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Update documentation - fix typo
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@jvsguerra
jvsguerra committed Jan 27, 2025
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2 changes: 1 addition & 1 deletion docs/_sources/package/tutorial/index.rst.txt
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Expand Up @@ -489,7 +489,7 @@ A spatial characterization, that includes volume, area and defining surface poin

* `pyKVFinder.spatial <../api_reference/spatial.html>`_

1. Performing constitutional characterization
6. Performing constitutional characterization
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.
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4 changes: 2 additions & 2 deletions docs/package/tutorial/index.html
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Expand Up @@ -58,7 +58,7 @@
<li class="toctree-l4"><a class="reference internal" href="#detecting-biomolecular-cavities">4. Detecting biomolecular cavities</a></li>
<li class="toctree-l4"><a class="reference internal" href="#detecting-biomolecular-cavities-with-ligand-adjustment">4.1 Detecting biomolecular cavities with ligand adjustment</a></li>
<li class="toctree-l4"><a class="reference internal" href="#performing-spatial-characterization">5. Performing spatial characterization</a></li>
<li class="toctree-l4"><a class="reference internal" href="#performing-constitutional-characterization">1. Performing constitutional characterization</a></li>
<li class="toctree-l4"><a class="reference internal" href="#performing-constitutional-characterization">6. Performing constitutional characterization</a></li>
<li class="toctree-l4"><a class="reference internal" href="#calculating-and-plotting-frequencies">6.1 Calculating and plotting frequencies</a></li>
<li class="toctree-l4"><a class="reference internal" href="#performing-hydropathy-characterization">7. Performing hydropathy characterization</a></li>
<li class="toctree-l4"><a class="reference internal" href="#performing-depth-characterization">8. Performing depth characterization</a></li>
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</div>
</section>
<section id="performing-constitutional-characterization">
<h4>1. Performing constitutional characterization<a class="headerlink" href="#performing-constitutional-characterization" title="Link to this heading"></a></h4>
<h4>6. Performing constitutional characterization<a class="headerlink" href="#performing-constitutional-characterization" title="Link to this heading"></a></h4>
<p>A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.</p>
<p><code class="docutils literal notranslate"><span class="pre">pyKVFinder.constitutional</span></code> takes the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) and a collection of detection parameters (<code class="docutils literal notranslate"><span class="pre">step</span></code>, <code class="docutils literal notranslate"><span class="pre">probe_in</span></code>, <code class="docutils literal notranslate"><span class="pre">ignore_backbone</span></code>), and returns a dictionary with interface residues of each cavity.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="c1"># Default ignore backbone contacts flag (ignore_backbone): False</span>
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2 changes: 1 addition & 1 deletion docs/source/package/tutorial/index.rst
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Expand Up @@ -489,7 +489,7 @@ A spatial characterization, that includes volume, area and defining surface poin

* `pyKVFinder.spatial <../api_reference/spatial.html>`_

1. Performing constitutional characterization
6. Performing constitutional characterization
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

A constitutional characterization, that identifies the interface residues, is performed on the detected 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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