rebuilt html docs for version 2.10.0-dev0 from branch develop with sphinx at 6939953

Author: github-actions

2.10.0-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="0fec7c7b48e04c6ab8092973a6cb602a" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="2ba53d09ab7f4d19a6c0b62878da9116" 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>

2.10.0-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 0x7fd055291600&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f191ce09150&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 0x7fd055fde020&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f1917b8d900&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 0x7fd057619390&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f1917a04eb0&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>

2.10.0-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: 29, 22, 25, 24, 32, 10, 55, 72, 23, 56, 51, 73, 6, 2, 70, 50, 3, 5, 57, 81, 54, 26, 52, 7, 1, 20, 21, 31, 30, 9. These can be defined manually using the keyword &#39;vdwradii&#39;
+<span class="ne">ValueError</span>: vdw radii for types: 31, 57, 2, 7, 56, 24, 32, 21, 1, 6, 26, 70, 81, 25, 52, 29, 10, 54, 73, 9, 22, 51, 50, 3, 30, 20, 5, 72, 55, 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>

2.10.0-dev0/_images/auxiliary-1.png

@@ -192,7 +192,7 @@
   <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> 2.10.0-dev0</p>
-<p><strong>Last updated:</strong> Sep 02, 2025</p>
+<p><strong>Last updated:</strong> Sep 05, 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>.

2.10.0-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([[0.42741063, 0.00922342, 0.6143326 ],</span>
-<span class="go">       [0.15383257, 0.9899378 , 0.77942884],</span>
-<span class="go">       [0.35516596, 0.31616712, 0.47718456],</span>
+<span class="go">array([[0.98901296, 0.921778  , 0.8471628 ],</span>
+<span class="go">       [0.8574938 , 0.8635229 , 0.551288  ],</span>
+<span class="go">       [0.736985  , 0.82266283, 0.22308916],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.02330471, 0.805696  , 0.8164346 ],</span>
-<span class="go">       [0.77810466, 0.07304598, 0.51572824],</span>
-<span class="go">       [0.37853596, 0.9646609 , 0.79172784]],</span>
+<span class="go">       [0.4237809 , 0.23401038, 0.9353551 ],</span>
+<span class="go">       [0.1719129 , 0.5352706 , 0.97872806],</span>
+<span class="go">       [0.10453048, 0.53918105, 0.7274322 ]],</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([[0.42741063, 0.00922342, 0.6143326 ],</span>
-<span class="go">       [0.15383257, 0.9899378 , 0.77942884],</span>
-<span class="go">       [0.35516596, 0.31616712, 0.47718456],</span>
+<span class="go">array([[0.98901296, 0.921778  , 0.8471628 ],</span>
+<span class="go">       [0.8574938 , 0.8635229 , 0.551288  ],</span>
+<span class="go">       [0.736985  , 0.82266283, 0.22308916],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.02330471, 0.805696  , 0.8164346 ],</span>
-<span class="go">       [0.77810466, 0.07304598, 0.51572824],</span>
-<span class="go">       [0.37853596, 0.9646609 , 0.79172784]],</span>
+<span class="go">       [0.4237809 , 0.23401038, 0.9353551 ],</span>
+<span class="go">       [0.1719129 , 0.5352706 , 0.97872806],</span>
+<span class="go">       [0.10453048, 0.53918105, 0.7274322 ]],</span>
 <span class="go">      shape=(47681, 3), dtype=float32)</span>
 </pre></div>
 </div>