rebuilt html docs for version 2.7.0-dev0 from branch develop with sph…

…inx at c2e6df9

2.7.0-dev0/_modules/MDAnalysis/analysis/dielectric.html

@@ -162,6 +162,10 @@ <h1>Source code for MDAnalysis.analysis.dielectric</h1><div class="highlight"><p
 <span class="sd">    the usual case if electrostatics are handled with a Ewald summation</span>
 <span class="sd">    technique. See [Neumann1983]_ for details on the derivation.</span>
 
+<span class="sd">    .. warning::</span>
+<span class="sd">      Applying this class requires that no free charges, such as ions or</span>
+<span class="sd">      charged fragments, are present in the simulation.</span>
+
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
 <span class="sd">    atomgroup : MDAnalysis.core.groups.AtomGroup</span>

2.7.0-dev0/documentation_pages/analysis/dielectric.html

@@ -147,6 +147,11 @@ <h1><span class="section-number">4.8.4. </span>Dielectric — <a class="referenc
 <p>is calculated for a system in tin foil boundary conditions, which is
 the usual case if electrostatics are handled with a Ewald summation
 technique. See <a class="reference internal" href="../references.html#neumann1983" id="id1"><span>[Neumann1983]</span></a> for details on the derivation.</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>Applying this class requires that no free charges, such as ions or
+charged fragments, are present in the simulation.</p>
+</div>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

2.7.0-dev0/documentation_pages/analysis/wbridge_analysis.html

@@ -1017,15 +1017,15 @@ <h2><span class="section-number">4.3.3.8. </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">'OD1',</span> <span class="pre">'O',</span> <span class="pre">'ND1',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'OG',</span> <span class="pre">'SG',</span> <span class="pre">'OH',</span> <span class="pre">'OD2',</span> <span class="pre">'OG1',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'OE1',</span> <span class="pre">'OE2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'OW',</span> <span class="pre">'O2',</span> <span class="pre">'O',</span> <span class="pre">'NT',</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="Permalink 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">('OE2',</span> <span class="pre">'SG',</span> <span class="pre">'OC2',</span> <span class="pre">'OH',</span> <span class="pre">'OD2',</span> <span class="pre">'OW',</span> <span class="pre">'OG1',</span> <span class="pre">'OC1',</span> <span class="pre">'ND1',</span> <span class="pre">'OE1',</span> <span class="pre">'OH2',</span> <span class="pre">'SD',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'O',</span> <span class="pre">'OD1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'SM',</span> <span class="pre">'OS',</span> <span class="pre">'O2',</span> <span class="pre">'OY',</span> <span class="pre">'NT',</span> <span class="pre">'OW',</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="Permalink 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">('N',</span> <span class="pre">'OH',</span> <span class="pre">'OH2',</span> <span class="pre">'NE1',</span> <span class="pre">'OW',</span> <span class="pre">'NE',</span> <span class="pre">'OG1',</span> <span class="pre">'NH1',</span> <span class="pre">'ND1',</span> <span class="pre">'NZ',</span> <span class="pre">'SG',</span> <span class="pre">'OG',</span> <span class="pre">'ND2',</span> <span class="pre">'NE2',</span> <span class="pre">'NH2'),</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="Permalink 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">'NE1',</span> <span class="pre">'OH2',</span> <span class="pre">'NE',</span> <span class="pre">'OH',</span> <span class="pre">'NH1',</span> <span class="pre">'NH2',</span> <span class="pre">'ND2',</span> <span class="pre">'NZ',</span> <span class="pre">'OW',</span> <span class="pre">'N',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'OG1',</span> <span class="pre">'ND1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'OH',</span> <span class="pre">'OW',</span> <span class="pre">'N',</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="Permalink 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>

2.7.0-dev0/index.html

@@ -103,7 +103,7 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 <dd class="field-odd"><p>2.7.0-dev0</p>
 </dd>
 <dt class="field-even">Date</dt>
-<dd class="field-even"><p>Aug 31, 2023</p>
+<dd class="field-even"><p>Sep 02, 2023</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

dev/_modules/MDAnalysis/analysis/dielectric.html

@@ -162,6 +162,10 @@ <h1>Source code for MDAnalysis.analysis.dielectric</h1><div class="highlight"><p
 <span class="sd">    the usual case if electrostatics are handled with a Ewald summation</span>
 <span class="sd">    technique. See [Neumann1983]_ for details on the derivation.</span>
 
+<span class="sd">    .. warning::</span>
+<span class="sd">      Applying this class requires that no free charges, such as ions or</span>
+<span class="sd">      charged fragments, are present in the simulation.</span>
+
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
 <span class="sd">    atomgroup : MDAnalysis.core.groups.AtomGroup</span>

dev/documentation_pages/analysis/dielectric.html

@@ -147,6 +147,11 @@ <h1><span class="section-number">4.8.4. </span>Dielectric — <a class="referenc
 <p>is calculated for a system in tin foil boundary conditions, which is
 the usual case if electrostatics are handled with a Ewald summation
 technique. See <a class="reference internal" href="../references.html#neumann1983" id="id1"><span>[Neumann1983]</span></a> for details on the derivation.</p>
+<div class="admonition warning">
+<p class="admonition-title">Warning</p>
+<p>Applying this class requires that no free charges, such as ions or
+charged fragments, are present in the simulation.</p>
+</div>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">

dev/documentation_pages/analysis/wbridge_analysis.html

@@ -1017,15 +1017,15 @@ <h2><span class="section-number">4.3.3.8. </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">'OD1',</span> <span class="pre">'O',</span> <span class="pre">'ND1',</span> <span class="pre">'SD',</span> <span class="pre">'OC2',</span> <span class="pre">'OG',</span> <span class="pre">'SG',</span> <span class="pre">'OH',</span> <span class="pre">'OD2',</span> <span class="pre">'OG1',</span> <span class="pre">'OC1',</span> <span class="pre">'NE2',</span> <span class="pre">'OE1',</span> <span class="pre">'OE2'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'N',</span> <span class="pre">'OY',</span> <span class="pre">'OW',</span> <span class="pre">'O2',</span> <span class="pre">'O',</span> <span class="pre">'NT',</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="Permalink 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">('OE2',</span> <span class="pre">'SG',</span> <span class="pre">'OC2',</span> <span class="pre">'OH',</span> <span class="pre">'OD2',</span> <span class="pre">'OW',</span> <span class="pre">'OG1',</span> <span class="pre">'OC1',</span> <span class="pre">'ND1',</span> <span class="pre">'OE1',</span> <span class="pre">'OH2',</span> <span class="pre">'SD',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'O',</span> <span class="pre">'OD1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OH',</span> <span class="pre">'SM',</span> <span class="pre">'OS',</span> <span class="pre">'O2',</span> <span class="pre">'OY',</span> <span class="pre">'NT',</span> <span class="pre">'OW',</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="Permalink 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">('N',</span> <span class="pre">'OH',</span> <span class="pre">'OH2',</span> <span class="pre">'NE1',</span> <span class="pre">'OW',</span> <span class="pre">'NE',</span> <span class="pre">'OG1',</span> <span class="pre">'NH1',</span> <span class="pre">'ND1',</span> <span class="pre">'NZ',</span> <span class="pre">'SG',</span> <span class="pre">'OG',</span> <span class="pre">'ND2',</span> <span class="pre">'NE2',</span> <span class="pre">'NH2'),</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="Permalink 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">'NE1',</span> <span class="pre">'OH2',</span> <span class="pre">'NE',</span> <span class="pre">'OH',</span> <span class="pre">'NH1',</span> <span class="pre">'NH2',</span> <span class="pre">'ND2',</span> <span class="pre">'NZ',</span> <span class="pre">'OW',</span> <span class="pre">'N',</span> <span class="pre">'NE2',</span> <span class="pre">'OG',</span> <span class="pre">'OG1',</span> <span class="pre">'ND1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('NT',</span> <span class="pre">'OH',</span> <span class="pre">'OW',</span> <span class="pre">'N',</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="Permalink 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/index.html

@@ -103,7 +103,7 @@ <h1>MDAnalysis documentation<a class="headerlink" href="#mdanalysis-documentatio
 <dd class="field-odd"><p>2.7.0-dev0</p>
 </dd>
 <dt class="field-even">Date</dt>
-<dd class="field-even"><p>Aug 31, 2023</p>
+<dd class="field-even"><p>Sep 02, 2023</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