Merged branch master into master

scoria/docs/build/html/FileIO.html → docs/build/html/FileIO.html

@@ -58,7 +58,7 @@ <h1>4. The FileIO Class<a class="headerlink" href="#the-fileio-class" title="Per
 <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-formats" title="Permalink to this headline">¶</a></h2>
 <p>Scoria can naitvely read and write PDB, PDBQT, and PYM files. It
 can also read multiframe PDB and PDBQT files. It also has the ability
-to import information from <a class="reference external" href="https://pythonhosted.org/MDAnalysis/documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup" title="(in MDAnalysis v0.15)"><code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code></a> objects.</p>
+to import information from <code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code> objects.</p>
 </div>
 <div class="section" id="module-scoria.FileIO">
 <span id="function-definitions"></span><h2>4.2. Function Definitions<a class="headerlink" href="#module-scoria.FileIO" title="Permalink to this headline">¶</a></h2>
@@ -71,7 +71,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 <dt id="scoria.FileIO.FileIO.load_MDAnalysis_into">
 <code class="descname">load_MDAnalysis_into</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_MDAnalysis_into" title="Permalink to this definition">¶</a></dt>
 <dd><p>Allows import of molecular structure with MDAnalysis.</p>
-<p>Requires the <a class="reference external" href="https://pythonhosted.org/MDAnalysis/documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup" title="(in MDAnalysis v0.15)"><code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code></a> library.</p>
+<p>Requires the <code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code> library.</p>
 <p>Should be called via the wrapper function
 <code class="xref py py-meth docutils literal"><span class="pre">load_via_MDAnalysis()</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -89,7 +89,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 <dt id="scoria.FileIO.FileIO.load_MDAnalysis_into_using_universe_object">
 <code class="descname">load_MDAnalysis_into_using_universe_object</code><span class="sig-paren">(</span><em>universe</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_MDAnalysis_into_using_universe_object" title="Permalink to this definition">¶</a></dt>
 <dd><p>Allows import of molecular structure from an MDAnalysis object.</p>
-<p>Requires the <a class="reference external" href="https://pythonhosted.org/MDAnalysis/documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup" title="(in MDAnalysis v0.15)"><code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code></a> library.</p>
+<p>Requires the <code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code> library.</p>
 <p>Should be called via the wrapper function
 <code class="xref py py-meth docutils literal"><span class="pre">load_via_MDAnalysis()</span></code></p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -105,7 +105,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 
 <dl class="method">
 <dt id="scoria.FileIO.FileIO.load_pdb_into">
-<code class="descname">load_pdb_into</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds_by_distance=True</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em>, <em>is_trajectory=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_into" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_pdb_into</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds_by_distance=False</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em>, <em>is_trajectory=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_into" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads the molecular data contained in a pdb file into the current
 scoria.Molecule object.</p>
 <p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.load_pdb_into" title="scoria.Molecule.Molecule.load_pdb_into"><code class="xref py py-meth docutils literal"><span class="pre">load_pdb_into()</span></code></a></p>
@@ -133,7 +133,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 
 <dl class="method">
 <dt id="scoria.FileIO.FileIO.load_pdb_into_using_file_object">
-<code class="descname">load_pdb_into_using_file_object</code><span class="sig-paren">(</span><em>file_obj</em>, <em>bonds_by_distance=True</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em>, <em>is_trajectory=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_into_using_file_object" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_pdb_into_using_file_object</code><span class="sig-paren">(</span><em>file_obj</em>, <em>bonds_by_distance=False</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em>, <em>is_trajectory=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_into_using_file_object" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads molecular data from a python file object (pdb formatted) into
 the current scoria.Molecule object. Note that most users will want
 to use the load_pdb_into() function instead, which is identical except
@@ -165,7 +165,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 
 <dl class="method">
 <dt id="scoria.FileIO.FileIO.load_pdb_trajectory_into">
-<code class="descname">load_pdb_trajectory_into</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds_by_distance=True</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_trajectory_into" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_pdb_trajectory_into</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds_by_distance=False</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_trajectory_into" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads the molecular data contained in a pdb trajectory file into the
 current scoria.Molecule object.</p>
 <p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.load_pdb_trajectory_into" title="scoria.Molecule.Molecule.load_pdb_trajectory_into"><code class="xref py py-meth docutils literal"><span class="pre">scoria.Molecule.Molecule.load_pdb_trajectory_into()</span></code></a></p>
@@ -192,7 +192,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 
 <dl class="method">
 <dt id="scoria.FileIO.FileIO.load_pdb_trajectory_into_using_file_object">
-<code class="descname">load_pdb_trajectory_into_using_file_object</code><span class="sig-paren">(</span><em>file_obj</em>, <em>bonds_by_distance=True</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_trajectory_into_using_file_object" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_pdb_trajectory_into_using_file_object</code><span class="sig-paren">(</span><em>file_obj</em>, <em>bonds_by_distance=False</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdb_trajectory_into_using_file_object" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads molecular data from a python file object (pdb trajectory
 formatted) into the current scoria.Molecule object. Note that most
 users will want to use the load_pdb_trajectory_into() function
@@ -286,7 +286,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 
 <dl class="method">
 <dt id="scoria.FileIO.FileIO.load_pdbqt_trajectory_into">
-<code class="descname">load_pdbqt_trajectory_into</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds_by_distance=True</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdbqt_trajectory_into" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_pdbqt_trajectory_into</code><span class="sig-paren">(</span><em>filename</em>, <em>bonds_by_distance=False</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdbqt_trajectory_into" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads the molecular data contained in a pdbqt trajectoy file (e.g., an
 AutoDock Vina output file) into the current scoria.Molecule
 object.</p>
@@ -313,7 +313,7 @@ <h2>4.1. File Types and Formats<a class="headerlink" href="#file-types-and-forma
 
 <dl class="method">
 <dt id="scoria.FileIO.FileIO.load_pdbqt_trajectory_into_using_file_object">
-<code class="descname">load_pdbqt_trajectory_into_using_file_object</code><span class="sig-paren">(</span><em>file_obj</em>, <em>bonds_by_distance=True</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdbqt_trajectory_into_using_file_object" title="Permalink to this definition">¶</a></dt>
+<code class="descname">load_pdbqt_trajectory_into_using_file_object</code><span class="sig-paren">(</span><em>file_obj</em>, <em>bonds_by_distance=False</em>, <em>serial_reindex=True</em>, <em>resseq_reindex=False</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.FileIO.FileIO.load_pdbqt_trajectory_into_using_file_object" title="Permalink to this definition">¶</a></dt>
 <dd><p>Loads molecular data from a python file object (pdbqt trajectory
 formatted) into the current scoria.Molecule object. Note that most
 users will want to use the load_pdbqt_trajectory_into() function

scoria/docs/build/html/Molecule.html → docs/build/html/Molecule.html

@@ -24,8 +24,8 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <link rel="top" title="scoria 2.0 documentation" href="index.html" />
-    <link rel="next" title="2. The AtomsAndBonds Class" href="AtomsAndBonds.html" />
-    <link rel="prev" title="Welcome to scoria’s documentation!" href="index.html" /> 
+    <link rel="next" title="2. Scoria Demo" href="Demo.html" />
+    <link rel="prev" title="Welcome to Scoria’s documentation!" href="index.html" /> 
   </head>
   <body role="document">
     <div class="related" role="navigation" aria-label="related navigation">
@@ -38,10 +38,10 @@ <h3>Navigation</h3>
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="AtomsAndBonds.html" title="2. The AtomsAndBonds Class"
+          <a href="Demo.html" title="2. Scoria Demo"
              accesskey="N">next</a> |</li>
         <li class="right" >
-          <a href="index.html" title="Welcome to scoria’s documentation!"
+          <a href="index.html" title="Welcome to Scoria’s documentation!"
              accesskey="P">previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">scoria 2.0 documentation</a> &#187;</li> 
       </ul>
@@ -1328,7 +1328,7 @@ <h2>1.1. Initiating and using the object<a class="headerlink" href="#initiating-
 <dt id="scoria.Molecule.Molecule.load_MDAnalysis_into">
 <code class="descname">load_MDAnalysis_into</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Molecule.Molecule.load_MDAnalysis_into" title="Permalink to this definition">¶</a></dt>
 <dd><p>Allows import of molecular structure with MDAnalysis</p>
-<p>Requires the <a class="reference external" href="https://pythonhosted.org/MDAnalysis/documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup" title="(in MDAnalysis v0.15)"><code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code></a> library.</p>
+<p>Requires the <code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code> library.</p>
 <p>Wrapper function for 
 <a class="reference internal" href="FileIO.html#scoria.FileIO.FileIO.load_MDAnalysis_into" title="scoria.FileIO.FileIO.load_MDAnalysis_into"><code class="xref py py-meth docutils literal"><span class="pre">load_MDAnalysis_into()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -1346,7 +1346,7 @@ <h2>1.1. Initiating and using the object<a class="headerlink" href="#initiating-
 <dt id="scoria.Molecule.Molecule.load_MDAnalysis_into_using_universe_object">
 <code class="descname">load_MDAnalysis_into_using_universe_object</code><span class="sig-paren">(</span><em>universe</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Molecule.Molecule.load_MDAnalysis_into_using_universe_object" title="Permalink to this definition">¶</a></dt>
 <dd><p>Allows import of molecular structure with MDAnalysis</p>
-<p>Requires the <a class="reference external" href="https://pythonhosted.org/MDAnalysis/documentation_pages/core/AtomGroup.html#module-MDAnalysis.core.AtomGroup" title="(in MDAnalysis v0.15)"><code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code></a> library.</p>
+<p>Requires the <code class="xref any docutils literal"><span class="pre">MDAnalysis</span></code> library.</p>
 <p>Wrapper function for 
 <a class="reference internal" href="FileIO.html#scoria.FileIO.FileIO.load_MDAnalysis_into_using_universe_object" title="scoria.FileIO.FileIO.load_MDAnalysis_into_using_universe_object"><code class="xref py py-meth docutils literal"><span class="pre">load_MDAnalysis_into_using_universe_object()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
@@ -2354,10 +2354,10 @@ <h3><a href="index.html">Table Of Contents</a></h3>
 
   <h4>Previous topic</h4>
   <p class="topless"><a href="index.html"
-                        title="previous chapter">Welcome to scoria&#8217;s documentation!</a></p>
+                        title="previous chapter">Welcome to Scoria&#8217;s documentation!</a></p>
   <h4>Next topic</h4>
-  <p class="topless"><a href="AtomsAndBonds.html"
-                        title="next chapter">2. The AtomsAndBonds Class</a></p>
+  <p class="topless"><a href="Demo.html"
+                        title="next chapter">2. Scoria Demo</a></p>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
@@ -2389,10 +2389,10 @@ <h3>Navigation</h3>
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="AtomsAndBonds.html" title="2. The AtomsAndBonds Class"
+          <a href="Demo.html" title="2. Scoria Demo"
              >next</a> |</li>
         <li class="right" >
-          <a href="index.html" title="Welcome to scoria’s documentation!"
+          <a href="index.html" title="Welcome to Scoria’s documentation!"
              >previous</a> |</li>
         <li class="nav-item nav-item-0"><a href="index.html">scoria 2.0 documentation</a> &#187;</li> 
       </ul>