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

…inx at 406f84d

2.8.0-dev0/atomgroup.html

@@ -242,7 +242,7 @@ <h3>Indexing and slicing<a class="headerlink" href="#indexing-and-slicing" title
 <span class="gh">Out[7]: </span><span class="go">array([0, 2, 4])</span>
 </pre></div>
 </div>
-<p>MDAnalysis also supports fancy indexing: passing a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> or a <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>.</p>
+<p>MDAnalysis also supports fancy indexing: passing a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> or a <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>.</p>
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [8]: </span><span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span>
 
 <span class="gp">In [9]: </span><span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span><span class="o">.</span><span class="n">indices</span>

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="e49fbd8f54bb45edaedf202d28b08620" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="fb1070cd6e144b71825bc8bea350829d" 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 0x7f45eb3cc7f0&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fa669b47220&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 0x7f45f1127160&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fa66aefafb0&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 0x7f45eaa060e0&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fa66c0ba5c0&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/formats/reference/ncdf.html

@@ -254,7 +254,7 @@ <h2>Reading in<a class="headerlink" href="#reading-in" title="Link to this headi
 <li><p>time: ps</p></li>
 </ul>
 </div></blockquote>
-<p>Currently, if other units are detected, MDAnalysis will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#NotImplementedError" title="(in Python v3.12)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">NotImplementedError</span></code></a>.</p>
+<p>Currently, if other units are detected, MDAnalysis will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#NotImplementedError" title="(in Python v3.13)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">NotImplementedError</span></code></a>.</p>
 </section>
 <section id="writing-out">
 <h2>Writing out<a class="headerlink" href="#writing-out" title="Link to this heading"></a></h2>

2.8.0-dev0/formats/reference/pqr.html

@@ -272,7 +272,7 @@ <h2>Reading in<a class="headerlink" href="#reading-in" title="Link to this headi
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">recordName</span> <span class="n">serial</span> <span class="n">atomName</span> <span class="n">residueName</span> <span class="n">residueNumber</span> <span class="n">X</span> <span class="n">Y</span> <span class="n">Z</span> <span class="n">charge</span> <span class="n">radius</span>
 </pre></div>
 </div>
-<p>Anything else will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code></a>.</p>
+<p>Anything else will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.13)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code></a>.</p>
 <p>The whitespace is the most important feature of this format: fields
 <em>must</em> be separated by at least one space or tab character.</p>
 </section>

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 04, 2024</p>
+<p><strong>Last updated:</strong> Oct 08, 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([[0.4925136 , 0.03463347, 0.08987161],</span>
-<span class="go">       [0.7390431 , 0.25437427, 0.08799985],</span>
-<span class="go">       [0.2464222 , 0.32855192, 0.13459331],</span>
+<span class="go">array([[0.67456794, 0.44370043, 0.4388902 ],</span>
+<span class="go">       [0.9182168 , 0.5429831 , 0.4007073 ],</span>
+<span class="go">       [0.42256373, 0.25019425, 0.62344104],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.4677765 , 0.6960034 , 0.35505942],</span>
-<span class="go">       [0.29870602, 0.3594374 , 0.37256014],</span>
-<span class="go">       [0.7553673 , 0.307522  , 0.9067642 ]], dtype=float32)</span>
+<span class="go">       [0.66889244, 0.04879748, 0.6862997 ],</span>
+<span class="go">       [0.6264734 , 0.03047601, 0.33831993],</span>
+<span class="go">       [0.54861754, 0.11238988, 0.6819914 ]], 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([[0.4925136 , 0.03463347, 0.08987161],</span>
-<span class="go">       [0.7390431 , 0.25437427, 0.08799985],</span>
-<span class="go">       [0.2464222 , 0.32855192, 0.13459331],</span>
+<span class="go">array([[0.67456794, 0.44370043, 0.4388902 ],</span>
+<span class="go">       [0.9182168 , 0.5429831 , 0.4007073 ],</span>
+<span class="go">       [0.42256373, 0.25019425, 0.62344104],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.4677765 , 0.6960034 , 0.35505942],</span>
-<span class="go">       [0.29870602, 0.3594374 , 0.37256014],</span>
-<span class="go">       [0.7553673 , 0.307522  , 0.9067642 ]], dtype=float32)</span>
+<span class="go">       [0.66889244, 0.04879748, 0.6862997 ],</span>
+<span class="go">       [0.6264734 , 0.03047601, 0.33831993],</span>
+<span class="go">       [0.54861754, 0.11238988, 0.6819914 ]], dtype=float32)</span>
 </pre></div>
 </div>
 </section>

2.8.0-dev0/selections.html

@@ -283,7 +283,7 @@ <h2>Selection Keywords<a class="headerlink" href="#selection-keywords" title="Li
 the string <code class="docutils literal notranslate"><span class="pre">GL*</span></code> selects all strings that start with “GL”,
 such as “GLU”, “GLY”, “GLX29”, “GLN”. <code class="docutils literal notranslate"><span class="pre">GL[YN]</span></code> will select all “GLY” and
 “GLN” strings. Any number of patterns can be included in the search.
-For more information on pattern matching, see the <a class="reference external" href="https://docs.python.org/3/library/fnmatch.html#module-fnmatch" title="(in Python v3.12)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">fnmatch</span></code></a> documentation.</p>
+For more information on pattern matching, see the <a class="reference external" href="https://docs.python.org/3/library/fnmatch.html#module-fnmatch" title="(in Python v3.13)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">fnmatch</span></code></a> documentation.</p>
 </li>
 </ul>
 <section id="simple-selections">

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>O</p></td>
-<td><p>C</p></td>
+<tr class="row-odd"><td><p>N</p></td>
 <td><p>CA</p></td>
-<td><p>N</p></td>
+<td><p>C</p></td>
+<td><p>O</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>RC</p></td>
-<td><p>THY</p></td>
-<td><p>DC5</p></td>
-<td><p>RG</p></td>
-<td><p>RG3</p></td>
-<td><p>RC3</p></td>
-<td><p>G</p></td>
+<tr class="row-odd"><td><p>DG3</p></td>
+<td><p>DT5</p></td>
+<td><p>DT</p></td>
+<td><p>RA5</p></td>
 <td><p>DG</p></td>
-</tr>
-<tr class="row-even"><td><p>T</p></td>
+<td><p>DA5</p></td>
 <td><p>RU3</p></td>
-<td><p>DC3</p></td>
-<td><p>RA3</p></td>
-<td><p>RG5</p></td>
-<td><p>RA5</p></td>
-<td><p>ADE</p></td>
-<td><p>DT3</p></td>
+<td><p>DC</p></td>
 </tr>
-<tr class="row-odd"><td><p>RA</p></td>
-<td><p>C</p></td>
-<td><p>A</p></td>
-<td><p>RU5</p></td>
+<tr class="row-even"><td><p>RG5</p></td>
+<td><p>DG5</p></td>
+<td><p>DA</p></td>
+<td><p>RC</p></td>
+<td><p>RC3</p></td>
 <td><p>URA</p></td>
-<td><p>DT</p></td>
-<td><p>DA5</p></td>
-<td><p>RC5</p></td>
+<td><p>G</p></td>
+<td><p>THY</p></td>
 </tr>
-<tr class="row-even"><td><p>RU</p></td>
-<td><p>DC</p></td>
-<td><p>DG5</p></td>
-<td><p>U</p></td>
-<td><p>CYT</p></td>
-<td><p>DT5</p></td>
+<tr class="row-odd"><td><p>RA3</p></td>
 <td><p>GUA</p></td>
-<td><p>DA</p></td>
+<td><p>T</p></td>
+<td><p>A</p></td>
+<td><p>RG</p></td>
+<td><p>RA</p></td>
+<td><p>CYT</p></td>
+<td><p>RU</p></td>
+</tr>
+<tr class="row-even"><td><p>DA3</p></td>
+<td><p>DT3</p></td>
+<td><p>DC5</p></td>
+<td><p>RC5</p></td>
+<td><p>ADE</p></td>
+<td><p>RU5</p></td>
+<td><p>RG3</p></td>
+<td><p>U</p></td>
 </tr>
-<tr class="row-odd"><td><p>DA3</p></td>
-<td><p>DG3</p></td>
+<tr class="row-odd"><td><p>C</p></td>
+<td><p>DC3</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>O3’</p></td>
-<td><p>P</p></td>
-<td><p>C3’</p></td>
-<td><p>O5’</p></td>
+<tr class="row-odd"><td><p>P</p></td>
+<td><p>O3’</p></td>
 <td><p>C5’</p></td>
+<td><p>O5’</p></td>
+<td><p>C3’</p></td>
 </tr>
 </tbody>
 </table>
@@ -416,22 +416,22 @@ <h3>Nucleic backbone<a class="headerlink" href="#nucleic-backbone" title="Link t
 <table class="docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p>N6</p></td>
-<td><p>C8</p></td>
-<td><p>N4</p></td>
 <td><p>C5M</p></td>
+<td><p>C5</p></td>
+<td><p>C6</p></td>
+<td><p>N9</p></td>
 <td><p>C4</p></td>
-<td><p>N7</p></td>
+<td><p>O2</p></td>
 <td><p>N2</p></td>
-<td><p>O4</p></td>
 </tr>
-<tr class="row-even"><td><p>O2</p></td>
-<td><p>N3</p></td>
-<td><p>C5</p></td>
-<td><p>C2</p></td>
-<td><p>C6</p></td>
+<tr class="row-even"><td><p>N7</p></td>
 <td><p>O6</p></td>
-<td><p>N9</p></td>
 <td><p>N1</p></td>
+<td><p>O4</p></td>
+<td><p>C2</p></td>
+<td><p>C8</p></td>
+<td><p>N3</p></td>
+<td><p>N4</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>C1’</p></td>
-<td><p>O4’</p></td>
-<td><p>C3’</p></td>
-<td><p>C4’</p></td>
+<tr class="row-odd"><td><p>C4’</p></td>
 <td><p>C2’</p></td>
+<td><p>C3’</p></td>
+<td><p>C1’</p></td>
+<td><p>O4’</p></td>
 </tr>
 </tbody>
 </table>