deploy: e08f6c5

MDAnalysis · Aug 12, 2023 · 19d1620 · 19d1620
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: d6553e4ae935533548bbb3a1c54c2249
+config: de78a6819362ea551fa527ae87f4944d
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/gridData/OpenDX.html b/_modules/gridData/OpenDX.html
diff --git a/_modules/gridData/core.html b/_modules/gridData/core.html
diff --git a/_modules/gridData/gOpenMol.html b/_modules/gridData/gOpenMol.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gridData.gOpenMol &mdash; GridDataFormats 1.0.1+2.g069e535 documentation</title>
+  <title>gridData.gOpenMol &mdash; GridDataFormats 1.0.1+5.ge08f6c5 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
@@ -13,13 +13,11 @@
   <![endif]-->
 
         <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-        <script src="../../_static/jquery.js"></script>
-        <script src="../../_static/underscore.js"></script>
-        <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../../_static/doctools.js"></script>
+        <script src="../../_static/sphinx_highlight.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within GridDataFormats 1.0.1+2.g069e535 documentation"
+          title="Search within GridDataFormats 1.0.1+5.ge08f6c5 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -30,15 +28,19 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search"  style="background: white" >
-            <a href="../../index.html">
-            <img src="../../_static/mdanalysis-griddataformats-logo.png" class="logo" alt="Logo"/>
+
+
+
+          <a href="../../index.html">
+
+              <img src="../../_static/mdanalysis-griddataformats-logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 1.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -49,6 +51,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/overview.html">Handling grids of data — <code class="xref py py-mod docutils literal notranslate"><span class="pre">gridData</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/basic.html">Basic use</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/core.html">Core functionality for storing n-D grids — <code class="xref py py-mod docutils literal notranslate"><span class="pre">gridData.core</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../gridData/core.html#gridData.core.Grid"><code class="docutils literal notranslate"><span class="pre">Grid</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../gridData/core.html#gridData.core.ndmeshgrid"><code class="docutils literal notranslate"><span class="pre">ndmeshgrid()</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/formats.html">Formats</a></li>
 </ul>
 
@@ -65,9 +69,9 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../../index.html" class="icon icon-home"></a> &raquo;</li>
-          <li><a href="../index.html">Module code</a> &raquo;</li>
-      <li>gridData.gOpenMol</li>
+      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">gridData.gOpenMol</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
@@ -225,7 +229,7 @@ <h1>Source code for gridData.gOpenMol</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot;Record(</span><span class="si">%(key)r</span><span class="s2">,</span><span class="si">%(bintype)r</span><span class="s2">,...)&quot;</span> <span class="o">%</span> <span class="nb">vars</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
 
 <div class="viewcode-block" id="Plt"><a class="viewcode-back" href="../../gridData/formats/gOpenMol.html#gridData.gOpenMol.Plt">[docs]</a><span class="k">class</span> <span class="nc">Plt</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;A class to represent a gOpenMol_ plt file.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;A class to represent a gOpenMol_ plt file.</span>
 
 <span class="sd">    Only reading is implemented; either supply a filename to the constructor</span>
 <span class="sd">      &gt;&gt;&gt; G = Plt(filename)</span>
@@ -281,7 +285,7 @@ <h1>Source code for gridData.gOpenMol</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
 
 <div class="viewcode-block" id="Plt.read"><a class="viewcode-back" href="../../gridData/formats/gOpenMol.html#gridData.gOpenMol.Plt.read">[docs]</a>    <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Populate the instance from the plt file *filename*.&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Populate the instance from the plt file *filename*.&quot;&quot;&quot;</span>
         <span class="kn">from</span> <span class="nn">struct</span> <span class="kn">import</span> <span class="n">calcsize</span><span class="p">,</span> <span class="n">unpack</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="n">filename</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
@@ -303,7 +307,7 @@ <h1>Source code for gridData.gOpenMol</h1><div class="highlight"><pre>
 
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">edges</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Edges of the grid cells, origin at centre of 0,0,..,0 grid cell.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Edges of the grid cells, origin at centre of 0,0,..,0 grid cell.</span>
 
 <span class="sd">        Only works for regular, orthonormal grids.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -318,7 +322,7 @@ <h1>Source code for gridData.gOpenMol</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">delta</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">_read_header</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pltfile</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Read header bytes, try all possibilities for byte order/size/alignment.&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Read header bytes, try all possibilities for byte order/size/alignment.&quot;&quot;&quot;</span>
         <span class="n">nheader</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">calcsize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_headerfmt</span><span class="p">)</span>
         <span class="n">names</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">key</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_header_struct</span><span class="p">]</span>
         <span class="n">binheader</span> <span class="o">=</span> <span class="n">pltfile</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">nheader</span><span class="p">)</span>
@@ -340,7 +344,7 @@ <h1>Source code for gridData.gOpenMol</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">header</span>
 
 <div class="viewcode-block" id="Plt.histogramdd"><a class="viewcode-back" href="../../gridData/formats/gOpenMol.html#gridData.gOpenMol.Plt.histogramdd">[docs]</a>    <span class="k">def</span> <span class="nf">histogramdd</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Return array data as (edges,grid), i.e. a numpy nD histogram.&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return array data as (edges,grid), i.e. a numpy nD histogram.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">)</span></div></div>
 </pre></div>
 

diff --git a/_modules/gridData/mrc.html b/_modules/gridData/mrc.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>gridData.mrc &mdash; GridDataFormats 1.0.1+2.g069e535 documentation</title>
+  <title>gridData.mrc &mdash; GridDataFormats 1.0.1+5.ge08f6c5 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
@@ -13,13 +13,11 @@
   <![endif]-->
 
         <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-        <script src="../../_static/jquery.js"></script>
-        <script src="../../_static/underscore.js"></script>
-        <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../../_static/doctools.js"></script>
+        <script src="../../_static/sphinx_highlight.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="search" type="application/opensearchdescription+xml"
-          title="Search within GridDataFormats 1.0.1+2.g069e535 documentation"
+          title="Search within GridDataFormats 1.0.1+5.ge08f6c5 documentation"
           href="../../_static/opensearch.xml"/>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -30,15 +28,19 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search"  style="background: white" >
-            <a href="../../index.html">
-            <img src="../../_static/mdanalysis-griddataformats-logo.png" class="logo" alt="Logo"/>
+
+
+
+          <a href="../../index.html">
+
+              <img src="../../_static/mdanalysis-griddataformats-logo.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 1.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -49,6 +51,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/overview.html">Handling grids of data — <code class="xref py py-mod docutils literal notranslate"><span class="pre">gridData</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/basic.html">Basic use</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/core.html">Core functionality for storing n-D grids — <code class="xref py py-mod docutils literal notranslate"><span class="pre">gridData.core</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../gridData/core.html#gridData.core.Grid"><code class="docutils literal notranslate"><span class="pre">Grid</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../gridData/core.html#gridData.core.ndmeshgrid"><code class="docutils literal notranslate"><span class="pre">ndmeshgrid()</span></code></a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../gridData/formats.html">Formats</a></li>
 </ul>
 
@@ -65,9 +69,9 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../../index.html" class="icon icon-home"></a> &raquo;</li>
-          <li><a href="../index.html">Module code</a> &raquo;</li>
-      <li>gridData.mrc</li>
+      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">gridData.mrc</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
@@ -113,7 +117,7 @@ <h1>Source code for gridData.mrc</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="MRC"><a class="viewcode-back" href="../../gridData/formats/mrc.html#gridData.mrc.MRC">[docs]</a><span class="k">class</span> <span class="nc">MRC</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Represent a MRC/CCP4 file.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Represent a MRC/CCP4 file.</span>
 
 <span class="sd">    Load `MRC/CCP4 2014 &lt;MRC2014 file format&gt;`_ 3D volumetric data with</span>
 <span class="sd">    the mrcfile_ library.</span>
@@ -171,7 +175,7 @@ <h1>Source code for gridData.mrc</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
 
 <div class="viewcode-block" id="MRC.read"><a class="viewcode-back" href="../../gridData/formats/mrc.html#gridData.mrc.MRC.read">[docs]</a>    <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Populate the instance from the MRC/CCP4 file *filename*.&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Populate the instance from the MRC/CCP4 file *filename*.&quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">filename</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="n">filename</span>
         <span class="k">with</span> <span class="n">mrcfile</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">mrc</span><span class="p">:</span>
@@ -209,12 +213,12 @@ <h1>Source code for gridData.mrc</h1><div class="highlight"><pre>
 
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">shape</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Shape of the :attr:`array`&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Shape of the :attr:`array`&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="o">.</span><span class="n">shape</span>
 
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">edges</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Edges of the grid cells, origin at centre of 0,0,0 grid cell.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Edges of the grid cells, origin at centre of 0,0,0 grid cell.</span>
 
 <span class="sd">        Only works for regular, orthonormal grids.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -224,7 +228,7 @@ <h1>Source code for gridData.mrc</h1><div class="highlight"><pre>
                 <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rank</span><span class="p">)]</span>
 
 <div class="viewcode-block" id="MRC.histogramdd"><a class="viewcode-back" href="../../gridData/formats/mrc.html#gridData.mrc.MRC.histogramdd">[docs]</a>    <span class="k">def</span> <span class="nf">histogramdd</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;Return array data as (edges,grid), i.e. a numpy nD histogram.&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return array data as (edges,grid), i.e. a numpy nD histogram.&quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">)</span></div></div>