Rename to scoria

durrantlab · Jan 13, 2017 · 269a02a · 269a02a
1 parent 474330c
commit 269a02a
Show file tree

Hide file tree

Showing 109 changed files with 1,571 additions and 1,553 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
 # List files you want to ignore here
 *.pym
 *.pyc
-pymolecule_tests_tmp
+scoria_tests_tmp
 rsync_htc.bash
diff --git a/README.md b/README.md
@@ -1,3 +1,3 @@
-# PyMolecule
+# scoria
 
-The PyMolecule library is a lightweight code base for importing, exporting, and manipulating molecular models. 
+The scoria library is a lightweight code base for importing, exporting, and manipulating molecular models. 
diff --git a/benchmarks.py b/benchmarks.py
@@ -1,3 +1,3 @@
-import pymolecule
-from pymolecule.Test import FileIOBenchmarks
+import scoria
+from scoria.Test import FileIOBenchmarks
 FileIOBenchmarks()
diff --git a/conda_setup.sh b/conda_setup.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
 conda config --add channels MDAnalysis
-conda create --name pymolecule numpy scipy mdanalysis
+conda create --name scoria numpy scipy mdanalysis
 
-source activate pymolecule
+source activate scoria
diff --git a/docs/Makefile b/docs/Makefile
@@ -91,9 +91,9 @@ qthelp:
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Pymolecule20.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/scoria0.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Pymolecule20.qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/scoria0.qhc"
 
 .PHONY: applehelp
 applehelp:
@@ -110,8 +110,8 @@ devhelp:
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/Pymolecule20"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Pymolecule20"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/scoria0"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/scoria0"
 	@echo "# devhelp"
 
 .PHONY: epub

diff --git a/docs/build/html/AtomsAndBonds.html b/docs/build/html/AtomsAndBonds.html
diff --git a/docs/build/html/FileIO.html b/docs/build/html/FileIO.html
diff --git a/docs/build/html/Geometry.html b/docs/build/html/Geometry.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>4. pymolecule.Geometry module &#8212; PyMolecule 2.0 documentation</title>
+    <title>4. scoria.Geometry module &#8212; scoria 2.0 documentation</title>
 
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -23,8 +23,8 @@
     <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>
-    <link rel="top" title="PyMolecule 2.0 documentation" href="index.html" />
-    <link rel="next" title="5. pymolecule.Information module" href="Information.html" />
+    <link rel="top" title="scoria 2.0 documentation" href="index.html" />
+    <link rel="next" title="5. scoria.Information module" href="Information.html" />
     <link rel="prev" title="3. The FileIO Class" href="FileIO.html" /> 
   </head>
   <body role="document">
@@ -38,12 +38,12 @@ <h3>Navigation</h3>
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="Information.html" title="5. pymolecule.Information module"
+          <a href="Information.html" title="5. scoria.Information module"
              accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="FileIO.html" title="3. The FileIO Class"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">PyMolecule 2.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">scoria 2.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -52,19 +52,19 @@ <h3>Navigation</h3>
         <div class="bodywrapper">
           <div class="body" role="main">
 
-  <div class="section" id="module-pymolecule.Geometry">
-<span id="pymolecule-geometry-module"></span><h1>4. pymolecule.Geometry module<a class="headerlink" href="#module-pymolecule.Geometry" title="Permalink to this headline">¶</a></h1>
+  <div class="section" id="module-scoria.Geometry">
+<span id="scoria-geometry-module"></span><h1>4. scoria.Geometry module<a class="headerlink" href="#module-scoria.Geometry" title="Permalink to this headline">¶</a></h1>
 <dl class="class">
-<dt id="pymolecule.Geometry.Geometry">
-<em class="property">class </em><code class="descclassname">pymolecule.Geometry.</code><code class="descname">Geometry</code><span class="sig-paren">(</span><em>parent_molecule_object</em><span class="sig-paren">)</span><a class="headerlink" href="#pymolecule.Geometry.Geometry" title="Permalink to this definition">¶</a></dt>
+<dt id="scoria.Geometry.Geometry">
+<em class="property">class </em><code class="descclassname">scoria.Geometry.</code><code class="descname">Geometry</code><span class="sig-paren">(</span><em>parent_molecule_object</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Geometry.Geometry" title="Permalink to this definition">¶</a></dt>
 <dd><p>A class containing a few geometry functions. Note that numpy should be
 used for most geometry functions.</p>
 <dl class="method">
-<dt id="pymolecule.Geometry.Geometry.get_angle_between_three_points">
-<code class="descname">get_angle_between_three_points</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em><span class="sig-paren">)</span><a class="headerlink" href="#pymolecule.Geometry.Geometry.get_angle_between_three_points" title="Permalink to this definition">¶</a></dt>
+<dt id="scoria.Geometry.Geometry.get_angle_between_three_points">
+<code class="descname">get_angle_between_three_points</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Geometry.Geometry.get_angle_between_three_points" title="Permalink to this definition">¶</a></dt>
 <dd><p>Computes the angle (in radians) formed by three points (numpy.array
 objects).</p>
-<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#pymolecule.Molecule.Molecule.get_angle_between_three_points" title="pymolecule.Molecule.Molecule.get_angle_between_three_points"><code class="xref py py-meth docutils literal"><span class="pre">get_angle_between_three_points()</span></code></a></p>
+<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.get_angle_between_three_points" title="scoria.Molecule.Molecule.get_angle_between_three_points"><code class="xref py py-meth docutils literal"><span class="pre">get_angle_between_three_points()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -88,11 +88,11 @@ <h3>Navigation</h3>
 </dd></dl>
 
 <dl class="method">
-<dt id="pymolecule.Geometry.Geometry.get_dihedral_angle">
-<code class="descname">get_dihedral_angle</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em>, <em>pt4</em><span class="sig-paren">)</span><a class="headerlink" href="#pymolecule.Geometry.Geometry.get_dihedral_angle" title="Permalink to this definition">¶</a></dt>
+<dt id="scoria.Geometry.Geometry.get_dihedral_angle">
+<code class="descname">get_dihedral_angle</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em>, <em>pt4</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Geometry.Geometry.get_dihedral_angle" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculates the dihedral angle formed by four points (numpy.array
 objects).</p>
-<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#pymolecule.Molecule.Molecule.get_dihedral_angle" title="pymolecule.Molecule.Molecule.get_dihedral_angle"><code class="xref py py-meth docutils literal"><span class="pre">get_dihedral_angle()</span></code></a></p>
+<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.get_dihedral_angle" title="scoria.Molecule.Molecule.get_dihedral_angle"><code class="xref py py-meth docutils literal"><span class="pre">get_dihedral_angle()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -118,11 +118,11 @@ <h3>Navigation</h3>
 </dd></dl>
 
 <dl class="method">
-<dt id="pymolecule.Geometry.Geometry.get_planarity_deviation">
-<code class="descname">get_planarity_deviation</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em>, <em>pt4</em><span class="sig-paren">)</span><a class="headerlink" href="#pymolecule.Geometry.Geometry.get_planarity_deviation" title="Permalink to this definition">¶</a></dt>
+<dt id="scoria.Geometry.Geometry.get_planarity_deviation">
+<code class="descname">get_planarity_deviation</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em>, <em>pt4</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Geometry.Geometry.get_planarity_deviation" title="Permalink to this definition">¶</a></dt>
 <dd><p>Determines how close four points (numpy.array objects) come to lying
 in a common plane.</p>
-<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#pymolecule.Molecule.Molecule.get_planarity_deviation" title="pymolecule.Molecule.Molecule.get_planarity_deviation"><code class="xref py py-meth docutils literal"><span class="pre">get_planarity_deviation()</span></code></a></p>
+<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.get_planarity_deviation" title="scoria.Molecule.Molecule.get_planarity_deviation"><code class="xref py py-meth docutils literal"><span class="pre">get_planarity_deviation()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -144,10 +144,10 @@ <h3>Navigation</h3>
 </dd></dl>
 
 <dl class="method">
-<dt id="pymolecule.Geometry.Geometry.is_planar">
-<code class="descname">is_planar</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em>, <em>pt4</em>, <em>planarity_cutoff=0.2</em><span class="sig-paren">)</span><a class="headerlink" href="#pymolecule.Geometry.Geometry.is_planar" title="Permalink to this definition">¶</a></dt>
+<dt id="scoria.Geometry.Geometry.is_planar">
+<code class="descname">is_planar</code><span class="sig-paren">(</span><em>pt1</em>, <em>pt2</em>, <em>pt3</em>, <em>pt4</em>, <em>planarity_cutoff=0.2</em><span class="sig-paren">)</span><a class="headerlink" href="#scoria.Geometry.Geometry.is_planar" title="Permalink to this definition">¶</a></dt>
 <dd><p>Checks whether four points (numpy.array) lie in a common plane.</p>
-<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#pymolecule.Molecule.Molecule.is_planar" title="pymolecule.Molecule.Molecule.is_planar"><code class="xref py py-meth docutils literal"><span class="pre">is_planar()</span></code></a></p>
+<p>Should be called via the wrapper function <a class="reference internal" href="Molecule.html#scoria.Molecule.Molecule.is_planar" title="scoria.Molecule.Molecule.is_planar"><code class="xref py py-meth docutils literal"><span class="pre">is_planar()</span></code></a></p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -185,7 +185,7 @@ <h4>Previous topic</h4>
                         title="previous chapter">3. The FileIO Class</a></p>
   <h4>Next topic</h4>
   <p class="topless"><a href="Information.html"
-                        title="next chapter">5. pymolecule.Information module</a></p>
+                        title="next chapter">5. scoria.Information module</a></p>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
@@ -217,12 +217,12 @@ <h3>Navigation</h3>
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="right" >
-          <a href="Information.html" title="5. pymolecule.Information module"
+          <a href="Information.html" title="5. scoria.Information module"
              >next</a> |</li>
         <li class="right" >
           <a href="FileIO.html" title="3. The FileIO Class"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">PyMolecule 2.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">scoria 2.0 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">