rebuilt html docs for version 2.11.0-dev0 from branch develop with sphinx at 8a8e7b2

Author: github-actions

2.11.0-dev0/_modules/MDAnalysis/transformations/nojump.html

@@ -262,6 +262,13 @@ <h1>Source code for MDAnalysis.transformations.nojump</h1><div class="highlight"
         <span class="k">except</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">LinAlgError</span><span class="p">:</span>
             <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Periodic box dimensions are not invertible at step </span><span class="si">{</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span><span class="si">}</span><span class="s2">&quot;</span>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">prev</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="s2">&quot;NoJump transformation must be applied starting from frame 0. &quot;</span>
+                <span class="sa">f</span><span class="s2">&quot;Currently at frame </span><span class="si">{</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span><span class="si">}</span><span class="s2">. Please reset trajectory to frame 0 before adding this transformation.&quot;</span>
+            <span class="p">)</span>
+
         <span class="k">if</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="c1"># We don&#39;t need to apply the transformation here. However, we need to</span>
             <span class="c1"># ensure we have the 0th frame coordinates in reduced form. We also need to</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">('OE1',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'O',</span> <span class="pre">'OC1',</span> <span class="pre">'SG',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'ND1',</span> <span class="pre">'OE2',</span> <span class="pre">'OD1',</span> <span class="pre">'OG1',</span> <span class="pre">'OH2',</span> <span class="pre">'OD2',</span> <span class="pre">'OW',</span> <span class="pre">'OH'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OY',</span> <span class="pre">'OS',</span> <span class="pre">'NT',</span> <span class="pre">'OH',</span> <span class="pre">'O',</span> <span class="pre">'OW',</span> <span class="pre">'SM',</span> <span class="pre">'N',</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>
+<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">('SD',</span> <span class="pre">'SG',</span> <span class="pre">'OH2',</span> <span class="pre">'OH',</span> <span class="pre">'OE1',</span> <span class="pre">'O',</span> <span class="pre">'ND1',</span> <span class="pre">'OC2',</span> <span class="pre">'OG1',</span> <span class="pre">'OE2',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'OW',</span> <span class="pre">'OD2',</span> <span class="pre">'OG',</span> <span class="pre">'OD1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'O2',</span> <span class="pre">'OW',</span> <span class="pre">'O',</span> <span class="pre">'OS',</span> <span class="pre">'NT',</span> <span class="pre">'OY',</span> <span class="pre">'SM',</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_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">('NZ',</span> <span class="pre">'OG1',</span> <span class="pre">'ND2',</span> <span class="pre">'OH2',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'NH2',</span> <span class="pre">'OW',</span> <span class="pre">'SG',</span> <span class="pre">'N',</span> <span class="pre">'NE1',</span> <span class="pre">'ND1',</span> <span class="pre">'OH',</span> <span class="pre">'NE',</span> <span class="pre">'NH1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N',</span> <span class="pre">'OH',</span> <span class="pre">'N3',</span> <span class="pre">'NT',</span> <span class="pre">'OW'),</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">'NH1',</span> <span class="pre">'OH',</span> <span class="pre">'NE',</span> <span class="pre">'NE2',</span> <span class="pre">'OW',</span> <span class="pre">'NH2',</span> <span class="pre">'OG',</span> <span class="pre">'NZ',</span> <span class="pre">'NE1',</span> <span class="pre">'ND2',</span> <span class="pre">'ND1',</span> <span class="pre">'N',</span> <span class="pre">'OG1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'OW',</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>

2.11.0-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>Jan 06, 2026</p>
+<dd class="field-even"><p>Jan 07, 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

@@ -262,6 +262,13 @@ <h1>Source code for MDAnalysis.transformations.nojump</h1><div class="highlight"
         <span class="k">except</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">LinAlgError</span><span class="p">:</span>
             <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Periodic box dimensions are not invertible at step </span><span class="si">{</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span><span class="si">}</span><span class="s2">&quot;</span>
             <span class="k">raise</span> <span class="n">NoDataError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">prev</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="s2">&quot;NoJump transformation must be applied starting from frame 0. &quot;</span>
+                <span class="sa">f</span><span class="s2">&quot;Currently at frame </span><span class="si">{</span><span class="n">ts</span><span class="o">.</span><span class="n">frame</span><span class="si">}</span><span class="s2">. Please reset trajectory to frame 0 before adding this transformation.&quot;</span>
+            <span class="p">)</span>
+
         <span class="k">if</span> <span class="n">ts</span><span class="o">.</span><span class="n">frame</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="c1"># We don&#39;t need to apply the transformation here. However, we need to</span>
             <span class="c1"># ensure we have the 0th frame coordinates in reduced form. We also need to</span>

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

dev/documentation_pages/analysis/wbridge_analysis.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>Jan 06, 2026</p>
+<dd class="field-even"><p>Jan 07, 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