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

@@ -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="757a3802c37b4dadb34c8442f5b1de0e" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="3cdf3a26456d4bb89851473560ae193b" 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 0x7f99ed953860&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f03ecd4e810&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 0x7f99e7df27b0&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f03ecf19e50&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 0x7f99e7373230&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f03ec88f1d0&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

@@ -363,23 +363,23 @@ <h3>Order of guessing<a class="headerlink" href="#order-of-guessing" title="Link
 <span class="g g-Whitespace">    </span><span class="mi">165</span> <span class="c1"># check if the topology already has the attribute to partially guess it</span>
 <span class="g g-Whitespace">    </span><span class="mi">166</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_universe</span><span class="o">.</span><span class="n">atoms</span><span class="p">,</span> <span class="n">attr_to_guess</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">force_guess</span><span class="p">:</span>
 
-<span class="nn">File ~/micromamba/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/guesser/default_guesser.py:438,</span> in <span class="ni">DefaultGuesser.guess_bonds</span><span class="nt">(self, atoms, coords)</span>
-<span class="g g-Whitespace">    </span><span class="mi">436</span> <span class="c1"># check that all types have a defined vdw</span>
-<span class="g g-Whitespace">    </span><span class="mi">437</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">val</span> <span class="ow">in</span> <span class="n">vdwradii</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">atomtypes</span><span class="p">)):</span>
-<span class="ne">--&gt; </span><span class="mi">438</span>     <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-<span class="g g-Whitespace">    </span><span class="mi">439</span>         <span class="p">(</span>
-<span class="g g-Whitespace">    </span><span class="mi">440</span>             <span class="s2">&quot;vdw radii for types: &quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">441</span>             <span class="o">+</span> <span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
-<span class="g g-Whitespace">    </span><span class="mi">442</span>                 <span class="p">[</span><span class="n">t</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">atomtypes</span><span class="p">)</span> <span class="k">if</span> <span class="n">t</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">vdwradii</span><span class="p">]</span>
-<span class="g g-Whitespace">    </span><span class="mi">443</span>             <span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">444</span>             <span class="o">+</span> <span class="s2">&quot;. These can be defined manually using the&quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">445</span>             <span class="o">+</span> <span class="sa">f</span><span class="s2">&quot; keyword &#39;vdwradii&#39;&quot;</span>
-<span class="g g-Whitespace">    </span><span class="mi">446</span>         <span class="p">)</span>
-<span class="g g-Whitespace">    </span><span class="mi">447</span>     <span class="p">)</span>
-<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: 29, 30, 10, 1, 52, 7, 57, 21, 26, 23, 5, 20, 3, 51, 55, 70, 72, 24, 56, 81, 9, 25, 54, 2, 22, 73, 6, 50, 31, 32. These can be defined manually using the keyword &#39;vdwradii&#39;
+<span class="nn">File ~/micromamba/envs/mda-user-guide/lib/python3.12/site-packages/MDAnalysis/guesser/default_guesser.py:441,</span> in <span class="ni">DefaultGuesser.guess_bonds</span><span class="nt">(self, atoms, coords)</span>
+<span class="g g-Whitespace">    </span><span class="mi">439</span> <span class="c1"># check that all types have a defined vdw</span>
+<span class="g g-Whitespace">    </span><span class="mi">440</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">val</span> <span class="ow">in</span> <span class="n">vdwradii</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">atomtypes</span><span class="p">)):</span>
+<span class="ne">--&gt; </span><span class="mi">441</span>     <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+<span class="g g-Whitespace">    </span><span class="mi">442</span>         <span class="p">(</span>
+<span class="g g-Whitespace">    </span><span class="mi">443</span>             <span class="s2">&quot;vdw radii for types: &quot;</span>
+<span class="g g-Whitespace">    </span><span class="mi">444</span>             <span class="o">+</span> <span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+<span class="g g-Whitespace">    </span><span class="mi">445</span>                 <span class="p">[</span><span class="n">t</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">atomtypes</span><span class="p">)</span> <span class="k">if</span> <span class="n">t</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">vdwradii</span><span class="p">]</span>
+<span class="g g-Whitespace">    </span><span class="mi">446</span>             <span class="p">)</span>
+<span class="g g-Whitespace">    </span><span class="mi">447</span>             <span class="o">+</span> <span class="s2">&quot;. These can be defined manually using the&quot;</span>
+<span class="g g-Whitespace">    </span><span class="mi">448</span>             <span class="o">+</span> <span class="sa">f</span><span class="s2">&quot; keyword &#39;vdwradii&#39;&quot;</span>
+<span class="g g-Whitespace">    </span><span class="mi">449</span>         <span class="p">)</span>
+<span class="g g-Whitespace">    </span><span class="mi">450</span>     <span class="p">)</span>
+<span class="g g-Whitespace">    </span><span class="mi">452</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">454</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: 5, 20, 72, 1, 73, 7, 81, 29, 3, 30, 54, 22, 70, 31, 9, 25, 51, 56, 52, 57, 6, 10, 23, 32, 26, 24, 21, 55, 50, 2. 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> Mar 24, 2026</p>
+<p><strong>Last updated:</strong> Mar 27, 2026</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([[0.15735286, 0.38165665, 0.0351738 ],</span>
-<span class="go">       [0.25182623, 0.62850213, 0.9313244 ],</span>
-<span class="go">       [0.26050243, 0.26548767, 0.1963082 ],</span>
+<span class="go">array([[0.6875658 , 0.78742814, 0.3906397 ],</span>
+<span class="go">       [0.70865184, 0.39357167, 0.7077977 ],</span>
+<span class="go">       [0.1239754 , 0.05433128, 0.82379866],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.44937775, 0.69725835, 0.7428036 ],</span>
-<span class="go">       [0.51406956, 0.0865438 , 0.9742243 ],</span>
-<span class="go">       [0.7896645 , 0.38141623, 0.5184715 ]],</span>
+<span class="go">       [0.05072585, 0.68809956, 0.43131375],</span>
+<span class="go">       [0.44890735, 0.4795402 , 0.09977882],</span>
+<span class="go">       [0.3389504 , 0.11222287, 0.7483889 ]],</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([[0.15735286, 0.38165665, 0.0351738 ],</span>
-<span class="go">       [0.25182623, 0.62850213, 0.9313244 ],</span>
-<span class="go">       [0.26050243, 0.26548767, 0.1963082 ],</span>
+<span class="go">array([[0.6875658 , 0.78742814, 0.3906397 ],</span>
+<span class="go">       [0.70865184, 0.39357167, 0.7077977 ],</span>
+<span class="go">       [0.1239754 , 0.05433128, 0.82379866],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.44937775, 0.69725835, 0.7428036 ],</span>
-<span class="go">       [0.51406956, 0.0865438 , 0.9742243 ],</span>
-<span class="go">       [0.7896645 , 0.38141623, 0.5184715 ]],</span>
+<span class="go">       [0.05072585, 0.68809956, 0.43131375],</span>
+<span class="go">       [0.44890735, 0.4795402 , 0.09977882],</span>
+<span class="go">       [0.3389504 , 0.11222287, 0.7483889 ]],</span>
 <span class="go">      shape=(47681, 3), dtype=float32)</span>
 </pre></div>
 </div>

2.11.0-dev0/index.html

@@ -332,10 +332,10 @@ <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>N</p></td>
-<td><p>C</p></td>
-<td><p>CA</p></td>
+<tr class="row-odd"><td><p>CA</p></td>
 <td><p>O</p></td>
+<td><p>C</p></td>
+<td><p>N</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>A</p></td>
-<td><p>THY</p></td>
-<td><p>C</p></td>
+<tr class="row-odd"><td><p>RC5</p></td>
+<td><p>RU5</p></td>
 <td><p>DG</p></td>
-<td><p>G</p></td>
-<td><p>T</p></td>
 <td><p>RG3</p></td>
-<td><p>DT3</p></td>
-</tr>
-<tr class="row-even"><td><p>DT5</p></td>
-<td><p>URA</p></td>
-<td><p>DC3</p></td>
-<td><p>RG5</p></td>
+<td><p>DC</p></td>
+<td><p>RA5</p></td>
+<td><p>RA</p></td>
 <td><p>RU3</p></td>
-<td><p>RC</p></td>
-<td><p>RA3</p></td>
-<td><p>DA</p></td>
 </tr>
-<tr class="row-odd"><td><p>DG5</p></td>
-<td><p>RU5</p></td>
-<td><p>RC5</p></td>
+<tr class="row-even"><td><p>G</p></td>
+<td><p>RA3</p></td>
+<td><p>DA3</p></td>
+<td><p>DT</p></td>
+<td><p>DT3</p></td>
+<td><p>C</p></td>
+<td><p>T</p></td>
 <td><p>CYT</p></td>
-<td><p>RA5</p></td>
+</tr>
+<tr class="row-odd"><td><p>A</p></td>
 <td><p>DC5</p></td>
-<td><p>DA5</p></td>
-<td><p>DC</p></td>
+<td><p>THY</p></td>
+<td><p>GUA</p></td>
+<td><p>DG3</p></td>
+<td><p>U</p></td>
+<td><p>RC</p></td>
+<td><p>DG5</p></td>
 </tr>
-<tr class="row-even"><td><p>DG3</p></td>
-<td><p>DA3</p></td>
+<tr class="row-even"><td><p>RG5</p></td>
+<td><p>DA</p></td>
+<td><p>URA</p></td>
+<td><p>RC3</p></td>
 <td><p>RU</p></td>
-<td><p>ADE</p></td>
+<td><p>DT5</p></td>
 <td><p>RG</p></td>
-<td><p>GUA</p></td>
-<td><p>RC3</p></td>
-<td><p>DT</p></td>
+<td><p>DC3</p></td>
 </tr>
-<tr class="row-odd"><td><p>U</p></td>
-<td><p>RA</p></td>
+<tr class="row-odd"><td><p>ADE</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>C5’</p></td>
-<td><p>O3’</p></td>
+<tr class="row-odd"><td><p>P</p></td>
 <td><p>C3’</p></td>
+<td><p>O3’</p></td>
 <td><p>O5’</p></td>
-<td><p>P</p></td>
+<td><p>C5’</p></td>
 </tr>
 </tbody>
 </table>
@@ -413,23 +413,23 @@ <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>
+<tr class="row-odd"><td><p>C2</p></td>
+<td><p>C5</p></td>
+<td><p>N2</p></td>
+<td><p>N3</p></td>
+<td><p>N4</p></td>
 <td><p>N7</p></td>
+<td><p>O6</p></td>
+<td><p>N1</p></td>
+</tr>
+<tr class="row-even"><td><p>N6</p></td>
+<td><p>C4</p></td>
+<td><p>O4</p></td>
 <td><p>C6</p></td>
 <td><p>C5M</p></td>
-<td><p>C2</p></td>
-<td><p>N4</p></td>
-<td><p>N2</p></td>
-<td><p>O4</p></td>
-</tr>
-<tr class="row-even"><td><p>C8</p></td>
-<td><p>O6</p></td>
-<td><p>N3</p></td>
 <td><p>N9</p></td>
-<td><p>C4</p></td>
-<td><p>N6</p></td>
+<td><p>C8</p></td>
 <td><p>O2</p></td>
-<td><p>C5</p></td>
 </tr>
 </tbody>
 </table>
@@ -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>C1’</p></td>
-<td><p>C4’</p></td>
-<td><p>O4’</p></td>
+<tr class="row-odd"><td><p>O4’</p></td>
 <td><p>C3’</p></td>
 <td><p>C2’</p></td>
+<td><p>C1’</p></td>
+<td><p>C4’</p></td>
 </tr>
 </tbody>
 </table>