rebuilt html docs for version 2.8.0-dev0 from branch develop with sph…

…inx at d2729f7

2.8.0-dev0/_modules/MDAnalysis/topology/ITPParser.html

@@ -747,7 +747,15 @@ <h1>Source code for MDAnalysis.topology.ITPParser</h1><div class="highlight"><pr
         <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span> <span class="ow">in</span> <span class="n">SYMB2Z</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">):</span>
             <span class="n">attrs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Elements</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elements</span><span class="p">,</span>
                          <span class="n">dtype</span><span class="o">=</span><span class="nb">object</span><span class="p">),</span> <span class="n">guessed</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
-
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span>
+                <span class="s2">&quot;The elements attribute has been populated by guessing &quot;</span>
+                <span class="s2">&quot;elements from atom types. This behaviour has been &quot;</span>
+                <span class="s2">&quot;temporarily added to the ITPParser as we transition &quot;</span>
+                <span class="s2">&quot;to the new guessing API. &quot;</span>
+                <span class="s2">&quot;This behavior will be removed in release 3.0. &quot;</span>
+                <span class="s2">&quot;Please see issue #4698 for more information. &quot;</span><span class="p">,</span>
+                <span class="ne">DeprecationWarning</span>
+            <span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;Element information is missing, elements attribute &quot;</span>
                           <span class="s2">&quot;will not be populated. If needed these can be &quot;</span>

2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html

@@ -1048,15 +1048,15 @@ <h2><span class="section-number">4.4.3.8. </span>Classes<a class="headerlink" hr
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS">
-<span class="sig-name descname"><span class="pre">DEFAULT_ACCEPTORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OE1',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'OE2',</span> <span class="pre">'OC2',</span> <span class="pre">'SD',</span> <span class="pre">'OC1',</span> <span class="pre">'OH2',</span> <span class="pre">'ND1',</span> <span class="pre">'OD1',</span> <span class="pre">'OD2',</span> <span class="pre">'SG',</span> <span class="pre">'OG',</span> <span class="pre">'NE2',</span> <span class="pre">'O',</span> <span class="pre">'OG1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'OW',</span> <span class="pre">'OY',</span> <span class="pre">'OH',</span> <span class="pre">'SM',</span> <span class="pre">'OS',</span> <span class="pre">'O2',</span> <span class="pre">'N',</span> <span class="pre">'O'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">DEFAULT_ACCEPTORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OH',</span> <span class="pre">'OG1',</span> <span class="pre">'ND1',</span> <span class="pre">'OW',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'O',</span> <span class="pre">'OD2',</span> <span class="pre">'OC2',</span> <span class="pre">'SD',</span> <span class="pre">'OG',</span> <span class="pre">'SG',</span> <span class="pre">'OE1',</span> <span class="pre">'OE2',</span> <span class="pre">'OH2',</span> <span class="pre">'OD1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'OS',</span> <span class="pre">'O',</span> <span class="pre">'NT',</span> <span class="pre">'OW',</span> <span class="pre">'OY',</span> <span class="pre">'N',</span> <span class="pre">'SM',</span> <span class="pre">'O2'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS" title="Link to this definition"></a></dt>
 <dd><p>default atom names that are treated as hydrogen <em>acceptors</em>
 (see <a class="reference internal" href="#default-atom-names-for-water-bridge-analysis"><span class="std std-ref">Default heavy atom names for CHARMM27 force field.</span></a>);
 use the keyword <cite>acceptors</cite> to add a list of additional acceptor names.</p>
 </dd></dl>
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS">
-<span class="sig-name descname"><span class="pre">DEFAULT_DONORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('NH1',</span> <span class="pre">'NE',</span> <span class="pre">'ND1',</span> <span class="pre">'OW',</span> <span class="pre">'NE1',</span> <span class="pre">'OH',</span> <span class="pre">'NH2',</span> <span class="pre">'OG1',</span> <span class="pre">'SG',</span> <span class="pre">'OG',</span> <span class="pre">'NZ',</span> <span class="pre">'N',</span> <span class="pre">'NE2',</span> <span class="pre">'ND2',</span> <span class="pre">'OH2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'N',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'N3'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">DEFAULT_DONORS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'CHARMM27':</span> <span class="pre">('OH',</span> <span class="pre">'NZ',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'NE1',</span> <span class="pre">'OG',</span> <span class="pre">'ND1',</span> <span class="pre">'NH2',</span> <span class="pre">'SG',</span> <span class="pre">'OW',</span> <span class="pre">'OH2',</span> <span class="pre">'N',</span> <span class="pre">'ND2',</span> <span class="pre">'NH1',</span> <span class="pre">'NE'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'OW',</span> <span class="pre">'N',</span> <span class="pre">'NT',</span> <span class="pre">'N3'),</span> <span class="pre">'other':</span> <span class="pre">()}</span></em><a class="headerlink" href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS" title="Link to this definition"></a></dt>
 <dd><p>default heavy atom names whose hydrogens are treated as <em>donors</em>
 (see <a class="reference internal" href="#default-atom-names-for-water-bridge-analysis"><span class="std std-ref">Default heavy atom names for CHARMM27 force field.</span></a>);
 use the keyword <cite>donors</cite> to add a list of additional donor names.</p>

2.8.0-dev0/documentation_pages/coordinates/GSD.html

@@ -214,7 +214,7 @@ <h2><span class="section-number">7.7.1. </span>Classes<a class="headerlink" href
 <p><span class="versionmodified added">Added in version 0.17.0.</span></p>
 </div>
 <div class="versionchanged">
-<p><span class="versionmodified changed">Changed in version 2.0.0: </span>Now use a picklable <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.HOOMDTrajectory" title="(in GSD v3.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">gsd.hoomd.HOOMDTrajectory</span></code></a>–
+<p><span class="versionmodified changed">Changed in version 2.0.0: </span>Now use a picklable <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.HOOMDTrajectory" title="(in GSD v3.4.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">gsd.hoomd.HOOMDTrajectory</span></code></a>–
 <a class="reference internal" href="#MDAnalysis.coordinates.GSD.GSDPicklable" title="MDAnalysis.coordinates.GSD.GSDPicklable"><code class="xref py py-class docutils literal notranslate"><span class="pre">GSDPicklable</span></code></a></p>
 </div>
 <div class="versionchanged">
@@ -899,10 +899,10 @@ <h2><span class="section-number">7.7.1. </span>Classes<a class="headerlink" href
 <dt class="sig sig-object py" id="MDAnalysis.coordinates.GSD.GSDPicklable">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">MDAnalysis.coordinates.GSD.</span></span><span class="sig-name descname"><span class="pre">GSDPicklable</span></span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GSD.html#GSDPicklable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysis.coordinates.GSD.GSDPicklable" title="Link to this definition"></a></dt>
 <dd><p>Hoomd GSD file object (read-only) that can be pickled.</p>
-<p>This class provides a file-like object (as by <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.open" title="(in GSD v3.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">gsd.hoomd.open()</span></code></a>,
+<p>This class provides a file-like object (as by <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.open" title="(in GSD v3.4.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">gsd.hoomd.open()</span></code></a>,
 namely <code class="xref py py-class docutils literal notranslate"><span class="pre">gsd.hoodm.HOOMDTrajectory</span></code>) that, unlike file objects,
 can be pickled. Only read mode is supported.</p>
-<p>When the file is pickled, filename and mode of <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.fl.html#gsd.fl.GSDFile" title="(in GSD v3.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">gsd.fl.GSDFile</span></code></a> in
+<p>When the file is pickled, filename and mode of <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.fl.html#gsd.fl.GSDFile" title="(in GSD v3.4.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">gsd.fl.GSDFile</span></code></a> in
 the file are saved. On unpickling, the file is opened by filename.
 This means that for a successful unpickle, the original file still has to
 be accessible with its filename.</p>
@@ -914,7 +914,7 @@ <h2><span class="section-number">7.7.1. </span>Classes<a class="headerlink" href
 </div>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>file</strong> (<a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.fl.html#gsd.fl.GSDFile" title="(in GSD v3.4.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">gsd.fl.GSDFile</span></code></a>) – File to access.</p>
+<dd class="field-odd"><p><strong>file</strong> (<a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.fl.html#gsd.fl.GSDFile" title="(in GSD v3.4.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">gsd.fl.GSDFile</span></code></a>) – File to access.</p>
 </dd>
 </dl>
 <p class="rubric">Example</p>
@@ -941,7 +941,7 @@ <h2><span class="section-number">7.7.1. </span>Classes<a class="headerlink" href
 <span class="sig-prename descclassname"><span class="pre">MDAnalysis.coordinates.GSD.</span></span><span class="sig-name descname"><span class="pre">gsd_pickle_open</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'r'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/coordinates/GSD.html#gsd_pickle_open"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysis.coordinates.GSD.gsd_pickle_open" title="Link to this definition"></a></dt>
 <dd><p>Open hoomd schema GSD file with pickle function implemented.</p>
 <p>This function returns a GSDPicklable object. It can be used as a
-context manager, and replace the built-in <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.open" title="(in GSD v3.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">gsd.hoomd.open()</span></code></a> function
+context manager, and replace the built-in <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.open" title="(in GSD v3.4.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">gsd.hoomd.open()</span></code></a> function
 in read mode that only returns an unpicklable file object.</p>
 <p>Schema version will depend on the version of gsd module.</p>
 <div class="admonition note">
@@ -979,7 +979,7 @@ <h2><span class="section-number">7.7.1. </span>Classes<a class="headerlink" href
 </div>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
-<p><a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.anyopen" title="MDAnalysis.lib.util.anyopen"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.util.anyopen()</span></code></a>, <a class="reference internal" href="../lib/picklable_file_io.html#MDAnalysis.lib.picklable_file_io.pickle_open" title="MDAnalysis.lib.picklable_file_io.pickle_open"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.picklable_file_io.pickle_open()</span></code></a>, <a class="reference internal" href="../lib/picklable_file_io.html#MDAnalysis.lib.picklable_file_io.bz2_pickle_open" title="MDAnalysis.lib.picklable_file_io.bz2_pickle_open"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.picklable_file_io.bz2_pickle_open()</span></code></a>, <a class="reference internal" href="../lib/picklable_file_io.html#MDAnalysis.lib.picklable_file_io.gzip_pickle_open" title="MDAnalysis.lib.picklable_file_io.gzip_pickle_open"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.picklable_file_io.gzip_pickle_open()</span></code></a>, <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.open" title="(in GSD v3.4.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">gsd.hoomd.open()</span></code></a></p>
+<p><a class="reference internal" href="../lib/util.html#MDAnalysis.lib.util.anyopen" title="MDAnalysis.lib.util.anyopen"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.util.anyopen()</span></code></a>, <a class="reference internal" href="../lib/picklable_file_io.html#MDAnalysis.lib.picklable_file_io.pickle_open" title="MDAnalysis.lib.picklable_file_io.pickle_open"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.picklable_file_io.pickle_open()</span></code></a>, <a class="reference internal" href="../lib/picklable_file_io.html#MDAnalysis.lib.picklable_file_io.bz2_pickle_open" title="MDAnalysis.lib.picklable_file_io.bz2_pickle_open"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.picklable_file_io.bz2_pickle_open()</span></code></a>, <a class="reference internal" href="../lib/picklable_file_io.html#MDAnalysis.lib.picklable_file_io.gzip_pickle_open" title="MDAnalysis.lib.picklable_file_io.gzip_pickle_open"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.lib.picklable_file_io.gzip_pickle_open()</span></code></a>, <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#gsd.hoomd.open" title="(in GSD v3.4.1)"><code class="xref py py-func docutils literal notranslate"><span class="pre">gsd.hoomd.open()</span></code></a></p>
 </div>
 <div class="versionadded">
 <p><span class="versionmodified added">Added in version 2.0.0.</span></p>

2.8.0-dev0/documentation_pages/coordinates/init.html

@@ -375,7 +375,7 @@ <h2><span class="section-number">7.1.4. </span>Supported coordinate formats<a cl
 <tr class="row-odd"><td><p>HOOMD <a class="footnote-reference brackets" href="#a" id="id7" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></a></p></td>
 <td><p>gsd</p></td>
 <td><p>r</p></td>
-<td><p>HOOMD GSD format (using <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#module-gsd.hoomd" title="(in GSD v3.4.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gsd.hoomd</span></code></a>).
+<td><p>HOOMD GSD format (using <a class="reference external" href="https://gsd.readthedocs.io/en/stable/python-module-gsd.hoomd.html#module-gsd.hoomd" title="(in GSD v3.4.1)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">gsd.hoomd</span></code></a>).
 Module <a class="reference internal" href="GSD.html#module-MDAnalysis.coordinates.GSD" title="MDAnalysis.coordinates.GSD"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.coordinates.GSD</span></code></a></p></td>
 </tr>
 <tr class="row-even"><td><p>GAMESS</p></td>

2.8.0-dev0/index.html

@@ -149,7 +149,7 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 <dd class="field-odd"><p>2.8.0-dev0</p>
 </dd>
 <dt class="field-even">Date<span class="colon">:</span></dt>
-<dd class="field-even"><p>Oct 20, 2024</p>
+<dd class="field-even"><p>Oct 24, 2024</p>
 </dd>
 </dl>
 <p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is an object-oriented python