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Update documentation for pyKVFinder tool and command in ChimeraX
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jvsguerra committed Oct 28, 2024
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4 changes: 2 additions & 2 deletions docs/_sources/plugins/chimerax/index.rst.txt
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Find Cavities
*************

The **pyKVFinder** package is integrated into `UCSF ChimeraX <https://www.cgl.ucsf.edu/chimerax/>`_ through a bundle, called **Find Cavities**. This bundle allows the user to run pyKVFinder in ChimeraX and visualize the results directly on the ChimeraX viewer.
The **pyKVFinder** package is integrated into `UCSF ChimeraX <https://www.cgl.ucsf.edu/chimerax/>`_ as the **Find Cavities** tool, available from version 1.9. This tool allows the user to run pyKVFinder in ChimeraX and visualize the results directly on the ChimeraX viewer.

Tool
====

The **Find Cavities** tool is available in ChimeraX starting from version 1.9. It can be accessed from:
The **Find Cavities** tool can be accessed from:

* ``Tools`` > ``Binding Analysis`` > ``Find Cavities``

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4 changes: 2 additions & 2 deletions docs/plugins/chimerax/index.html
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<section id="find-cavities">
<h1>Find Cavities<a class="headerlink" href="#find-cavities" title="Link to this heading"></a></h1>
<p>The <strong>pyKVFinder</strong> package is integrated into <a class="reference external" href="https://www.cgl.ucsf.edu/chimerax/">UCSF ChimeraX</a> through a bundle, called <strong>Find Cavities</strong>. This bundle allows the user to run pyKVFinder in ChimeraX and visualize the results directly on the ChimeraX viewer.</p>
<p>The <strong>pyKVFinder</strong> package is integrated into <a class="reference external" href="https://www.cgl.ucsf.edu/chimerax/">UCSF ChimeraX</a> as the <strong>Find Cavities</strong> tool, available from version 1.9. This tool allows the user to run pyKVFinder in ChimeraX and visualize the results directly on the ChimeraX viewer.</p>
<section id="tool">
<h2>Tool<a class="headerlink" href="#tool" title="Link to this heading"></a></h2>
<p>The <strong>Find Cavities</strong> tool is available in ChimeraX starting from version 1.9. It can be accessed from:</p>
<p>The <strong>Find Cavities</strong> tool can be accessed from:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">Tools</span></code> &gt; <code class="docutils literal notranslate"><span class="pre">Binding</span> <span class="pre">Analysis</span></code> &gt; <code class="docutils literal notranslate"><span class="pre">Find</span> <span class="pre">Cavities</span></code></p></li>
</ul>
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2 changes: 1 addition & 1 deletion docs/searchindex.js
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4 changes: 2 additions & 2 deletions docs/source/plugins/chimerax/index.rst
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Find Cavities
*************

The **pyKVFinder** package is integrated into `UCSF ChimeraX <https://www.cgl.ucsf.edu/chimerax/>`_ through a bundle, called **Find Cavities**. This bundle allows the user to run pyKVFinder in ChimeraX and visualize the results directly on the ChimeraX viewer.
The **pyKVFinder** package is integrated into `UCSF ChimeraX <https://www.cgl.ucsf.edu/chimerax/>`_ as the **Find Cavities** tool, available from version 1.9. This tool allows the user to run pyKVFinder in ChimeraX and visualize the results directly on the ChimeraX viewer.

Tool
====

The **Find Cavities** tool is available in ChimeraX starting from version 1.9. It can be accessed from:
The **Find Cavities** tool can be accessed from:

* ``Tools`` > ``Binding Analysis`` > ``Find Cavities``

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Coverage

Coverage Report
FileStmtsMissCoverMissing
pyKVFinder
   grid.py72911285%918, 922, 2243–2263, 2400–2477, 2749–2766, 2867–2936
   main.py3616981%93, 97, 105, 114, 142–148, 495, 660, 1061, 1068, 1078, 1089, 1108, 1113–1114, 1340, 1345, 1351, 1358, 1361–1364, 1368–1373, 1385, 1395, 1424–1425, 1430–1431, 1436–1437, 1497–1502, 1508, 1513–1518, 1578, 1580, 1593, 1704, 1706, 1712, 1714, 1720, 1725, 1729, 1782–1792, 1818
   utils.py312698%571, 603, 606–608, 630
TOTAL140218787% 

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