Commit bbe6d227 authored by pjropp's avatar pjropp
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Documentation update

parent d9b6ff86
......@@ -58,7 +58,7 @@
<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 @@ object.</p>
<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 @@ inizalize a MDAnalysis.Universe object.</td>
<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 @@ import.</td>
<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 @@ is multi-frame.</li>
<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 @@ is multi-frame.</li>
<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 @@ reindex the pdb resseq field. False by default.</li>
<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 @@ is multi-frame.</li>
<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 @@ reindex the pdb resseq field. False by default.</li>
<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
......
......@@ -24,8 +24,8 @@
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<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" />
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......@@ -38,10 +38,10 @@
<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" >
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......@@ -1328,7 +1328,7 @@ default is 0.2.</li>
<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 @@ inizalize a MDAnalysis.Universe object.</td>
<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 @@ amount to move each atom along the x, y, and z coordinates.</td>
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......@@ -2389,10 +2389,10 @@ amount to move each atom along the x, y, and z coordinates.</td>
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<a href="AtomsAndBonds.html" title="2. The AtomsAndBonds Class"
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<li class="right" >
<a href="index.html" title="Welcome to scoria’s documentation!"
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<li class="nav-item nav-item-0"><a href="index.html">scoria 2.0 documentation</a> &#187;</li>
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