rebuilt html docs for version 2.11.0-dev0 from branch develop with sphinx at 12dcfc3

Author: github-actions

2.11.0-dev0/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf

@@ -715,7 +715,7 @@ <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="b4890dc7bbf14de2858984a9d1d1b8aa" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="4b530786ccbb4e80b5173ac9005cae3b" 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>

2.11.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html

@@ -261,7 +261,7 @@ <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 0x7f12492c5700&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9c7870d190&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>
@@ -460,7 +460,7 @@ <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 0x7f1243859460&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9c78cdf620&gt;</span>
 </pre></div>
 </div>
 <p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
@@ -575,7 +575,7 @@ <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="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </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 0x7f1242524ad0&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f9c727261b0&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>

2.11.0-dev0/examples/constructing_universe.html

@@ -347,12 +347,12 @@ <h3>Order of guessing<a class="headerlink" href="#order-of-guessing" title="Link
 <span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">32</span><span class="p">],</span> <span class="n">line</span> <span class="mi">1</span>
 <span class="ne">----&gt; </span><span class="mi">1</span> <span class="n">u</span><span class="o">.</span><span class="n">guess_TopologyAttrs</span><span class="p">(</span><span class="n">to_guess</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;bonds&quot;</span><span class="p">])</span>
 
-<span class="nn">File ~/micromamba/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:1911,</span> in <span class="ni">Universe.guess_TopologyAttrs</span><span class="nt">(self, context, to_guess, force_guess, error_if_missing, **kwargs)</span>
-<span class="g g-Whitespace">   </span><span class="mi">1909</span> <span class="n">fg</span> <span class="o">=</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">force_guess</span>
-<span class="g g-Whitespace">   </span><span class="mi">1910</span> <span class="k">try</span><span class="p">:</span>
-<span class="ne">-&gt; </span><span class="mi">1911</span>     <span class="n">values</span> <span class="o">=</span> <span class="n">guesser</span><span class="o">.</span><span class="n">guess_attr</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">fg</span><span class="p">)</span>
-<span class="g g-Whitespace">   </span><span class="mi">1912</span> <span class="k">except</span> <span class="n">NoDataError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
-<span class="g g-Whitespace">   </span><span class="mi">1913</span>     <span class="k">if</span> <span class="n">error_if_missing</span> <span class="ow">or</span> <span class="n">fg</span><span class="p">:</span>
+<span class="nn">File ~/micromamba/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/core/universe.py:1935,</span> in <span class="ni">Universe.guess_TopologyAttrs</span><span class="nt">(self, context, to_guess, force_guess, error_if_missing, **kwargs)</span>
+<span class="g g-Whitespace">   </span><span class="mi">1933</span> <span class="n">fg</span> <span class="o">=</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">force_guess</span>
+<span class="g g-Whitespace">   </span><span class="mi">1934</span> <span class="k">try</span><span class="p">:</span>
+<span class="ne">-&gt; </span><span class="mi">1935</span>     <span class="n">values</span> <span class="o">=</span> <span class="n">guesser</span><span class="o">.</span><span class="n">guess_attr</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">fg</span><span class="p">)</span>
+<span class="g g-Whitespace">   </span><span class="mi">1936</span> <span class="k">except</span> <span class="n">NoDataError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+<span class="g g-Whitespace">   </span><span class="mi">1937</span>     <span class="k">if</span> <span class="n">error_if_missing</span> <span class="ow">or</span> <span class="n">fg</span><span class="p">:</span>
 
 <span class="nn">File ~/micromamba/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/guesser/base.py:163,</span> in <span class="ni">GuesserBase.guess_attr</span><span class="nt">(self, attr_to_guess, force_guess)</span>
 <span class="g g-Whitespace">    </span><span class="mi">159</span> <span class="c1"># Connection attributes should be just returned as they are always</span>
@@ -379,7 +379,7 @@ <h3>Order of guessing<a class="headerlink" href="#order-of-guessing" title="Link
 <span class="g g-Whitespace">    </span><span class="mi">449</span> <span class="n">lower_bound</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;lower_bound&quot;</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
 <span class="g g-Whitespace">    </span><span class="mi">451</span> <span class="n">box</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;box&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
 
-<span class="ne">ValueError</span>: vdw radii for types: 3, 30, 26, 6, 81, 24, 9, 56, 7, 10, 52, 51, 21, 54, 25, 31, 29, 1, 70, 2, 73, 23, 5, 50, 32, 20, 57, 72, 55, 22. These can be defined manually using the keyword &#39;vdwradii&#39;
+<span class="ne">ValueError</span>: vdw radii for types: 72, 6, 54, 7, 26, 24, 25, 10, 5, 56, 2, 21, 57, 29, 32, 52, 50, 55, 31, 81, 30, 3, 51, 1, 20, 9, 22, 70, 73, 23. These can be defined manually using the keyword &#39;vdwradii&#39;
 </pre></div>
 </div>
 <p>However, the snippet below will re-guess the types, and now bond-guessing can work as the elements have vdW radii defined:</p>

2.11.0-dev0/formats/auxiliary.html

@@ -190,7 +190,7 @@
   <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> 2.11.0-dev0</p>
-<p><strong>Last updated:</strong> Nov 14, 2025</p>
+<p><strong>Last updated:</strong> Nov 18, 2025</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>.

2.11.0-dev0/guessing.html

@@ -320,13 +320,13 @@ <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([[0.25009313, 0.5773151 , 0.6917117 ],</span>
-<span class="go">       [0.09441383, 0.18819465, 0.31852555],</span>
-<span class="go">       [0.45390674, 0.4766085 , 0.37601155],</span>
+<span class="go">array([[0.26797223, 0.38690624, 0.69587946],</span>
+<span class="go">       [0.16045298, 0.42770648, 0.23505129],</span>
+<span class="go">       [0.704188  , 0.7275821 , 0.91988504],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.77226627, 0.00268798, 0.70273584],</span>
-<span class="go">       [0.77817786, 0.26999992, 0.09424755],</span>
-<span class="go">       [0.9061668 , 0.6645001 , 0.5726216 ]],</span>
+<span class="go">       [0.9841226 , 0.33841234, 0.36142474],</span>
+<span class="go">       [0.74384415, 0.7097269 , 0.19336794],</span>
+<span class="go">       [0.34026566, 0.78603977, 0.53190196]],</span>
 <span class="go">      shape=(47681, 3), dtype=float32)</span>
 </pre></div>
 </div>
@@ -335,13 +335,13 @@ <h4>Building trajectories in memory<a class="headerlink" href="#building-traject
 
 <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([[0.25009313, 0.5773151 , 0.6917117 ],</span>
-<span class="go">       [0.09441383, 0.18819465, 0.31852555],</span>
-<span class="go">       [0.45390674, 0.4766085 , 0.37601155],</span>
+<span class="go">array([[0.26797223, 0.38690624, 0.69587946],</span>
+<span class="go">       [0.16045298, 0.42770648, 0.23505129],</span>
+<span class="go">       [0.704188  , 0.7275821 , 0.91988504],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.77226627, 0.00268798, 0.70273584],</span>
-<span class="go">       [0.77817786, 0.26999992, 0.09424755],</span>
-<span class="go">       [0.9061668 , 0.6645001 , 0.5726216 ]],</span>
+<span class="go">       [0.9841226 , 0.33841234, 0.36142474],</span>
+<span class="go">       [0.74384415, 0.7097269 , 0.19336794],</span>
+<span class="go">       [0.34026566, 0.78603977, 0.53190196]],</span>
 <span class="go">      shape=(47681, 3), dtype=float32)</span>
 </pre></div>
 </div>

2.11.0-dev0/index.html

@@ -334,8 +334,8 @@ <h3>Protein backbone<a class="headerlink" href="#protein-backbone" title="Link t
 <tbody>
 <tr class="row-odd"><td><p>N</p></td>
 <td><p>C</p></td>
-<td><p>O</p></td>
 <td><p>CA</p></td>
+<td><p>O</p></td>
 </tr>
 </tbody>
 </table>
@@ -347,44 +347,44 @@ <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>RA3</p></td>
-<td><p>DT</p></td>
+<tr class="row-odd"><td><p>CYT</p></td>
+<td><p>RA</p></td>
+<td><p>DG3</p></td>
 <td><p>RU3</p></td>
-<td><p>A</p></td>
-<td><p>RA5</p></td>
-<td><p>C</p></td>
 <td><p>T</p></td>
-<td><p>DA5</p></td>
-</tr>
-<tr class="row-even"><td><p>GUA</p></td>
-<td><p>DC5</p></td>
-<td><p>RA</p></td>
+<td><p>RC</p></td>
 <td><p>U</p></td>
+<td><p>DA3</p></td>
+</tr>
+<tr class="row-even"><td><p>DC</p></td>
+<td><p>DG</p></td>
 <td><p>RG</p></td>
 <td><p>DC3</p></td>
 <td><p>RC5</p></td>
-<td><p>DT5</p></td>
+<td><p>GUA</p></td>
+<td><p>RA3</p></td>
+<td><p>RC3</p></td>
 </tr>
-<tr class="row-odd"><td><p>THY</p></td>
+<tr class="row-odd"><td><p>DT</p></td>
+<td><p>RU</p></td>
+<td><p>DG5</p></td>
+<td><p>URA</p></td>
 <td><p>DT3</p></td>
-<td><p>RU5</p></td>
-<td><p>ADE</p></td>
-<td><p>RG5</p></td>
+<td><p>DT5</p></td>
 <td><p>DA</p></td>
-<td><p>DG3</p></td>
-<td><p>RC3</p></td>
+<td><p>RG5</p></td>
 </tr>
-<tr class="row-even"><td><p>RU</p></td>
-<td><p>DC</p></td>
-<td><p>RC</p></td>
-<td><p>DG</p></td>
-<td><p>RG3</p></td>
-<td><p>CYT</p></td>
-<td><p>DA3</p></td>
+<tr class="row-even"><td><p>RU5</p></td>
+<td><p>C</p></td>
+<td><p>RA5</p></td>
 <td><p>G</p></td>
+<td><p>ADE</p></td>
+<td><p>RG3</p></td>
+<td><p>THY</p></td>
+<td><p>DC5</p></td>
 </tr>
-<tr class="row-odd"><td><p>URA</p></td>
-<td><p>DG5</p></td>
+<tr class="row-odd"><td><p>A</p></td>
+<td><p>DA5</p></td>
 <td></td>
 <td></td>
 <td></td>
@@ -399,11 +399,11 @@ <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>C3’</p></td>
 <td><p>O3’</p></td>
 <td><p>P</p></td>
-<td><p>C3’</p></td>
+<td><p>O5’</p></td>
+<td><p>C5’</p></td>
 </tr>
 </tbody>
 </table>
@@ -413,22 +413,22 @@ <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>O2</p></td>
-<td><p>O4</p></td>
-<td><p>N4</p></td>
-<td><p>N1</p></td>
+<tr class="row-odd"><td><p>N2</p></td>
 <td><p>N3</p></td>
+<td><p>C5</p></td>
 <td><p>C2</p></td>
-<td><p>N9</p></td>
 <td><p>O6</p></td>
-</tr>
-<tr class="row-even"><td><p>C6</p></td>
+<td><p>N4</p></td>
 <td><p>C5M</p></td>
-<td><p>C5</p></td>
-<td><p>N2</p></td>
+<td><p>N9</p></td>
+</tr>
+<tr class="row-even"><td><p>O2</p></td>
+<td><p>C6</p></td>
 <td><p>N6</p></td>
-<td><p>C8</p></td>
+<td><p>N1</p></td>
 <td><p>C4</p></td>
+<td><p>O4</p></td>
+<td><p>C8</p></td>
 <td><p>N7</p></td>
 </tr>
 </tbody>
@@ -439,11 +439,11 @@ <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>C2’</p></td>
+<tr class="row-odd"><td><p>C3’</p></td>
 <td><p>C4’</p></td>
+<td><p>O4’</p></td>
+<td><p>C2’</p></td>
 <td><p>C1’</p></td>
-<td><p>C3’</p></td>
 </tr>
 </tbody>
 </table>