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

Author: github-actions

2.11.0-dev0/_downloads/35d4323e5cc041e33705e58839d7a259/auxiliary-1.hires.png

@@ -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="5571be83e11d4287b7c3e842dd4a5508" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="b4890dc7bbf14de2858984a9d1d1b8aa" 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/_downloads/899668c9e2e17d4c2fc64131d19cdebc/auxiliary-1.pdf

@@ -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 0x7faf23804b90&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f12492c5700&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 0x7faf23ceeba0&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f1243859460&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 0x7faf2363e120&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f1242524ad0&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/_downloads/e26175fa4b43d8229a32471a3e7c7831/auxiliary-1.png

@@ -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: 20, 21, 10, 30, 50, 32, 23, 52, 72, 2, 26, 9, 31, 1, 81, 57, 3, 55, 54, 29, 24, 70, 5, 25, 73, 7, 56, 51, 22, 6. These can be defined manually using the keyword &#39;vdwradii&#39;
+<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;
 </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/_images/auxiliary-1.png

@@ -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 11, 2025</p>
+<p><strong>Last updated:</strong> Nov 14, 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/examples/analysis/hydrogen_bonds/hbonds.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([[0.43428072, 0.6591771 , 0.8340298 ],</span>
-<span class="go">       [0.22990876, 0.74337006, 0.4288904 ],</span>
-<span class="go">       [0.80040604, 0.60976034, 0.28898978],</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">       ...,</span>
-<span class="go">       [0.8136455 , 0.9867994 , 0.9866304 ],</span>
-<span class="go">       [0.41428906, 0.52284384, 0.9664641 ],</span>
-<span class="go">       [0.03519778, 0.4686935 , 0.11677959]],</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">      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([[0.43428072, 0.6591771 , 0.8340298 ],</span>
-<span class="go">       [0.22990876, 0.74337006, 0.4288904 ],</span>
-<span class="go">       [0.80040604, 0.60976034, 0.28898978],</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">       ...,</span>
-<span class="go">       [0.8136455 , 0.9867994 , 0.9866304 ],</span>
-<span class="go">       [0.41428906, 0.52284384, 0.9664641 ],</span>
-<span class="go">       [0.03519778, 0.4686935 , 0.11677959]],</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">      shape=(47681, 3), dtype=float32)</span>
 </pre></div>
 </div>