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2 changes: 1 addition & 1 deletion 2.8.0-dev0/_modules/MDAnalysis/guesser/tables.html
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Expand Up @@ -192,7 +192,7 @@ <h1>Source code for MDAnalysis.guesser.tables</h1><div class="highlight"><pre>


<div class="viewcode-block" id="kv2dict">
<a class="viewcode-back" href="../../../documentation_pages/guesser_modules/tables.html#MDAnalysis.guesser.tables.kv2dict">[docs]</a>
<a class="viewcode-back" href="../../../documentation_pages/topology/tables.html#MDAnalysis.guesser.tables.kv2dict">[docs]</a>
<span class="k">def</span> <span class="nf">kv2dict</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">convertor</span><span class="p">:</span> <span class="n">Any</span> <span class="o">=</span> <span class="nb">str</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Primitive ad-hoc parser of a key-value record list.</span>

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Expand Up @@ -282,6 +282,7 @@ <h1>All modules for which code is available</h1>
<li><a href="MDAnalysis/topology/TXYZParser.html">MDAnalysis.topology.TXYZParser</a></li>
<li><a href="MDAnalysis/topology/XYZParser.html">MDAnalysis.topology.XYZParser</a></li>
<li><a href="MDAnalysis/topology/base.html">MDAnalysis.topology.base</a></li>
<li><a href="MDAnalysis/topology/guessers.html">MDAnalysis.topology.guessers</a></li>
<li><a href="MDAnalysis/topology/tpr/obj.html">MDAnalysis.topology.tpr.obj</a></li>
<li><a href="MDAnalysis/topology/tpr/utils.html">MDAnalysis.topology.tpr.utils</a></li>
<li><a href="MDAnalysis/transformations/base.html">MDAnalysis.transformations.base</a></li>
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@@ -0,0 +1,2 @@
.. automodule:: MDAnalysis.topology.guessers
:members:
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.. automodule:: MDAnalysis.topology.tables
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Expand Up @@ -60,3 +60,5 @@ the topology readers.
topology/base
topology/core
topology/tpr_util
topology/guessers
topology/tables
4 changes: 2 additions & 2 deletions 2.8.0-dev0/documentation_pages/analysis/wbridge_analysis.html
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Expand Up @@ -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">('SD',</span> <span class="pre">'OE2',</span> <span class="pre">'OH2',</span> <span class="pre">'NE2',</span> <span class="pre">'OH',</span> <span class="pre">'OE1',</span> <span class="pre">'OW',</span> <span class="pre">'OD1',</span> <span class="pre">'O',</span> <span class="pre">'SG',</span> <span class="pre">'OD2',</span> <span class="pre">'OG',</span> <span class="pre">'OC1',</span> <span class="pre">'OC2',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('OW',</span> <span class="pre">'NT',</span> <span class="pre">'O',</span> <span class="pre">'OS',</span> <span class="pre">'SM',</span> <span class="pre">'O2',</span> <span class="pre">'OY',</span> <span class="pre">'OH',</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>
<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">('OC1',</span> <span class="pre">'OD1',</span> <span class="pre">'OD2',</span> <span class="pre">'OC2',</span> <span class="pre">'OH2',</span> <span class="pre">'ND1',</span> <span class="pre">'OH',</span> <span class="pre">'OE2',</span> <span class="pre">'SG',</span> <span class="pre">'O',</span> <span class="pre">'OG',</span> <span class="pre">'NE2',</span> <span class="pre">'SD',</span> <span class="pre">'OW',</span> <span class="pre">'OE1',</span> <span class="pre">'OG1'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('O',</span> <span class="pre">'NT',</span> <span class="pre">'O2',</span> <span class="pre">'OW',</span> <span class="pre">'OS',</span> <span class="pre">'OY',</span> <span class="pre">'OH',</span> <span class="pre">'N',</span> <span class="pre">'SM'),</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">('OW',</span> <span class="pre">'NZ',</span> <span class="pre">'SG',</span> <span class="pre">'NH2',</span> <span class="pre">'NH1',</span> <span class="pre">'OG',</span> <span class="pre">'OH2',</span> <span class="pre">'OH',</span> <span class="pre">'OG1',</span> <span class="pre">'ND2',</span> <span class="pre">'NE1',</span> <span class="pre">'NE2',</span> <span class="pre">'ND1',</span> <span class="pre">'NE',</span> <span class="pre">'N'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N3',</span> <span class="pre">'NT',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</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>
<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">'OG',</span> <span class="pre">'NH2',</span> <span class="pre">'NE1',</span> <span class="pre">'NE2',</span> <span class="pre">'OW',</span> <span class="pre">'OH',</span> <span class="pre">'OH2',</span> <span class="pre">'NH1',</span> <span class="pre">'ND1',</span> <span class="pre">'OG1',</span> <span class="pre">'NE',</span> <span class="pre">'ND2',</span> <span class="pre">'N',</span> <span class="pre">'SG'),</span> <span class="pre">'GLYCAM06':</span> <span class="pre">('N3',</span> <span class="pre">'N',</span> <span class="pre">'OH',</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>
<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>
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Expand Up @@ -1490,7 +1490,7 @@ <h3><span class="section-number">12.2.2.1.1. </span>Collections<a class="headerl
</dl>
<div class="admonition seealso">
<p class="admonition-title">See also</p>
<p><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers.guess_bonds()</span></code>, <code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers.guess_angles()</span></code>, <code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers.guess_dihedrals()</span></code></p>
<p><a class="reference internal" href="../topology/guessers.html#MDAnalysis.topology.guessers.guess_bonds" title="MDAnalysis.topology.guessers.guess_bonds"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers.guess_bonds()</span></code></a>, <a class="reference internal" href="../topology/guessers.html#MDAnalysis.topology.guessers.guess_angles" title="MDAnalysis.topology.guessers.guess_angles"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers.guess_angles()</span></code></a>, <a class="reference internal" href="../topology/guessers.html#MDAnalysis.topology.guessers.guess_dihedrals" title="MDAnalysis.topology.guessers.guess_dihedrals"><code class="xref py py-func docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers.guess_dihedrals()</span></code></a></p>
</div>
<div class="versionadded">
<p><span class="versionmodified added">Added in version 0.10.0.</span></p>
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<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="6.1.2.1. Context-specific guessers — MDAnalysis.guesser" href="guesser_modules/init.html" />
<link rel="prev" title="5.26. Utility functions for the TPR topology parser" href="topology/tpr_util.html" />
<link rel="prev" title="5.28. MDAnalysis topology tables" href="topology/tables.html" />
</head>

<body class="wy-body-for-nav">
Expand Down Expand Up @@ -225,7 +225,7 @@ <h3><span class="section-number">6.1.2. </span>Guessing using <a class="referenc
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="topology/tpr_util.html" class="btn btn-neutral float-left" title="5.26. Utility functions for the TPR topology parser" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="topology/tables.html" class="btn btn-neutral float-left" title="5.28. MDAnalysis topology tables" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="guesser_modules/init.html" class="btn btn-neutral float-right" title="6.1.2.1. Context-specific guessers — MDAnalysis.guesser" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>

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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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<li class="toctree-l2"><a class="reference internal" href="base.html">5.24. Base topology reader classes — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.base</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core.html">5.25. Common functions for topology building — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.core</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tpr_util.html">5.26. Utility functions for the TPR topology parser</a></li>
<li class="toctree-l2"><a class="reference internal" href="guessers.html">5.27. Guessing unknown Topology information — <code class="xref py py-mod docutils literal notranslate"><span class="pre">MDAnalysis.topology.guessers</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="tables.html">5.28. MDAnalysis topology tables</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="../guesser_modules.html">6. Guesser modules</a></li>
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