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

…inx at b0da13f

2.8.0-dev0/_sources/contributing_docs.rst.txt

@@ -231,6 +231,7 @@ defines flags that you can also pass directly to pytest.
 For example, if you wanted to test the `hole2` notebook::
 
     pytest --nbval --nbval-current-env --nbval-sanitize-with ./sanitize_output.cfg ../doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb
+
 Where ``--nbval`` tells pytest to use nbval to test Jupyter notebooks, ``--nbval-current-env``
 to use the currently loaded python environment (make sure you actually loaded your environment)
 instead of trying to use the one that was used when the notebook was saved  and
@@ -239,6 +240,7 @@ for example::
 
     regex: (.*B \[0.*B/s\])
     replace: DOWNLOAD
+
 This tells pytest to scan the outputs of all cells and replace the matching string with the word
 *DOWNLOAD*. This is called *sanitization*.
 
@@ -384,7 +386,5 @@ For each time you add changes to another branch later, just merge into gh-pages
     cd doc/
     make github
 
-
-
 .. _nbsphinx: https://nbsphinx.readthedocs.io
 .. _ReviewNB: https://www.reviewnb.com/

2.8.0-dev0/examples/constructing_universe.html

@@ -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="813f3c045dab4abe852f234784e358fb" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="e7a62196afe949acad151e11715c661d" 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>

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 0x7f9f3dfc1120&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fc145b81ea0&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 0x7f9f3f38bf10&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fc1471c2d70&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 0x7f9f3d955180&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fc1460fe1d0&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/index.html

@@ -194,7 +194,7 @@
   <section id="welcome-to-mdanalysis-user-guide-s-documentation">
 <h1>Welcome to MDAnalysis User Guide’s documentation!<a class="headerlink" href="#welcome-to-mdanalysis-user-guide-s-documentation" title="Link to this heading"></a></h1>
 <p><strong>MDAnalysis version:</strong> 2.8.0-dev0</p>
-<p><strong>Last updated:</strong> Oct 13, 2024</p>
+<p><strong>Last updated:</strong> Oct 14, 2024</p>
 <p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is a Python
 toolkit to analyse molecular dynamics files and trajectories in <a class="reference internal" href="formats/index.html#formats"><span class="std std-ref">many popular formats</span></a>. MDAnalysis can write
 most of these formats, too, together with atom selections for use in <a class="reference internal" href="formats/selection_exporters.html#selection-exporters"><span class="std std-ref">visualisation tools or other analysis programs</span></a>.

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([[0.5946307 , 0.18919976, 0.44233742],</span>
-<span class="go">       [0.5949025 , 0.9947764 , 0.6217801 ],</span>
-<span class="go">       [0.9149371 , 0.6625653 , 0.798835  ],</span>
+<span class="go">array([[0.43275654, 0.05787423, 0.09639952],</span>
+<span class="go">       [0.12101547, 0.72229546, 0.06255616],</span>
+<span class="go">       [0.7702801 , 0.17550863, 0.76324135],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.7360544 , 0.5006215 , 0.67056286],</span>
-<span class="go">       [0.7761591 , 0.55651474, 0.64369595],</span>
-<span class="go">       [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)</span>
+<span class="go">       [0.3037213 , 0.02933419, 0.89408046],</span>
+<span class="go">       [0.94700533, 0.15484135, 0.73815924],</span>
+<span class="go">       [0.0986912 , 0.3056773 , 0.62667555]], 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([[0.5946307 , 0.18919976, 0.44233742],</span>
-<span class="go">       [0.5949025 , 0.9947764 , 0.6217801 ],</span>
-<span class="go">       [0.9149371 , 0.6625653 , 0.798835  ],</span>
+<span class="go">array([[0.43275654, 0.05787423, 0.09639952],</span>
+<span class="go">       [0.12101547, 0.72229546, 0.06255616],</span>
+<span class="go">       [0.7702801 , 0.17550863, 0.76324135],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.7360544 , 0.5006215 , 0.67056286],</span>
-<span class="go">       [0.7761591 , 0.55651474, 0.64369595],</span>
-<span class="go">       [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)</span>
+<span class="go">       [0.3037213 , 0.02933419, 0.89408046],</span>
+<span class="go">       [0.94700533, 0.15484135, 0.73815924],</span>
+<span class="go">       [0.0986912 , 0.3056773 , 0.62667555]], dtype=float32)</span>
 </pre></div>
 </div>
 </section>

2.8.0-dev0/standard_selections.html

@@ -334,9 +334,9 @@ <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>
+<tr class="row-odd"><td><p>O</p></td>
+<td><p>CA</p></td>
 <td><p>C</p></td>
-<td><p>O</p></td>
 <td><p>N</p></td>
 </tr>
 </tbody>
@@ -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>RU</p></td>
-<td><p>RG3</p></td>
-<td><p>RC5</p></td>
-<td><p>RG</p></td>
-<td><p>RA</p></td>
+<tr class="row-odd"><td><p>DG3</p></td>
+<td><p>DA</p></td>
+<td><p>G</p></td>
 <td><p>DC5</p></td>
-<td><p>CYT</p></td>
-<td><p>DG5</p></td>
-</tr>
-<tr class="row-even"><td><p>RA5</p></td>
-<td><p>RC3</p></td>
-<td><p>RC</p></td>
-<td><p>DA3</p></td>
-<td><p>DG</p></td>
-<td><p>URA</p></td>
-<td><p>DT</p></td>
-<td><p>RG5</p></td>
+<td><p>RA5</p></td>
+<td><p>U</p></td>
+<td><p>RU3</p></td>
+<td><p>C</p></td>
 </tr>
-<tr class="row-odd"><td><p>DG3</p></td>
-<td><p>DT3</p></td>
+<tr class="row-even"><td><p>DC3</p></td>
 <td><p>RA3</p></td>
-<td><p>DC3</p></td>
-<td><p>RU3</p></td>
-<td><p>DT5</p></td>
+<td><p>ADE</p></td>
+<td><p>RG3</p></td>
 <td><p>A</p></td>
-<td><p>DC</p></td>
+<td><p>DA3</p></td>
+<td><p>RA</p></td>
+<td><p>DT3</p></td>
 </tr>
-<tr class="row-even"><td><p>DA5</p></td>
-<td><p>ADE</p></td>
-<td><p>DA</p></td>
-<td><p>G</p></td>
-<td><p>U</p></td>
-<td><p>GUA</p></td>
+<tr class="row-odd"><td><p>DA5</p></td>
+<td><p>DC</p></td>
+<td><p>RG5</p></td>
 <td><p>T</p></td>
+<td><p>THY</p></td>
+<td><p>CYT</p></td>
+<td><p>DT5</p></td>
 <td><p>RU5</p></td>
 </tr>
-<tr class="row-odd"><td><p>C</p></td>
-<td><p>THY</p></td>
+<tr class="row-even"><td><p>RC5</p></td>
+<td><p>GUA</p></td>
+<td><p>DG</p></td>
+<td><p>RG</p></td>
+<td><p>RC3</p></td>
+<td><p>RC</p></td>
+<td><p>RU</p></td>
+<td><p>URA</p></td>
+</tr>
+<tr class="row-odd"><td><p>DT</p></td>
+<td><p>DG5</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>O5’</p></td>
-<td><p>C5’</p></td>
+<tr class="row-odd"><td><p>P</p></td>
 <td><p>C3’</p></td>
-<td><p>P</p></td>
 <td><p>O3’</p></td>
+<td><p>O5’</p></td>
+<td><p>C5’</p></td>
 </tr>
 </tbody>
 </table>
@@ -415,23 +415,23 @@ <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>N1</p></td>
-<td><p>O2</p></td>
-<td><p>N9</p></td>
+<tr class="row-odd"><td><p>C5</p></td>
 <td><p>N6</p></td>
+<td><p>C8</p></td>
 <td><p>N7</p></td>
-<td><p>N2</p></td>
-<td><p>O6</p></td>
 <td><p>C2</p></td>
-</tr>
-<tr class="row-even"><td><p>N4</p></td>
-<td><p>C8</p></td>
 <td><p>O4</p></td>
-<td><p>C5M</p></td>
-<td><p>C6</p></td>
-<td><p>C5</p></td>
 <td><p>N3</p></td>
+<td><p>N1</p></td>
+</tr>
+<tr class="row-even"><td><p>N2</p></td>
+<td><p>O2</p></td>
+<td><p>N9</p></td>
 <td><p>C4</p></td>
+<td><p>C6</p></td>
+<td><p>N4</p></td>
+<td><p>C5M</p></td>
+<td><p>O6</p></td>
 </tr>
 </tbody>
 </table>
@@ -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>O4’</p></td>
-<td><p>C1’</p></td>
-<td><p>C2’</p></td>
+<tr class="row-odd"><td><p>C1’</p></td>
 <td><p>C3’</p></td>
 <td><p>C4’</p></td>
+<td><p>O4’</p></td>
+<td><p>C2’</p></td>
 </tr>
 </tbody>
 </table>