rebuilt html docs for version 2.8.0-dev0 from branch develop with sph…

…inx at 406f84d

2.8.0-dev0/_sources/examples/constructing_universe.ipynb.txt

@@ -1031,7 +1031,7 @@
     "<center>\n",
     "<div style=\"width:800px; text-align:center;\">\n",
     "\n",
-    "![no_overlap_view](images/constructing-universe_domain-view.png)\n",
+    "![domain-view](images/constructing-universe_domain-view.png)\n",
     "    \n",
     "</div>\n",
     "</center>"

2.8.0-dev0/examples/constructing_universe.html

@@ -706,7 +706,7 @@ <h2>Merging with a protein<a class="headerlink" href="#Merging-with-a-protein" t
 </pre></div>
 </div>
 </div>
-<center><div style="width:800px; text-align:center;"><p><img alt="no_overlap_view" src="../_images/constructing-universe_domain-view.png" /></p>
+<center><div style="width:800px; text-align:center;"><p><img alt="no_overlap_view" src="../_images/constructing-universe_no-overlap-view.png" /></p>
 </div></center></section>
 <section id="Adding-a-new-segment">
 <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title="Link to this heading"></a></h2>
@@ -717,7 +717,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
 <li><p>NMP: residues 30-59 (blue)</p></li>
 <li><p>LID: residues 122-159 (yellow)</p></li>
 </ul>
-<p><img alt="63e5d447341a4d91a578db7ea6e51393" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="c89ea66639b045488b7ef200ee542546" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
 <div class="nbinput docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[26]:
 </pre></div>
@@ -814,7 +814,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
 </pre></div>
 </div>
 </div>
-<center><div style="width:800px; text-align:center;"><p><img alt="no_overlap_view" src="../_images/constructing-universe_domain-view.png" /></p>
+<center><div style="width:800px; text-align:center;"><p><img alt="domain-view" src="../_images/constructing-universe_domain-view.png" /></p>
 </div></center></section>
 <section id="Tiling-into-a-larger-Universe">
 <h2>Tiling into a larger Universe<a class="headerlink" href="#Tiling-into-a-larger-Universe" title="Link to this heading"></a></h2>

2.8.0-dev0/examples/constructing_universe.ipynb

@@ -1031,7 +1031,7 @@
     "<center>\n",
     "<div style=\"width:800px; text-align:center;\">\n",
     "\n",
-    "![no_overlap_view](images/constructing-universe_domain-view.png)\n",
+    "![domain-view](images/constructing-universe_domain-view.png)\n",
     "    \n",
     "</div>\n",
     "</center>"

2.8.0-dev0/formats/auxiliary.html

@@ -263,7 +263,7 @@ <h2>Reading data directly<a class="headerlink" href="#reading-data-directly" tit
 <span class="gp">In [3]: </span><span class="n">aux</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="n">XVG_BZ2</span><span class="p">)</span>
 
 <span class="gp">In [4]: </span><span class="n">aux</span>
-<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fde5f954250&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f06c1a41ed0&gt;</span>
 </pre></div>
 </div>
 <p>In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.</p>
@@ -462,7 +462,7 @@ <h2>Recreating auxiliaries<a class="headerlink" href="#recreating-auxiliaries" t
 <span class="gp">In [30]: </span><span class="k">del</span> <span class="n">aux</span>
 
 <span class="gp">In [31]: </span><span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="o">**</span><span class="n">description</span><span class="p">)</span>
-<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fde66eed390&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f06c1f3f310&gt;</span>
 </pre></div>
 </div>
 <p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
@@ -577,7 +577,7 @@ <h2>Standalone Usage<a class="headerlink" href="#standalone-usage" title="Link t
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [45]: </span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 
 <span class="gp">In [46]: </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Time&quot;</span><span class="p">],</span> <span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Temperature&quot;</span><span class="p">])</span>
-<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fde6500e650&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f06c19740a0&gt;]</span>
 
 <span class="gp">In [47]: </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Temperature [K]&quot;</span><span class="p">)</span>
 <span class="gh">Out[47]: </span><span class="go">Text(0, 0.5, &#39;Temperature [K]&#39;)</span>

2.8.0-dev0/reading_and_writing.html

@@ -322,27 +322,27 @@ <h4>Building trajectories in memory<a class="headerlink" href="#building-traject
 
 <span class="gp">In [16]: </span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
 <span class="gh">Out[16]: </span>
-<span class="go">array([[0.7333103 , 0.2709559 , 0.01008517],</span>
-<span class="go">       [0.63832605, 0.00579721, 0.45592576],</span>
-<span class="go">       [0.4069619 , 0.4723249 , 0.6068874 ],</span>
+<span class="go">array([[0.4985685 , 0.4481248 , 0.7366852 ],</span>
+<span class="go">       [0.6066934 , 0.9468767 , 0.57959056],</span>
+<span class="go">       [0.11703162, 0.556185  , 0.66504943],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.30106223, 0.0804872 , 0.13362622],</span>
-<span class="go">       [0.2962001 , 0.09005761, 0.68332994],</span>
-<span class="go">       [0.79022497, 0.8548461 , 0.764362  ]], dtype=float32)</span>
+<span class="go">       [0.8067174 , 0.4116918 , 0.6045624 ],</span>
+<span class="go">       [0.47088104, 0.91593075, 0.70687884],</span>
+<span class="go">       [0.38909045, 0.9656515 , 0.31426218]], dtype=float32)</span>
 </pre></div>
 </div>
 <p>or they can be directly passed in when creating a Universe.</p>
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [17]: </span><span class="n">universe2</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PDB</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="n">MemoryReader</span><span class="p">)</span>
 
 <span class="gp">In [18]: </span><span class="n">universe2</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
 <span class="gh">Out[18]: </span>
-<span class="go">array([[0.7333103 , 0.2709559 , 0.01008517],</span>
-<span class="go">       [0.63832605, 0.00579721, 0.45592576],</span>
-<span class="go">       [0.4069619 , 0.4723249 , 0.6068874 ],</span>
+<span class="go">array([[0.4985685 , 0.4481248 , 0.7366852 ],</span>
+<span class="go">       [0.6066934 , 0.9468767 , 0.57959056],</span>
+<span class="go">       [0.11703162, 0.556185  , 0.66504943],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.30106223, 0.0804872 , 0.13362622],</span>
-<span class="go">       [0.2962001 , 0.09005761, 0.68332994],</span>
-<span class="go">       [0.79022497, 0.8548461 , 0.764362  ]], dtype=float32)</span>
+<span class="go">       [0.8067174 , 0.4116918 , 0.6045624 ],</span>
+<span class="go">       [0.47088104, 0.91593075, 0.70687884],</span>
+<span class="go">       [0.38909045, 0.9656515 , 0.31426218]], dtype=float32)</span>
 </pre></div>
 </div>
 </section>

2.8.0-dev0/standard_selections.html

@@ -334,10 +334,10 @@ <h3>Protein backbone<a class="headerlink" href="#protein-backbone" title="Link t
 <p>Protein backbone atoms in MDAnalysis belong to a recognised protein residue and have the atom names:</p>
 <table class="docutils align-default">
 <tbody>
-<tr class="row-odd"><td><p>CA</p></td>
-<td><p>N</p></td>
+<tr class="row-odd"><td><p>N</p></td>
 <td><p>O</p></td>
 <td><p>C</p></td>
+<td><p>CA</p></td>
 </tr>
 </tbody>
 </table>
@@ -349,44 +349,44 @@ <h3>Protein backbone<a class="headerlink" href="#protein-backbone" title="Link t
 <p>The below names are drawn from largely from the CHARMM force field.</p>
 <table class="docutils align-default">
 <tbody>
-<tr class="row-odd"><td><p>DC5</p></td>
-<td><p>C</p></td>
-<td><p>DT5</p></td>
-<td><p>RU</p></td>
-<td><p>CYT</p></td>
-<td><p>THY</p></td>
+<tr class="row-odd"><td><p>DC3</p></td>
+<td><p>RG3</p></td>
+<td><p>RC</p></td>
+<td><p>T</p></td>
+<td><p>DC5</p></td>
+<td><p>RC5</p></td>
+<td><p>DG</p></td>
 <td><p>RC3</p></td>
-<td><p>RA5</p></td>
 </tr>
-<tr class="row-even"><td><p>T</p></td>
-<td><p>DA3</p></td>
-<td><p>DT</p></td>
-<td><p>DG3</p></td>
-<td><p>G</p></td>
-<td><p>DT3</p></td>
-<td><p>U</p></td>
-<td><p>DA</p></td>
-</tr>
-<tr class="row-odd"><td><p>RU5</p></td>
+<tr class="row-even"><td><p>THY</p></td>
 <td><p>DC</p></td>
-<td><p>DG</p></td>
-<td><p>DC3</p></td>
-<td><p>RC5</p></td>
-<td><p>RU3</p></td>
-<td><p>RG3</p></td>
-<td><p>RG</p></td>
-</tr>
-<tr class="row-even"><td><p>RA3</p></td>
-<td><p>GUA</p></td>
+<td><p>G</p></td>
 <td><p>RA</p></td>
-<td><p>RC</p></td>
-<td><p>DA5</p></td>
+<td><p>RG5</p></td>
+<td><p>RU5</p></td>
+<td><p>GUA</p></td>
+<td><p>DT</p></td>
+</tr>
+<tr class="row-odd"><td><p>DA</p></td>
 <td><p>URA</p></td>
+<td><p>RG</p></td>
+<td><p>U</p></td>
+<td><p>CYT</p></td>
 <td><p>A</p></td>
+<td><p>DT5</p></td>
+<td><p>DG5</p></td>
+</tr>
+<tr class="row-even"><td><p>DA5</p></td>
+<td><p>DT3</p></td>
+<td><p>RA5</p></td>
+<td><p>RU3</p></td>
+<td><p>RU</p></td>
+<td><p>DA3</p></td>
+<td><p>C</p></td>
 <td><p>ADE</p></td>
 </tr>
-<tr class="row-odd"><td><p>DG5</p></td>
-<td><p>RG5</p></td>
+<tr class="row-odd"><td><p>RA3</p></td>
+<td><p>DG3</p></td>
 <td></td>
 <td></td>
 <td></td>
@@ -401,11 +401,11 @@ <h3>Nucleic backbone<a class="headerlink" href="#nucleic-backbone" title="Link t
 <p>Nucleic backbone atoms in MDAnalysis belong to a recognised nucleic acid residue and have the atom names:</p>
 <table class="docutils align-default">
 <tbody>
-<tr class="row-odd"><td><p>P</p></td>
-<td><p>C3’</p></td>
-<td><p>O3’</p></td>
-<td><p>C5’</p></td>
+<tr class="row-odd"><td><p>C3’</p></td>
 <td><p>O5’</p></td>
+<td><p>P</p></td>
+<td><p>C5’</p></td>
+<td><p>O3’</p></td>
 </tr>
 </tbody>
 </table>
@@ -415,22 +415,22 @@ <h3>Nucleic backbone<a class="headerlink" href="#nucleic-backbone" title="Link t
 <p>Nucleobase atoms from nucleic acid residues are recognised based on their names in CHARMM.</p>
 <table class="docutils align-default">
 <tbody>
-<tr class="row-odd"><td><p>N7</p></td>
-<td><p>N3</p></td>
-<td><p>N4</p></td>
+<tr class="row-odd"><td><p>N2</p></td>
 <td><p>N6</p></td>
+<td><p>C5</p></td>
+<td><p>N7</p></td>
+<td><p>N9</p></td>
+<td><p>O4</p></td>
 <td><p>N1</p></td>
-<td><p>O2</p></td>
-<td><p>C6</p></td>
-<td><p>N2</p></td>
+<td><p>C5M</p></td>
 </tr>
-<tr class="row-even"><td><p>C8</p></td>
-<td><p>C4</p></td>
+<tr class="row-even"><td><p>N4</p></td>
+<td><p>C8</p></td>
+<td><p>C6</p></td>
+<td><p>O2</p></td>
 <td><p>C2</p></td>
-<td><p>O4</p></td>
-<td><p>N9</p></td>
-<td><p>C5M</p></td>
-<td><p>C5</p></td>
+<td><p>C4</p></td>
+<td><p>N3</p></td>
 <td><p>O6</p></td>
 </tr>
 </tbody>
@@ -441,11 +441,11 @@ <h3>Nucleic sugars<a class="headerlink" href="#nucleic-sugars" title="Link to th
 <p>Nucleic sugar atoms from nucleic acid residues are recognised by MDAnalysis if they have the atom names:</p>
 <table class="docutils align-default">
 <tbody>
-<tr class="row-odd"><td><p>C3’</p></td>
-<td><p>C4’</p></td>
-<td><p>C1’</p></td>
-<td><p>O4’</p></td>
+<tr class="row-odd"><td><p>O4’</p></td>
 <td><p>C2’</p></td>
+<td><p>C3’</p></td>
+<td><p>C1’</p></td>
+<td><p>C4’</p></td>
 </tr>
 </tbody>
 </table>

dev/_sources/examples/constructing_universe.ipynb.txt

@@ -1031,7 +1031,7 @@
     "<center>\n",
     "<div style=\"width:800px; text-align:center;\">\n",
     "\n",
-    "![no_overlap_view](images/constructing-universe_domain-view.png)\n",
+    "![domain-view](images/constructing-universe_domain-view.png)\n",
     "    \n",
     "</div>\n",
     "</center>"

dev/examples/constructing_universe.html

@@ -706,7 +706,7 @@ <h2>Merging with a protein<a class="headerlink" href="#Merging-with-a-protein" t
 </pre></div>
 </div>
 </div>
-<center><div style="width:800px; text-align:center;"><p><img alt="no_overlap_view" src="../_images/constructing-universe_domain-view.png" /></p>
+<center><div style="width:800px; text-align:center;"><p><img alt="no_overlap_view" src="../_images/constructing-universe_no-overlap-view.png" /></p>
 </div></center></section>
 <section id="Adding-a-new-segment">
 <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title="Link to this heading"></a></h2>
@@ -717,7 +717,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
 <li><p>NMP: residues 30-59 (blue)</p></li>
 <li><p>LID: residues 122-159 (yellow)</p></li>
 </ul>
-<p><img alt="63e5d447341a4d91a578db7ea6e51393" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="c89ea66639b045488b7ef200ee542546" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
 <div class="nbinput docutils container">
 <div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[26]:
 </pre></div>
@@ -814,7 +814,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
 </pre></div>
 </div>
 </div>
-<center><div style="width:800px; text-align:center;"><p><img alt="no_overlap_view" src="../_images/constructing-universe_domain-view.png" /></p>
+<center><div style="width:800px; text-align:center;"><p><img alt="domain-view" src="../_images/constructing-universe_domain-view.png" /></p>
 </div></center></section>
 <section id="Tiling-into-a-larger-Universe">
 <h2>Tiling into a larger Universe<a class="headerlink" href="#Tiling-into-a-larger-Universe" title="Link to this heading"></a></h2>

dev/examples/constructing_universe.ipynb

@@ -1031,7 +1031,7 @@
     "<center>\n",
     "<div style=\"width:800px; text-align:center;\">\n",
     "\n",
-    "![no_overlap_view](images/constructing-universe_domain-view.png)\n",
+    "![domain-view](images/constructing-universe_domain-view.png)\n",
     "    \n",
     "</div>\n",
     "</center>"

dev/formats/auxiliary.html

@@ -263,7 +263,7 @@ <h2>Reading data directly<a class="headerlink" href="#reading-data-directly" tit
 <span class="gp">In [3]: </span><span class="n">aux</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="n">XVG_BZ2</span><span class="p">)</span>
 
 <span class="gp">In [4]: </span><span class="n">aux</span>
-<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fde5f954250&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f06c1a41ed0&gt;</span>
 </pre></div>
 </div>
 <p>In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.</p>
@@ -462,7 +462,7 @@ <h2>Recreating auxiliaries<a class="headerlink" href="#recreating-auxiliaries" t
 <span class="gp">In [30]: </span><span class="k">del</span> <span class="n">aux</span>
 
 <span class="gp">In [31]: </span><span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="o">**</span><span class="n">description</span><span class="p">)</span>
-<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fde66eed390&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f06c1f3f310&gt;</span>
 </pre></div>
 </div>
 <p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
@@ -577,7 +577,7 @@ <h2>Standalone Usage<a class="headerlink" href="#standalone-usage" title="Link t
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [45]: </span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 
 <span class="gp">In [46]: </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Time&quot;</span><span class="p">],</span> <span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Temperature&quot;</span><span class="p">])</span>
-<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fde6500e650&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f06c19740a0&gt;]</span>
 
 <span class="gp">In [47]: </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Temperature [K]&quot;</span><span class="p">)</span>
 <span class="gh">Out[47]: </span><span class="go">Text(0, 0.5, &#39;Temperature [K]&#39;)</span>