rebuilt html docs for version 2.9.0-dev0 from branch develop with sph…

…inx at 1e95ff7

2.9.0-dev0/examples/constructing_universe.html

@@ -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="209f8c5bcb0a447ba7f60116e2ad2c0a" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="b19d92875ca044e386d703015a0e778f" 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>

2.9.0-dev0/formats/auxiliary.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 0x7fc083712b00&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f972b5fb280&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 0x7fc08a0c7a00&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9732e6fa90&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="nn">matplotlib.pyplot</span> <span class="k">as</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 0x7fc0884b0790&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f9730ee7490&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>

2.9.0-dev0/index.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> 2.9.0-dev0</p>
-<p><strong>Last updated:</strong> Nov 29, 2024</p>
+<p><strong>Last updated:</strong> Dec 03, 2024</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>.

2.9.0-dev0/reading_and_writing.html

@@ -320,27 +320,27 @@ <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([[0.8580664 , 0.7531802 , 0.8636146 ],</span>
-<span class="go">       [0.9920289 , 0.04813056, 0.51556283],</span>
-<span class="go">       [0.49463013, 0.31598002, 0.942926  ],</span>
+<span class="go">array([[0.37988022, 0.51656055, 0.15907744],</span>
+<span class="go">       [0.72099   , 0.4801856 , 0.2797198 ],</span>
+<span class="go">       [0.8629845 , 0.06931261, 0.9472692 ],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.5120667 , 0.1280541 , 0.175151  ],</span>
-<span class="go">       [0.9157625 , 0.4990046 , 0.10934538],</span>
-<span class="go">       [0.528182  , 0.8287255 , 0.44734144]], dtype=float32)</span>
+<span class="go">       [0.8358833 , 0.11555139, 0.40879834],</span>
+<span class="go">       [0.16805787, 0.9488844 , 0.9357962 ],</span>
+<span class="go">       [0.6872807 , 0.50745964, 0.24288727]], dtype=float32)</span>
 </pre></div>
 </div>
 <p>or they can be directly passed in when creating a Universe.</p>
 <div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [17]: </span><span class="n">universe2</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PDB</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="n">MemoryReader</span><span class="p">)</span>
 
 <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([[0.8580664 , 0.7531802 , 0.8636146 ],</span>
-<span class="go">       [0.9920289 , 0.04813056, 0.51556283],</span>
-<span class="go">       [0.49463013, 0.31598002, 0.942926  ],</span>
+<span class="go">array([[0.37988022, 0.51656055, 0.15907744],</span>
+<span class="go">       [0.72099   , 0.4801856 , 0.2797198 ],</span>
+<span class="go">       [0.8629845 , 0.06931261, 0.9472692 ],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.5120667 , 0.1280541 , 0.175151  ],</span>
-<span class="go">       [0.9157625 , 0.4990046 , 0.10934538],</span>
-<span class="go">       [0.528182  , 0.8287255 , 0.44734144]], dtype=float32)</span>
+<span class="go">       [0.8358833 , 0.11555139, 0.40879834],</span>
+<span class="go">       [0.16805787, 0.9488844 , 0.9357962 ],</span>
+<span class="go">       [0.6872807 , 0.50745964, 0.24288727]], dtype=float32)</span>
 </pre></div>
 </div>
 </section>

2.9.0-dev0/standard_selections.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>
+<tr class="row-odd"><td><p>O</p></td>
+<td><p>N</p></td>
 <td><p>CA</p></td>
-<td><p>O</p></td>
+<td><p>C</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>G</p></td>
-<td><p>RG5</p></td>
-<td><p>RG</p></td>
-<td><p>RU5</p></td>
-<td><p>A</p></td>
-<td><p>T</p></td>
-<td><p>DT</p></td>
-<td><p>RC5</p></td>
-</tr>
-<tr class="row-even"><td><p>URA</p></td>
+<tr class="row-odd"><td><p>THY</p></td>
+<td><p>DG3</p></td>
+<td><p>RU</p></td>
+<td><p>ADE</p></td>
 <td><p>RU3</p></td>
-<td><p>DA5</p></td>
+<td><p>RA3</p></td>
+<td><p>DC</p></td>
+<td><p>RG3</p></td>
+</tr>
+<tr class="row-even"><td><p>RG5</p></td>
 <td><p>DA</p></td>
-<td><p>DG5</p></td>
-<td><p>RU</p></td>
+<td><p>DT</p></td>
 <td><p>RC3</p></td>
-<td><p>DG</p></td>
-</tr>
-<tr class="row-odd"><td><p>ADE</p></td>
-<td><p>DC3</p></td>
-<td><p>GUA</p></td>
-<td><p>DA3</p></td>
-<td><p>THY</p></td>
 <td><p>RC</p></td>
-<td><p>RA5</p></td>
+<td><p>C</p></td>
+<td><p>DG5</p></td>
+<td><p>DT5</p></td>
+</tr>
+<tr class="row-odd"><td><p>T</p></td>
 <td><p>U</p></td>
+<td><p>GUA</p></td>
+<td><p>RG</p></td>
+<td><p>A</p></td>
+<td><p>G</p></td>
+<td><p>RU5</p></td>
+<td><p>DG</p></td>
 </tr>
-<tr class="row-even"><td><p>C</p></td>
-<td><p>DG3</p></td>
-<td><p>DC</p></td>
-<td><p>DT5</p></td>
-<td><p>DC5</p></td>
-<td><p>RG3</p></td>
+<tr class="row-even"><td><p>DA5</p></td>
+<td><p>RA5</p></td>
+<td><p>RA</p></td>
+<td><p>DA3</p></td>
+<td><p>DT3</p></td>
+<td><p>DC3</p></td>
 <td><p>CYT</p></td>
-<td><p>RA3</p></td>
+<td><p>URA</p></td>
 </tr>
-<tr class="row-odd"><td><p>DT3</p></td>
-<td><p>RA</p></td>
+<tr class="row-odd"><td><p>DC5</p></td>
+<td><p>RC5</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>O3’</p></td>
+<tr class="row-odd"><td><p>P</p></td>
+<td><p>O3’</p></td>
 <td><p>C5’</p></td>
-<td><p>P</p></td>
-<td><p>O5’</p></td>
 <td><p>C3’</p></td>
+<td><p>O5’</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>O6</p></td>
-<td><p>C5</p></td>
-<td><p>N9</p></td>
-<td><p>C2</p></td>
+<tr class="row-odd"><td><p>C6</p></td>
+<td><p>C8</p></td>
 <td><p>N4</p></td>
-<td><p>N3</p></td>
 <td><p>O2</p></td>
+<td><p>N6</p></td>
 <td><p>O4</p></td>
-</tr>
-<tr class="row-even"><td><p>N6</p></td>
-<td><p>C6</p></td>
-<td><p>N1</p></td>
-<td><p>N7</p></td>
 <td><p>N2</p></td>
-<td><p>C8</p></td>
 <td><p>C4</p></td>
+</tr>
+<tr class="row-even"><td><p>N1</p></td>
+<td><p>O6</p></td>
+<td><p>N9</p></td>
+<td><p>N3</p></td>
+<td><p>N7</p></td>
+<td><p>C2</p></td>
 <td><p>C5M</p></td>
+<td><p>C5</p></td>
 </tr>
 </tbody>
 </table>
@@ -439,10 +439,10 @@ <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>O4’</p></td>
-<td><p>C1’</p></td>
+<tr class="row-odd"><td><p>C4’</p></td>
 <td><p>C2’</p></td>
-<td><p>C4’</p></td>
+<td><p>C1’</p></td>
+<td><p>O4’</p></td>
 <td><p>C3’</p></td>
 </tr>
 </tbody>

2.9.0-dev0/testing.html

@@ -433,13 +433,13 @@ <h4>Testing exceptions and warnings<a class="headerlink" href="#testing-exceptio
 </section>
 <section id="failing-tests">
 <h4>Failing tests<a class="headerlink" href="#failing-tests" title="Link to this heading"></a></h4>
-<p>To mark an expected failure, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.xfail" title="(in pytest v8.4.0.dev223)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.xfail()</span></code></a> decorator:</p>
+<p>To mark an expected failure, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.xfail" title="(in pytest v8.4.0.dev250)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.xfail()</span></code></a> decorator:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">xfail</span>
 <span class="k">def</span> <span class="nf">tested_expected_failure</span><span class="p">():</span>
     <span class="k">assert</span> <span class="mi">1</span> <span class="o">==</span> <span class="mi">2</span>
 </pre></div>
 </div>
-<p>To manually fail a test, make a call to <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fail" title="(in pytest v8.4.0.dev223)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fail()</span></code></a>:</p>
+<p>To manually fail a test, make a call to <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fail" title="(in pytest v8.4.0.dev250)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fail()</span></code></a>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">test_open</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tmpdir</span><span class="p">):</span>
     <span class="n">outfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">tmpdir</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;lammps-writer-test.dcd&#39;</span><span class="p">))</span>
     <span class="k">try</span><span class="p">:</span>
@@ -452,7 +452,7 @@ <h4>Failing tests<a class="headerlink" href="#failing-tests" title="Link to this
 </section>
 <section id="skipping-tests">
 <h4>Skipping tests<a class="headerlink" href="#skipping-tests" title="Link to this heading"></a></h4>
-<p>To skip tests based on a condition, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.skipif" title="(in pytest v8.4.0.dev223)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.skipif(condition)</span></code></a> decorator:</p>
+<p>To skip tests based on a condition, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.skipif" title="(in pytest v8.4.0.dev250)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.skipif(condition)</span></code></a> decorator:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">shares_memory</span>
@@ -467,7 +467,7 @@ <h4>Skipping tests<a class="headerlink" href="#skipping-tests" title="Link to th
     <span class="k">assert</span> <span class="ow">not</span> <span class="n">np</span><span class="o">.</span><span class="n">shares_memory</span><span class="p">(</span><span class="n">original</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">positions</span><span class="p">,</span> <span class="n">copy</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">positions</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>To skip a test if a module is not available for importing, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.importorskip" title="(in pytest v8.4.0.dev223)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.importorskip('module_name')</span></code></a></p>
+<p>To skip a test if a module is not available for importing, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.importorskip" title="(in pytest v8.4.0.dev250)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.importorskip('module_name')</span></code></a></p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">test_write_trajectory_netCDF4</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
     <span class="n">pytest</span><span class="o">.</span><span class="n">importorskip</span><span class="p">(</span><span class="s2">&quot;netCDF4&quot;</span><span class="p">)</span>
     <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_test_write_trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">outfile</span><span class="p">)</span>
@@ -477,7 +477,7 @@ <h4>Skipping tests<a class="headerlink" href="#skipping-tests" title="Link to th
 </section>
 <section id="fixtures">
 <h3>Fixtures<a class="headerlink" href="#fixtures" title="Link to this heading"></a></h3>
-<p>Use <a class="reference external" href="https://docs.pytest.org/en/latest/fixture.html">fixtures</a> as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fixture" title="(in pytest v8.4.0.dev223)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fixture()</span></code></a> decorator, over a function that returns the object you need:</p>
+<p>Use <a class="reference external" href="https://docs.pytest.org/en/latest/fixture.html">fixtures</a> as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fixture" title="(in pytest v8.4.0.dev250)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fixture()</span></code></a> decorator, over a function that returns the object you need:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@pytest</span><span class="o">.</span><span class="n">fixture</span>
 <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
     <span class="k">return</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref_filename</span><span class="p">)</span>