exec_program:8,clone:8,common:[8,0],model:[],make_directori:8,runtimeerror:[1,6],given:[0,1],free:8,standard:8,headlin:8,reason:8,base:[0,6],term:8,put:[8,0,4],org:8,basi:8,could:[8,6],keep:8,turn:[8,0],clash_sc_scor:1,place:8,think:8,first:[8,5],oper:8,softwar:8,major:8,suffix:0,obviou:8,prevent:8,feel:8,sidechains_pymod:8,number:[1,6],yourself:[8,4],restrict:8,mai:[8,4,6],alreadi:8,done:8,least:[8,4],blank:8,stabl:8,miss:[0,1,6],exit_statu:0,differ:[8,4],script:[8,0,4],top:[8,4],perfectli:8,mkdir:8,system:[8,4,5],messag:[8,0],tradition:0,attach:6,stori:8,master:8,too:8,termin:0,scheme:8,"final":[8,6],store:[8,1,6],shell:[4,0],option:[8,0,4],tool:0,copi:[8,6],restrict_chain:6,openstructur:[0,1,2,3,4,5,6,7,8,9,10],part:8,pars:0,boost_include_dir:8,mostli:8,rst:8,conop:8,exactli:4,than:8,kind:8,grep:4,target:[8,4],whenev:8,provid:[8,4],seamlessli:8,tree:8,unrecognis:0,project:8,find_packag:8,reus:6,str:[0,6],were:8,posit:[0,1],toward:8,markup:8,pre:8,python_binari:8,sometim:8,mind:8,argument:[],packag:8,manner:8,have:[8,4,1,6],"__main__":8,need:[8,0,4],fasta:6,tidi:8,cmake_current_source_dir:8,optimis:8,rmsdto:1,imagin:8,built:8,advic:8,inform:6,diverg:8,self:8,also:[8,0,4,6],without:[8,0,6],take:[8,6],which:[8,4,6,7],thoroughli:8,noth:8,singl:[8,6],"_opt":8,sure:8,distribut:8,clash:1,track:0,buildrawmodel:6,compress:0,strict:8,somethingtest:8,fragment:1,hotfix:8,"class":8,charg:8,renam:5,url:8,doc:[8,4],later:8,cover:[8,0,7],doe:[8,0,6],ext:0,declar:8,clean:[8,4],usual:[8,4],someth:8,came:8,cmakelist:[8,4],show:8,dbg:8,attachview:6,bring:8,permiss:8,add_doc_sourc:8,fine:8,find:8,help:[8,4],involv:8,access:1,onli:[8,0,6],locat:4,explain:8,configur:[8,4],activ:8,state:[8,4],should:[8,0],score:1,suppos:[8,1],templat:6,folder:8,move:8,hit:8,unus:8,variou:4,get:[8,4],watch:8,cannot:8,loadpdb:6,report:[8,6],toolbox:8,requir:[8,4,1],setup_compiler_flag:8,add_changelog_to_doc:8,candit:1,enabl:0,"2b1":4,gather:[8,7],whether:0,"float":1,integr:8,contain:[8,0,4,6,9],python_root:4,where:8,remov:4,view:8,user:[],set:[8,0,1,4,6],seq:8,allatom_scor:1,frame:8,around:8,ost_include_dir:8,see:8,temporarili:8,result:[4,6],smng:5,arg:8,testcas:8,reserv:0,sport:8,servic:8,subject:8,awar:8,statu:8,detect:0,parent:6,review:8,version_great:8,enumer:8,label:8,figur:8,header_stage_path:8,subdir:8,simplest:8,"import":[8,0,4,6],awai:8,paramet:[0,1,6],approach:8,attribut:8,accord:8,extend:8,sole:8,cmake_cxx_compiler_vers:8,test_your_modul:8,solv:8,come:[8,0],addit:[8,0],fail:[8,1],extens:[0,1],howev:1,disable_doctest:[8,4],promod3_version_patch:8,tutori:8,grain:8,fno:8,modif:6,whole:[8,6],pdb:[0,6],comment:8,sidechains_rst:8,"1ake":6,point:[8,4,1],cxx:8,overview:8,unittest:8,argumentpars:0,pop:8,walk:8,residu:[1,6],header:[8,4],param:1,codetest:8,test_submodule1:8,assum:8,torsion:1,quit:8,template_structur:6,evalu:8,coupl:8,rebuild:[8,4],three:8,been:8,sinc:[8,0,4],compon:8,trigger:8,besid:4,treat:[8,6],basic:[8,4,6],ost_root:[8,4],popul:[8,4],seq_alg:8,tini:8,quickli:8,life:[8,1],convert:6,ani:8,coordin:[],togeth:8,input:0,fileexist:0,educ:8,those:[8,4],"case":8,cmake_c_compiler_vers:8,uncertain:8,look:[8,0],raw:9,testfileexistsfals:8,straight:8,properti:8,commerci:8,formatt:8,calcul:1,match:[8,6],abov:8,error:0,per:[8,7],dost_root:[8,4],loop:9,stage_dir:8,spawn:8,real:8,test_sidechain:8,helper:1,readi:4,sidechain:[8,1,6],henc:8,non:8,itself:8,clutter:8,conf:[8,4],protein:[9,6],dedic:[8,4],sever:[8,4],reviv:8,disabl:8,develop:8,fedora:8,etc:8,author:8,suggest:8,belong:8,savepdb:6,same:[4,1],"while":[8,0],member:[8,6],binari:8,drawback:8,admir:8,document:5,conflict:8,complet:[8,6],http:8,cmakecach:4,optim:[8,4],bienchen:8,argpars:0,hand:4,driven:8,moment:8,rais:[1,6],disable_linkcheck:[8,4],initi:5,extern:8,respons:8,stack:8,expand:8,recent:8,task:8,off:[8,6],pymod:8,nevertheless:8,macro:8,builder:4,well:[8,4,1,6],exampl:[8,4,6],command:8,branchnam:8,thi:[0,1,4,6,7,8,9],endif:8,gzip:0,everyth:8,academ:8,loss:8,spend:8,latest:4,cmake_support:8,clash_scor:1,just:[8,4],entri:8,mol:8,reduced_scor:1,obtain:6,rest:[0,1,2,3,4,5,6,7,8,9,10],touch:8,web:[8,4],loopcandid:1,restructuredtext:[0,1,2,3,4,5,6,7,8,9,10],makefil:[8,4],except:8,littl:8,add:[8,1],densiti:1,els:8,save:8,boost_root:4,bin:8,advis:8,format:8,handl:6,specimen:0,setup_stag:8,piec:8,source2:8,source1:8,know:4,background:4,elabor:8,bit:[8,4],cmake_compiler_is_gnucxx:8,mod:8,eigen3_include_dir:4,insert:[1,6],like:[8,4,6],success:[0,1],incred:6,manual:[8,4],html:[8,4,5],test_:8,test_awesome_featur:8,"boolean":0,either:[8,6],output:[8,0],hook:8,page:[8,3,4],www:8,right:[8,4],often:[8,0],acknowledg:8,some:[8,0,4],begin:8,resolv:8,intern:8,proper:8,librari:8,qmean:[8,4],thu:0,txt:[8,4],lead:0,avoid:8,definit:8,legal:8,exit:0,select:6,recognis:8,sequenc:[9,1,6],condit:8,amino:6,core:8,plu:8,cmake_source_dir:8,backbon:[1,6],step:8,promot:8,repositori:[8,5],"__name__":8,cmake_minimum_requir:8,intervent:8,mmcif:0,stage:[],chapter:8,src:8,about:[8,6],actual:[8,1],most:[8,0,6],materi:8,manag:8,coars:8,commit:8,ost_doc_url:8,produc:4,qmean_root:[8,4],within:[8,4],automat:[8,0],due:[1,6],promod3_version_str:8,empti:8,cmake_cxx_flag:8,cmake_module_path:8,announc:8,your:[],merg:8,git:5,fill:8,log:8,wai:[8,4],pictur:8,qmean_include_dir:8,support:[8,0],renumb:6,custom:8,avail:[8,4],lost:8,sortbycorrel:1,much:[8,6],interfac:8,includ:[8,0,5],lot:[8,0],suit:8,forward:8,parse_arg:0,unfortun:8,"function":8,headach:8,unexpect:4,enough:8,tupl:0,forg:8,wno:8,back:8,link:[8,4],atom:[1,6],don:[8,4],line:8,inlin:8,"true":[8,0,1,6],bug:8,pull:[8,4],tripl:0,immedi:8,consist:8,possibl:[8,6],"default":[8,4],type:[0,1,6],insertinto:1,displai:0,below:8,otherwis:8,problem:8,similar:4,testutil:8,featur:8,creat:[8,4],"int":0,certain:4,utilis:[8,0],fellow:8,incomplet:6,exist:[8,0,1],file:8,dqmean_root:[8,4],deuterium:6,check:[8,0,4],probabl:[8,4],echo:8,again:[8,4],calpha:6,when:[8,6],detail:[8,6],other:[8,4,6],bool:[0,1],seem:8,test:[],you:[8,0,4],phosphoserin:6,nice:8,correl:1,bb_list:1,toentiti:1,additional_make_clean_fil:8,determin:0,rawmodelingresult:6,devot:7,cmake_build_typ:8,add_subdirectori:8,briefli:8,consid:8,gap:[1,6],homolog:7,doptim:8,fatal_error:8,stai:8,reduc:1,sphinx:[0,1,2,3,4,5,6,7,8,9,10],algorithm:6,project_binary_dir:8,directori:[],descript:8,pseudo:6,rule:8,ignor:6,time:[8,6],push:8},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:attribute","4":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","class","Python class"]},filenames:["core/argcheck","meld/loop","users","index","buildsystem","changelog","meld/rawmodel","core/index","contributing","meld/index","developers"],titles:["<tt class=\"docutils literal\"><span class=\"pre\">argcheck</span></tt> - Standard tests for command line arguments","Loop Modeling","Documentation For Users","Welcome to ProMod3&#8217;s documentation!","Building ProMod3","Changelog","Raw Coordinate Modeling","<tt class=\"docutils literal\"><span class=\"pre\">core</span></tt> - ProMod3 core functionality","Contributing","<tt class=\"docutils literal\"><span class=\"pre\">meld</span></tt> - Coordinate modeling","Documentation For Developes"],objects:{"promod3.core.argcheck":{FileExtension:[0,1,1,""],FileExists:[0,1,1,""]},"sm.meld.LoopCandidate":{correl:[1,3,1,""],clash_score:[1,3,1,""],allatom_score:[1,3,1,""],score:[1,3,1,""],reduced_score:[1,3,1,""],torsion_score:[1,3,1,""],InsertInto:[1,2,1,""],gap:[1,3,1,""],clash_sc_score:[1,3,1,""],ToEntity:[1,2,1,""],clash_bb_score:[1,3,1,""],coords:[1,3,1,""],packing_score:[1,3,1,""],RmsdTo:[1,2,1,""]},"sm.meld":{LoopCandidate:[1,4,1,""],LoopCandidates:[1,4,1,""],BuildRawModel:[6,1,1,""],RawModelingResult:[6,4,1,""]},"sm.meld.RawModelingResult":{model:[6,3,1,""],gaps:[6,3,1,""]},"sm.meld.LoopCandidates":{SortByScore:[1,2,1,""],model:[1,3,1,""],SortByCorrel:[1,2,1,""],Add:[1,2,1,""]},promod3:{core:[7,0,1,""],meld:[9,0,1,""]}},titleterms:{pre:[0,7,9],model:[9,1,6],own:8,modul:8,argument:0,indic:3,raw:6,api:[1,6],file:0,tabl:3,argcheck:0,your:8,unit:8,git:8,develop:10,welcom:3,start:8,parti:8,make:4,write:8,how:8,build:4,branch:8,test:[8,0],document:[8,3,10,2],promod3:[4,3,7],meld:9,"function":7,core:7,liter:[0,7,9],run:4,contribut:8,standard:0,coordin:[9,6],user:2,releas:5,cmake:[8,4],line:0,"class":[0,7,9],stage:8,third:8,changelog:5,directori:8,docutil:[0,7,9],introduct:[0,6],structur:8,issu:8,command:0,span:[0,7,9],chang:5,licens:8,loop:1,depend:4}})
\ No newline at end of file
diff --git a/doc/html/users.html b/doc/html/users.html
index 1a37587fdd946ddb792483677bd3853567f0414d..c8ec2e27d2c360173a4329367603feb19db3c4c7 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -110,7 +110,7 @@
     </div>
     <div class="footer">
         &copy; Copyright 2013, Bienchen.
-      Last updated on Aug 07 11:54, 2014.
+      Last updated on Aug 11 08:42, 2014.
       Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
     </div>
   </body>