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Add documentation for pyKVFinder tool and command in ChimeraX
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../plugins/cli/index.html">Command-line interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="../plugins/pymol/index.html">PyMOL pyKVFinder Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="../plugins/chimerax/index.html">ChimeraX</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">About</span></p>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/cli/index.html">Command-line interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/pymol/index.html">PyMOL pyKVFinder Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/chimerax/index.html">ChimeraX</a></li>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/cli/index.html">Command-line interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/pymol/index.html">PyMOL pyKVFinder Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/chimerax/index.html">ChimeraX</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../../plugins/cli/index.html">Command-line interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/pymol/index.html">PyMOL pyKVFinder Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../plugins/chimerax/index.html">ChimeraX</a></li>
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Funding
*******

This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], and Brazilian Center for Research in Energy and Materials (CNPEM).
This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) [Grant Number 88887.928702/2023-00], and Brazilian Center for Research in Energy and Materials (CNPEM).

*******
License
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Command-line interface <plugins/cli/index>
PyMOL pyKVFinder Tools <plugins/pymol/index>
ChimeraX <plugins/chimerax/index>

.. toctree::
:maxdepth: 1
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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.

Tool
====

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

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

or,

* ``Tools`` > ``Structure Analysis`` > ``Find Cavities``

For further details on Find Cavities tool, please refer to https://www.cgl.ucsf.edu/chimerax/docs/user/tools/findcavities.html.

Command
=======

The Find Cavities tool uses the **kvfinder** command. The command can be used in the ChimeraX command line interface (CLI) as follows:

.. code-block::
kvfinder model-spec [ probeIn r1 ] [ probeOut r2 ] [ removalDistance d ] [ volumeCutoff minvol ] [ gridSpacing s ] [ showTool true | false ] [ surfaceType SAS | SES ] [ boxOrigin x,y,z ] [ boxExtent length | lx,ly,lz ]
For further details on kvfinder command, please refer to https://www.cgl.ucsf.edu/chimerax/docs/user/commands/kvfinder.html.
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PyMOL pyKVFinder Tools
**********************

pyKVFinder package is integrated into PyMOL through a plugin, called PyMOL pyKVFinder Tools. This plugin allows the user to run pyKVFinder on PyMOL and visualize the results directly on the PyMOL viewer.
The **pyKVFinder** package is integrated into `PyMOL <https://pymol.org/>`_ through a plugin, called **PyMOL pyKVFinder Tools**. This plugin allows the user to run pyKVFinder in PyMOL and visualize the results directly on the PyMOL viewer.

Installation
============
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<script src="../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="prev" title="Supramolecular cage cavity detection" href="../plugins/pymol/tutorial/cage-cavity-detection.html" />
<link rel="prev" title="Find Cavities" href="../plugins/chimerax/index.html" />
</head>

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<ul>
<li class="toctree-l1"><a class="reference internal" href="../plugins/cli/index.html">Command-line interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="../plugins/pymol/index.html">PyMOL pyKVFinder Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="../plugins/chimerax/index.html">ChimeraX</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">About</span></p>
<ul class="current">
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</section>
<section id="funding">
<h1>Funding<a class="headerlink" href="#funding" title="Link to this heading"></a></h1>
<p>This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], and Brazilian Center for Research in Energy and Materials (CNPEM).</p>
<p>This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) [Grant Number 88887.928702/2023-00], and Brazilian Center for Research in Energy and Materials (CNPEM).</p>
</section>
<section id="license">
<h1>License<a class="headerlink" href="#license" title="Link to this heading"></a></h1>
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</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="../plugins/pymol/tutorial/cage-cavity-detection.html" class="btn btn-neutral float-left" title="Supramolecular cage cavity detection" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<li class="toctree-l1"><a class="reference internal" href="plugins/cli/index.html">Command-line interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="plugins/pymol/index.html">PyMOL pyKVFinder Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="plugins/chimerax/index.html">ChimeraX</a></li>
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<li class="toctree-l1"><a class="reference internal" href="plugins/pymol/index.html">PyMOL pyKVFinder Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="plugins/chimerax/index.html">ChimeraX</a></li>
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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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