rebuilt html docs for version 2.10.0-dev0 from branch develop with sphinx at b280419

Author: github-actions

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

@@ -240,7 +240,7 @@ <h3>Indexing and slicing<a class="headerlink" href="#indexing-and-slicing" title
 <span class="gh">Out[7]: </span><span class="go">array([0, 2, 4])</span>
 </pre></div>
 </div>
-<p>MDAnalysis also supports fancy indexing: passing a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> or a <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>.</p>
+<p>MDAnalysis also supports fancy indexing: passing a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> or a <a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>.</p>
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [8]: </span><span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span>
 
 <span class="gp">In [9]: </span><span class="n">u</span><span class="o">.</span><span class="n">atoms</span><span class="p">[</span><span class="n">indices</span><span class="p">]</span><span class="o">.</span><span class="n">indices</span>

2.10.0-dev0/atomgroup.html

@@ -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="1ea55ea7a3d44bfc879a2c040a3b3c47" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="e18fc54209f44382a12f21dad32b2451" 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/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 0x7fd84db69420&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7ff9a6ca79d0&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 0x7fd84dbd1c60&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7ff9a6e7c550&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 0x7fd84dce32e0&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7ff9a53ba110&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/examples/constructing_universe.html

@@ -252,7 +252,7 @@ <h2>Reading in<a class="headerlink" href="#reading-in" title="Link to this headi
 <li><p>time: ps</p></li>
 </ul>
 </div></blockquote>
-<p>Currently, if other units are detected, MDAnalysis will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#NotImplementedError" title="(in Python v3.13)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">NotImplementedError</span></code></a>.</p>
+<p>Currently, if other units are detected, MDAnalysis will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#NotImplementedError" title="(in Python v3.14)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">NotImplementedError</span></code></a>.</p>
 </section>
 <section id="writing-out">
 <h2>Writing out<a class="headerlink" href="#writing-out" title="Link to this heading"></a></h2>

2.10.0-dev0/formats/auxiliary.html

@@ -270,7 +270,7 @@ <h2>Reading in<a class="headerlink" href="#reading-in" title="Link to this headi
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">recordName</span> <span class="n">serial</span> <span class="n">atomName</span> <span class="n">residueName</span> <span class="n">residueNumber</span> <span class="n">X</span> <span class="n">Y</span> <span class="n">Z</span> <span class="n">charge</span> <span class="n">radius</span>
 </pre></div>
 </div>
-<p>Anything else will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.13)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code></a>.</p>
+<p>Anything else will raise a <a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.14)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code></a>.</p>
 <p>The whitespace is the most important feature of this format: fields
 <em>must</em> be separated by at least one space or tab character.</p>
 </section>

2.10.0-dev0/formats/reference/ncdf.html

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

@@ -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> Oct 07, 2025</p>
+<p><strong>Last updated:</strong> Oct 10, 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/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([[0.9698846 , 0.14219682, 0.7391416 ],</span>
-<span class="go">       [0.6978703 , 0.1957222 , 0.12173621],</span>
-<span class="go">       [0.39957583, 0.3693786 , 0.9720357 ],</span>
+<span class="go">array([[0.32602644, 0.7631936 , 0.9825418 ],</span>
+<span class="go">       [0.86445165, 0.92658633, 0.18274422],</span>
+<span class="go">       [0.9522029 , 0.5776288 , 0.6540529 ],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.91838706, 0.67035335, 0.69712627],</span>
-<span class="go">       [0.17226447, 0.20847343, 0.53334886],</span>
-<span class="go">       [0.5842144 , 0.04168625, 0.5767456 ]],</span>
+<span class="go">       [0.7257803 , 0.04970659, 0.9932215 ],</span>
+<span class="go">       [0.68967   , 0.5157973 , 0.06989766],</span>
+<span class="go">       [0.05291706, 0.8925698 , 0.42598587]],</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([[0.9698846 , 0.14219682, 0.7391416 ],</span>
-<span class="go">       [0.6978703 , 0.1957222 , 0.12173621],</span>
-<span class="go">       [0.39957583, 0.3693786 , 0.9720357 ],</span>
+<span class="go">array([[0.32602644, 0.7631936 , 0.9825418 ],</span>
+<span class="go">       [0.86445165, 0.92658633, 0.18274422],</span>
+<span class="go">       [0.9522029 , 0.5776288 , 0.6540529 ],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.91838706, 0.67035335, 0.69712627],</span>
-<span class="go">       [0.17226447, 0.20847343, 0.53334886],</span>
-<span class="go">       [0.5842144 , 0.04168625, 0.5767456 ]],</span>
+<span class="go">       [0.7257803 , 0.04970659, 0.9932215 ],</span>
+<span class="go">       [0.68967   , 0.5157973 , 0.06989766],</span>
+<span class="go">       [0.05291706, 0.8925698 , 0.42598587]],</span>
 <span class="go">      shape=(47681, 3), dtype=float32)</span>
 </pre></div>
 </div>