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2.11.0-dev0/documentation_pages/analysis/wbridge_analysis.html

@@ -1049,15 +1049,15 @@ <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">('OH',</span> <span class="pre">'OH2',</span> <span class="pre">'OD2',</span> <span class="pre">'NE2',</span> <span class="pre">'ND1',</span> <span class="pre">'SD',</span> <span class="pre">'OC1',</span> <span class="pre">'OE1',</span> <span class="pre">'OC2',</span> <span class="pre">'OG',</span> <span class="pre">'O',</span> <span class="pre">'SG',</span> <span class="pre">'OE2',</span> <span class="pre">'OG1',</span> <span class="pre">'OW',</span> <span class="pre">'OD1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'OY',</span> <span class="pre">'N',</span> <span class="pre">'NT',</span> <span class="pre">'O',</span> <span class="pre">'O2',</span> <span class="pre">'SM',</span> <span class="pre">'OS',</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_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">('ND1',</span> <span class="pre">'O',</span> <span class="pre">'OD1',</span> <span class="pre">'OE2',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'OH2',</span> <span class="pre">'OC1',</span> <span class="pre">'OW',</span> <span class="pre">'OC2',</span> <span class="pre">'SG',</span> <span class="pre">'SD',</span> <span class="pre">'OG',</span> <span class="pre">'OE1',</span> <span class="pre">'OD2',</span> <span class="pre">'OH'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('O2',</span> <span class="pre">'O',</span> <span class="pre">'N',</span> <span class="pre">'SM',</span> <span class="pre">'OW',</span> <span class="pre">'OS',</span> <span class="pre">'OY',</span> <span class="pre">'OH',</span> <span class="pre">'NT'),</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">('OH',</span> <span class="pre">'OG',</span> <span class="pre">'OH2',</span> <span class="pre">'N',</span> <span class="pre">'NE',</span> <span class="pre">'NE2',</span> <span class="pre">'NH2',</span> <span class="pre">'SG',</span> <span class="pre">'ND2',</span> <span class="pre">'NZ',</span> <span class="pre">'ND1',</span> <span class="pre">'NH1',</span> <span class="pre">'NE1',</span> <span class="pre">'OG1',</span> <span class="pre">'OW'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'N3',</span> <span class="pre">'N',</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">('ND1',</span> <span class="pre">'OG',</span> <span class="pre">'N',</span> <span class="pre">'NH1',</span> <span class="pre">'NE1',</span> <span class="pre">'NE2',</span> <span class="pre">'NZ',</span> <span class="pre">'OG1',</span> <span class="pre">'OH2',</span> <span class="pre">'OW',</span> <span class="pre">'NH2',</span> <span class="pre">'SG',</span> <span class="pre">'OH',</span> <span class="pre">'NE',</span> <span class="pre">'ND2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OW',</span> <span class="pre">'N3',</span> <span class="pre">'N',</span> <span class="pre">'OH',</span> <span class="pre">'NT'),</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

@@ -1049,15 +1049,15 @@ <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">('OH',</span> <span class="pre">'OH2',</span> <span class="pre">'OD2',</span> <span class="pre">'NE2',</span> <span class="pre">'ND1',</span> <span class="pre">'SD',</span> <span class="pre">'OC1',</span> <span class="pre">'OE1',</span> <span class="pre">'OC2',</span> <span class="pre">'OG',</span> <span class="pre">'O',</span> <span class="pre">'SG',</span> <span class="pre">'OE2',</span> <span class="pre">'OG1',</span> <span class="pre">'OW',</span> <span class="pre">'OD1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'OY',</span> <span class="pre">'N',</span> <span class="pre">'NT',</span> <span class="pre">'O',</span> <span class="pre">'O2',</span> <span class="pre">'SM',</span> <span class="pre">'OS',</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_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">('ND1',</span> <span class="pre">'O',</span> <span class="pre">'OD1',</span> <span class="pre">'OE2',</span> <span class="pre">'NE2',</span> <span class="pre">'OG1',</span> <span class="pre">'OH2',</span> <span class="pre">'OC1',</span> <span class="pre">'OW',</span> <span class="pre">'OC2',</span> <span class="pre">'SG',</span> <span class="pre">'SD',</span> <span class="pre">'OG',</span> <span class="pre">'OE1',</span> <span class="pre">'OD2',</span> <span class="pre">'OH'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('O2',</span> <span class="pre">'O',</span> <span class="pre">'N',</span> <span class="pre">'SM',</span> <span class="pre">'OW',</span> <span class="pre">'OS',</span> <span class="pre">'OY',</span> <span class="pre">'OH',</span> <span class="pre">'NT'),</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">('OH',</span> <span class="pre">'OG',</span> <span class="pre">'OH2',</span> <span class="pre">'N',</span> <span class="pre">'NE',</span> <span class="pre">'NE2',</span> <span class="pre">'NH2',</span> <span class="pre">'SG',</span> <span class="pre">'ND2',</span> <span class="pre">'NZ',</span> <span class="pre">'ND1',</span> <span class="pre">'NH1',</span> <span class="pre">'NE1',</span> <span class="pre">'OG1',</span> <span class="pre">'OW'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'N3',</span> <span class="pre">'N',</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">('ND1',</span> <span class="pre">'OG',</span> <span class="pre">'N',</span> <span class="pre">'NH1',</span> <span class="pre">'NE1',</span> <span class="pre">'NE2',</span> <span class="pre">'NZ',</span> <span class="pre">'OG1',</span> <span class="pre">'OH2',</span> <span class="pre">'OW',</span> <span class="pre">'NH2',</span> <span class="pre">'SG',</span> <span class="pre">'OH',</span> <span class="pre">'NE',</span> <span class="pre">'ND2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OW',</span> <span class="pre">'N3',</span> <span class="pre">'N',</span> <span class="pre">'OH',</span> <span class="pre">'NT'),</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>