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

@@ -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="d1eecba420af412094d4391f52a405c0" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="14eefe35f2b542c7a9fd19cd40460698" 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 0x7f7236c51e50&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f69ae7285f0&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 0x7f7236c79280&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f69aea60350&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 0x7f7236326ed0&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f69b54f6fc0&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">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: 9, 10, 32, 51, 26, 31, 7, 2, 70, 25, 54, 22, 29, 81, 50, 30, 52, 73, 24, 23, 6, 5, 21, 72, 55, 57, 20, 56, 3, 1. These can be defined manually using the keyword &#39;vdwradii&#39;
+<span class="ne">ValueError</span>: vdw radii for types: 55, 1, 21, 25, 23, 56, 7, 70, 30, 51, 6, 32, 81, 9, 73, 24, 5, 2, 31, 10, 22, 72, 52, 54, 57, 20, 26, 3, 29, 50. 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> Apr 21, 2026</p>
+<p><strong>Last updated:</strong> Apr 24, 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/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([[0.2353398 , 0.9638517 , 0.7066329 ],</span>
-<span class="go">       [0.40192217, 0.8810793 , 0.6095617 ],</span>
-<span class="go">       [0.8027306 , 0.7627569 , 0.35185593],</span>
+<span class="go">array([[0.8455031 , 0.23796308, 0.50634354],</span>
+<span class="go">       [0.14672625, 0.56461364, 0.74592525],</span>
+<span class="go">       [0.89599395, 0.79423636, 0.61019397],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.68539596, 0.89203113, 0.7951874 ],</span>
-<span class="go">       [0.796618  , 0.3804505 , 0.11035424],</span>
-<span class="go">       [0.2108357 , 0.48776805, 0.23092575]],</span>
+<span class="go">       [0.46275496, 0.13015974, 0.39076182],</span>
+<span class="go">       [0.7224128 , 0.82141334, 0.4341583 ],</span>
+<span class="go">       [0.35195768, 0.47419393, 0.6789639 ]],</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([[0.2353398 , 0.9638517 , 0.7066329 ],</span>
-<span class="go">       [0.40192217, 0.8810793 , 0.6095617 ],</span>
-<span class="go">       [0.8027306 , 0.7627569 , 0.35185593],</span>
+<span class="go">array([[0.8455031 , 0.23796308, 0.50634354],</span>
+<span class="go">       [0.14672625, 0.56461364, 0.74592525],</span>
+<span class="go">       [0.89599395, 0.79423636, 0.61019397],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.68539596, 0.89203113, 0.7951874 ],</span>
-<span class="go">       [0.796618  , 0.3804505 , 0.11035424],</span>
-<span class="go">       [0.2108357 , 0.48776805, 0.23092575]],</span>
+<span class="go">       [0.46275496, 0.13015974, 0.39076182],</span>
+<span class="go">       [0.7224128 , 0.82141334, 0.4341583 ],</span>
+<span class="go">       [0.35195768, 0.47419393, 0.6789639 ]],</span>
 <span class="go">      shape=(47681, 3), dtype=float32)</span>
 </pre></div>
 </div>