Update docs for version 1.5.1

BSC-CNS-EAPM · Jun 7, 2018 · 14b1b20 · 14b1b20
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diff --git a/AdaptivePELE/docs/Changelog.rst b/AdaptivePELE/docs/Changelog.rst
@@ -6,6 +6,28 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_.
 
+1.5.1 - 2018-06-07
+--------------------
+
+New features:
+.............
+
+    - The extractCoords script now works seemesly with pdb or xtc trajectories
+
+Behaviour changes from previous version:
+........................................
+
+
+    - Improve the speed of handling xtc trajectories by switching to the
+      low-level API of mdtraj
+    - Optimize and parallelize extractCoords script from the freeEnergies
+      subpackage, change the multiprocess module to multiprocessing
+
+Bug fixes:
+..........
+
+    - Fix several bugs in extractCoords script
+
 1.5 - 2018-05-11
 -------------------------------
 

diff --git a/AdaptivePELE/docs/conf.py b/AdaptivePELE/docs/conf.py
@@ -17,6 +17,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #sys.path.insert(0, os.path.abspath('.'))
+import AdaptivePELE as a
 
 # -- General configuration -----------------------------------------------------
 
@@ -48,7 +49,8 @@
 # built documents.
 #
 # The short X.Y version.
-version = 'v1.5'
+
+version = 'v%s' % a.__version__
 # The full version, including alpha/beta/rc tags.
 release = ''
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,12 +16,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
     - Optimize and parallelize extractCoords script from the freeEnergies
       subpackage, change the multiprocess module to multiprocessing
 
-
 ### Bug fixes:
 
     - Fix several bugs in extractCoords script
 
-
 ## [1.5] - 2018-05-11
 
 ### New features:

diff --git a/docs/AdaptivePELE.analysis.html b/docs/AdaptivePELE.analysis.html
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 

diff --git a/docs/AdaptivePELE.atomset.html b/docs/AdaptivePELE.atomset.html
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 
@@ -389,11 +389,6 @@ <h1>atomset Package<a class="headerlink" href="#atomset-package" title="Permalin
 </table>
 </dd></dl>
 
-<dl class="method">
-<dt id="AdaptivePELE.atomset.atomset.PDB.createSelectionString">
-<code class="descname">createSelectionString</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#AdaptivePELE.atomset.atomset.PDB.createSelectionString" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
 <dl class="method">
 <dt id="AdaptivePELE.atomset.atomset.PDB.extractCOM">
 <code class="descname">extractCOM</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#AdaptivePELE.atomset.atomset.PDB.extractCOM" title="Permalink to this definition">¶</a></dt>

diff --git a/docs/AdaptivePELE.clustering.html b/docs/AdaptivePELE.clustering.html
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 
@@ -88,7 +88,7 @@
 
                 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="Examples.html">User Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Problems.html">Frequently Asked Questions</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="AdaptivePELE.html">AdaptivePELE – Package Description</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.adaptiveSampling"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.automateRoundsAdaptive"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
@@ -110,6 +110,7 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
 </ul>
 
 

diff --git a/docs/AdaptivePELE.html b/docs/AdaptivePELE.html
@@ -64,7 +64,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 

diff --git a/docs/AdaptivePELE.simulation.html b/docs/AdaptivePELE.simulation.html
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 
@@ -88,7 +88,7 @@
 
                 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="Examples.html">User Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Problems.html">Frequently Asked Questions</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="AdaptivePELE.html">AdaptivePELE – Package Description</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.adaptiveSampling"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.automateRoundsAdaptive"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
@@ -108,6 +108,7 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
 </ul>
 
 

diff --git a/docs/AdaptivePELE.spawning.html b/docs/AdaptivePELE.spawning.html
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 
@@ -88,7 +88,7 @@
 
                 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="Examples.html">User Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Problems.html">Frequently Asked Questions</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="AdaptivePELE.html">AdaptivePELE – Package Description</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.adaptiveSampling"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.automateRoundsAdaptive"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
@@ -110,6 +110,7 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
 </ul>
 
 

diff --git a/docs/AdaptivePELE.utilities.html b/docs/AdaptivePELE.utilities.html
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 
@@ -88,7 +88,7 @@
 
                 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="Examples.html">User Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Problems.html">Frequently Asked Questions</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="AdaptivePELE.html">AdaptivePELE – Package Description</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.adaptiveSampling"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.automateRoundsAdaptive"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
@@ -108,6 +108,7 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
 </ul>
 
 
@@ -501,6 +502,11 @@ <h1>utilities Package<a class="headerlink" href="#utilities-package" title="Perm
 </table>
 </dd></dl>
 
+<dl class="function">
+<dt id="AdaptivePELE.utilities.utilities.writeObject">
+<code class="descclassname">AdaptivePELE.utilities.utilities.</code><code class="descname">writeObject</code><span class="sig-paren">(</span><em>filename</em>, <em>object_to_write</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/AdaptivePELE/utilities/utilities.html#writeObject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#AdaptivePELE.utilities.utilities.writeObject" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
 <dl class="function">
 <dt id="AdaptivePELE.utilities.utilities.write_PDB_clusters">
 <code class="descclassname">AdaptivePELE.utilities.utilities.</code><code class="descname">write_PDB_clusters</code><span class="sig-paren">(</span><em>pmf_xyzg</em>, <em>title=u'clusters.pdb'</em>, <em>use_beta=False</em>, <em>elements=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/AdaptivePELE/utilities/utilities.html#write_PDB_clusters"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#AdaptivePELE.utilities.utilities.write_PDB_clusters" title="Permalink to this definition">¶</a></dt>

diff --git a/docs/AdaptivePELE.validator.html b/docs/AdaptivePELE.validator.html
@@ -35,6 +35,7 @@
         <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="AdaptivePELE  documentation" href="index.html"/>
         <link rel="up" title="AdaptivePELE – Package Description" href="AdaptivePELE.html"/>
+        <link rel="next" title="Changelog" href="Changelog.html"/>
         <link rel="prev" title="utilities Package" href="AdaptivePELE.utilities.html"/> 
 
 
@@ -64,7 +65,7 @@
 
 
               <div class="version">
-                v1.5
+                v1.5.1
               </div>
 
 
@@ -87,7 +88,7 @@
 
                 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="Examples.html">User Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Problems.html">Frequently Asked Questions</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="AdaptivePELE.html">AdaptivePELE – Package Description</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.adaptiveSampling"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.automateRoundsAdaptive"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
@@ -106,6 +107,7 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="Changelog.html">Changelog</a></li>
 </ul>
 
 
@@ -238,6 +240,8 @@ <h1>validator Package<a class="headerlink" href="#validator-package" title="Perm
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
+        <a href="Changelog.html" class="btn btn-neutral float-right" title="Changelog" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+
 
         <a href="AdaptivePELE.utilities.html" class="btn btn-neutral" title="utilities Package" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-Original file line number
+Diff line change
@@ Expand Up / @@ -65,7 +65,7 @@ @@
                   <div class="version">
-                    v1.5
+                    v1.5.1
                   </div>
@@ Expand Down @@