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

…inx at 48e9e01

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

2.8.0-dev0/documentation_pages/topology/tables.html

@@ -206,7 +206,7 @@
 <a class="reference internal" href="#MDAnalysis.topology.tables.kv2dict" title="MDAnalysis.topology.tables.kv2dict"><code class="xref py py-func docutils literal notranslate"><span class="pre">kv2dict()</span></code></a> for explanation of the file format.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="MDAnalysis.topology.tables.kv2dict">
-<span class="sig-prename descclassname"><span class="pre">MDAnalysis.topology.tables.</span></span><span class="sig-name descname"><span class="pre">kv2dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">convertor=&lt;class</span> <span class="pre">'str'&gt;</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tables.html#kv2dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysis.topology.tables.kv2dict" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">MDAnalysis.topology.tables.</span></span><span class="sig-name descname"><span class="pre">kv2dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">convertor:</span> <span class="pre">~typing.Any</span> <span class="pre">=</span> <span class="pre">&lt;class</span> <span class="pre">'str'&gt;</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/topology/tables.html#kv2dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysis.topology.tables.kv2dict" title="Link to this definition"></a></dt>
 <dd><p>Primitive ad-hoc parser of a key-value record list.</p>
 <ul class="simple">
 <li><p>The string <em>s</em> should contain each key-value pair on a separate

2.8.0-dev0/index.html

@@ -150,7 +150,7 @@ <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 13, 2024</p>
+<dd class="field-even"><p>Oct 15, 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