rebuilt html docs for version 2.11.0-dev0 from branch develop with sphinx at e6c1b44

Author: github-actions

2.11.0-dev0/_modules/MDAnalysis/topology/TPRParser.html

@@ -211,6 +211,7 @@ <h1>Source code for MDAnalysis.topology.TPRParser</h1><div class="highlight"><pr
 <span class="sd">   133        28             2024.1               yes</span>
 <span class="sd">   134        28             2024.4               yes</span>
 <span class="sd">   137        28             2025.0               yes</span>
+<span class="sd">   138        29             2026.0               yes</span>
 <span class="sd">   ========== ============== ==================== =====</span>
 
 <span class="sd">.. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported.</span>

2.11.0-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">('OH2',</span> <span class="pre">'OW',</span> <span class="pre">'OG',</span> <span class="pre">'ND1',</span> <span class="pre">'OE2',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'OD2',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'OD1',</span> <span class="pre">'OG1',</span> <span class="pre">'O',</span> <span class="pre">'OH',</span> <span class="pre">'OE1',</span> <span class="pre">'SG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('SM',</span> <span class="pre">'NT',</span> <span class="pre">'O2',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'OS'),</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">('OC2',</span> <span class="pre">'OC1',</span> <span class="pre">'SD',</span> <span class="pre">'OH2',</span> <span class="pre">'OG',</span> <span class="pre">'OD2',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'OE1',</span> <span class="pre">'OD1',</span> <span class="pre">'OE2',</span> <span class="pre">'OH',</span> <span class="pre">'ND1',</span> <span class="pre">'NE2',</span> <span class="pre">'SG',</span> <span class="pre">'OG1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'OH',</span> <span class="pre">'O2',</span> <span class="pre">'O',</span> <span class="pre">'OW',</span> <span class="pre">'SM',</span> <span class="pre">'OS'),</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">('NE2',</span> <span class="pre">'NE1',</span> <span class="pre">'NZ',</span> <span class="pre">'OH2',</span> <span class="pre">'OW',</span> <span class="pre">'OG1',</span> <span class="pre">'OH',</span> <span class="pre">'NH2',</span> <span class="pre">'NH1',</span> <span class="pre">'N',</span> <span class="pre">'OG',</span> <span class="pre">'ND1',</span> <span class="pre">'NE',</span> <span class="pre">'SG',</span> <span class="pre">'ND2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N',</span> <span class="pre">'NT',</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">('SG',</span> <span class="pre">'OH2',</span> <span class="pre">'OG',</span> <span class="pre">'N',</span> <span class="pre">'NE1',</span> <span class="pre">'OH',</span> <span class="pre">'NH2',</span> <span class="pre">'OW',</span> <span class="pre">'NE2',</span> <span class="pre">'NH1',</span> <span class="pre">'ND2',</span> <span class="pre">'OG1',</span> <span class="pre">'NE',</span> <span class="pre">'ND1',</span> <span class="pre">'NZ'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'NT',</span> <span class="pre">'OW',</span> <span class="pre">'N3',</span> <span class="pre">'N'),</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>

2.11.0-dev0/documentation_pages/topology/TPRParser.html

@@ -279,6 +279,11 @@
 <td><p>2025.0</p></td>
 <td><p>yes</p></td>
 </tr>
+<tr class="row-even"><td><p>138</p></td>
+<td><p>29</p></td>
+<td><p>2026.0</p></td>
+<td><p>yes</p></td>
+</tr>
 </tbody>
 </table>
 <aside class="footnote-list brackets">

2.11.0-dev0/documentation_pages/topology/tpr_util.html

@@ -190,7 +190,7 @@ <h1><span class="section-number">5.26. </span>Utility functions for the TPR topo
 <a class="reference internal" href="TPRParser.html#module-MDAnalysis.topology.TPRParser" title="MDAnalysis.topology.TPRParser"><code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.TPRParser</span></code></a> module.</p>
 <dl class="py data">
 <dt class="sig sig-object py" id="MDAnalysis.topology.tpr.SUPPORTED_VERSIONS">
-<span class="sig-prename descclassname"><span class="pre">MDAnalysis.topology.tpr.</span></span><span class="sig-name descname"><span class="pre">SUPPORTED_VERSIONS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">(58,</span> <span class="pre">73,</span> <span class="pre">83,</span> <span class="pre">100,</span> <span class="pre">103,</span> <span class="pre">110,</span> <span class="pre">112,</span> <span class="pre">116,</span> <span class="pre">119,</span> <span class="pre">122,</span> <span class="pre">127,</span> <span class="pre">129,</span> <span class="pre">133,</span> <span class="pre">134,</span> <span class="pre">137)</span></em><a class="headerlink" href="#MDAnalysis.topology.tpr.SUPPORTED_VERSIONS" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">MDAnalysis.topology.tpr.</span></span><span class="sig-name descname"><span class="pre">SUPPORTED_VERSIONS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">(58,</span> <span class="pre">73,</span> <span class="pre">83,</span> <span class="pre">100,</span> <span class="pre">103,</span> <span class="pre">110,</span> <span class="pre">112,</span> <span class="pre">116,</span> <span class="pre">119,</span> <span class="pre">122,</span> <span class="pre">127,</span> <span class="pre">129,</span> <span class="pre">133,</span> <span class="pre">134,</span> <span class="pre">137,</span> <span class="pre">138)</span></em><a class="headerlink" href="#MDAnalysis.topology.tpr.SUPPORTED_VERSIONS" title="Link to this definition"></a></dt>
 <dd><p>Built-in immutable sequence.</p>
 <p>If no argument is given, the constructor returns an empty tuple.
 If iterable is specified the tuple is initialized from iterable’s items.</p>
@@ -212,7 +212,7 @@ <h1><span class="section-number">5.26. </span>Utility functions for the TPR topo
 </section>
 <dl class="py data">
 <dt class="sig sig-object py" id="MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS">
-<span class="sig-prename descclassname"><span class="pre">MDAnalysis.topology.tpr.setting.</span></span><span class="sig-name descname"><span class="pre">SUPPORTED_VERSIONS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">(58,</span> <span class="pre">73,</span> <span class="pre">83,</span> <span class="pre">100,</span> <span class="pre">103,</span> <span class="pre">110,</span> <span class="pre">112,</span> <span class="pre">116,</span> <span class="pre">119,</span> <span class="pre">122,</span> <span class="pre">127,</span> <span class="pre">129,</span> <span class="pre">133,</span> <span class="pre">134,</span> <span class="pre">137)</span></em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">MDAnalysis.topology.tpr.setting.</span></span><span class="sig-name descname"><span class="pre">SUPPORTED_VERSIONS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">(58,</span> <span class="pre">73,</span> <span class="pre">83,</span> <span class="pre">100,</span> <span class="pre">103,</span> <span class="pre">110,</span> <span class="pre">112,</span> <span class="pre">116,</span> <span class="pre">119,</span> <span class="pre">122,</span> <span class="pre">127,</span> <span class="pre">129,</span> <span class="pre">133,</span> <span class="pre">134,</span> <span class="pre">137,</span> <span class="pre">138)</span></em><a class="headerlink" href="#MDAnalysis.topology.tpr.setting.SUPPORTED_VERSIONS" title="Link to this definition"></a></dt>
 <dd><p>Gromacs TPR file format versions that can be read by the TPRParser.</p>
 </dd></dl>
 

2.11.0-dev0/index.html

@@ -148,7 +148,7 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 <dd class="field-odd"><p>2.11.0-dev0</p>
 </dd>
 <dt class="field-even">Date<span class="colon">:</span></dt>
-<dd class="field-even"><p>Feb 02, 2026</p>
+<dd class="field-even"><p>Feb 06, 2026</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

2.11.0-dev0/searchindex.js

@@ -211,6 +211,7 @@ <h1>Source code for MDAnalysis.topology.TPRParser</h1><div class="highlight"><pr
 <span class="sd">   133        28             2024.1               yes</span>
 <span class="sd">   134        28             2024.4               yes</span>
 <span class="sd">   137        28             2025.0               yes</span>
+<span class="sd">   138        29             2026.0               yes</span>
 <span class="sd">   ========== ============== ==================== =====</span>
 
 <span class="sd">.. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported.</span>

dev/_modules/MDAnalysis/topology/TPRParser.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">('OH2',</span> <span class="pre">'OW',</span> <span class="pre">'OG',</span> <span class="pre">'ND1',</span> <span class="pre">'OE2',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'OD2',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'OD1',</span> <span class="pre">'OG1',</span> <span class="pre">'O',</span> <span class="pre">'OH',</span> <span class="pre">'OE1',</span> <span class="pre">'SG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('SM',</span> <span class="pre">'NT',</span> <span class="pre">'O2',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'OS'),</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">('OC2',</span> <span class="pre">'OC1',</span> <span class="pre">'SD',</span> <span class="pre">'OH2',</span> <span class="pre">'OG',</span> <span class="pre">'OD2',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'OE1',</span> <span class="pre">'OD1',</span> <span class="pre">'OE2',</span> <span class="pre">'OH',</span> <span class="pre">'ND1',</span> <span class="pre">'NE2',</span> <span class="pre">'SG',</span> <span class="pre">'OG1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'OH',</span> <span class="pre">'O2',</span> <span class="pre">'O',</span> <span class="pre">'OW',</span> <span class="pre">'SM',</span> <span class="pre">'OS'),</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">('NE2',</span> <span class="pre">'NE1',</span> <span class="pre">'NZ',</span> <span class="pre">'OH2',</span> <span class="pre">'OW',</span> <span class="pre">'OG1',</span> <span class="pre">'OH',</span> <span class="pre">'NH2',</span> <span class="pre">'NH1',</span> <span class="pre">'N',</span> <span class="pre">'OG',</span> <span class="pre">'ND1',</span> <span class="pre">'NE',</span> <span class="pre">'SG',</span> <span class="pre">'ND2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N',</span> <span class="pre">'NT',</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">('SG',</span> <span class="pre">'OH2',</span> <span class="pre">'OG',</span> <span class="pre">'N',</span> <span class="pre">'NE1',</span> <span class="pre">'OH',</span> <span class="pre">'NH2',</span> <span class="pre">'OW',</span> <span class="pre">'NE2',</span> <span class="pre">'NH1',</span> <span class="pre">'ND2',</span> <span class="pre">'OG1',</span> <span class="pre">'NE',</span> <span class="pre">'ND1',</span> <span class="pre">'NZ'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'NT',</span> <span class="pre">'OW',</span> <span class="pre">'N3',</span> <span class="pre">'N'),</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>

dev/documentation_pages/analysis/wbridge_analysis.html

@@ -279,6 +279,11 @@
 <td><p>2025.0</p></td>
 <td><p>yes</p></td>
 </tr>
+<tr class="row-even"><td><p>138</p></td>
+<td><p>29</p></td>
+<td><p>2026.0</p></td>
+<td><p>yes</p></td>
+</tr>
 </tbody>
 </table>
 <aside class="footnote-list brackets">