Update documentation - fix typo

LBC-LNBio · Jan 27, 2025 · 3179a00 · 3179a00 · github-actions · Jan 27, 2025
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diff --git a/docs/.doctrees/about/index.doctree b/docs/.doctrees/about/index.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/package/api_reference/Molecule.doctree b/docs/.doctrees/package/api_reference/Molecule.doctree
diff --git a/docs/.doctrees/package/api_reference/box_file_template.doctree b/docs/.doctrees/package/api_reference/box_file_template.doctree
diff --git a/docs/.doctrees/package/api_reference/calculate_frequencies.doctree b/docs/.doctrees/package/api_reference/calculate_frequencies.doctree
diff --git a/docs/.doctrees/package/api_reference/constitutional.doctree b/docs/.doctrees/package/api_reference/constitutional.doctree
diff --git a/docs/.doctrees/package/api_reference/depth.doctree b/docs/.doctrees/package/api_reference/depth.doctree
diff --git a/docs/.doctrees/package/api_reference/detect.doctree b/docs/.doctrees/package/api_reference/detect.doctree
diff --git a/docs/.doctrees/package/api_reference/export.doctree b/docs/.doctrees/package/api_reference/export.doctree
diff --git a/docs/.doctrees/package/api_reference/export_openings.doctree b/docs/.doctrees/package/api_reference/export_openings.doctree
diff --git a/docs/.doctrees/package/api_reference/get_vertices.doctree b/docs/.doctrees/package/api_reference/get_vertices.doctree
diff --git a/docs/.doctrees/package/api_reference/get_vertices_from_file.doctree b/docs/.doctrees/package/api_reference/get_vertices_from_file.doctree
diff --git a/docs/.doctrees/package/api_reference/hydropathy.doctree b/docs/.doctrees/package/api_reference/hydropathy.doctree
diff --git a/docs/.doctrees/package/api_reference/hydrophobicity_scale_file_template.doctree b/docs/.doctrees/package/api_reference/hydrophobicity_scale_file_template.doctree
diff --git a/docs/.doctrees/package/api_reference/index.doctree b/docs/.doctrees/package/api_reference/index.doctree
diff --git a/docs/.doctrees/package/api_reference/openings.doctree b/docs/.doctrees/package/api_reference/openings.doctree
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diff --git a/docs/.doctrees/package/api_reference/pyKVFinderResults.doctree b/docs/.doctrees/package/api_reference/pyKVFinderResults.doctree
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diff --git a/docs/.doctrees/package/api_reference/vdw_file_template.doctree b/docs/.doctrees/package/api_reference/vdw_file_template.doctree
diff --git a/docs/.doctrees/package/api_reference/write_results.doctree b/docs/.doctrees/package/api_reference/write_results.doctree
diff --git a/docs/.doctrees/package/examples/index.doctree b/docs/.doctrees/package/examples/index.doctree
diff --git a/docs/.doctrees/package/installation/index.doctree b/docs/.doctrees/package/installation/index.doctree
diff --git a/docs/.doctrees/package/tutorial/index.doctree b/docs/.doctrees/package/tutorial/index.doctree
diff --git a/docs/.doctrees/plugins/chimerax/index.doctree b/docs/.doctrees/plugins/chimerax/index.doctree
diff --git a/docs/.doctrees/plugins/cli/index.doctree b/docs/.doctrees/plugins/cli/index.doctree
diff --git a/docs/.doctrees/plugins/pymol/index.doctree b/docs/.doctrees/plugins/pymol/index.doctree
diff --git a/docs/.doctrees/plugins/pymol/tutorial/biomolecular-cavity-detection.doctree b/docs/.doctrees/plugins/pymol/tutorial/biomolecular-cavity-detection.doctree
diff --git a/docs/.doctrees/plugins/pymol/tutorial/cage-cavity-detection.doctree b/docs/.doctrees/plugins/pymol/tutorial/cage-cavity-detection.doctree
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -1,23 +1,21 @@
+
+
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Overview: module code &mdash; pyKVFinder 0.7.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
 
 
     <link rel="shortcut icon" href="../_static/icon.ico"/>
-  <!--[if lt IE 9]>
-    <script src="../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
-
-        <script src="../_static/jquery.js?v=5d32c60e"></script>
-        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=6dfdf7c3"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../_static/documentation_options.js?v=6dfdf7c3"></script>
+      <script src="../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -35,9 +33,6 @@
             pyKVFinder
               <img src="../_static/logo.png" class="logo" alt="Logo"/>
           </a>
-              <div class="version">
-                0.7
-              </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
     <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />

diff --git a/docs/_modules/pyKVFinder/grid.html b/docs/_modules/pyKVFinder/grid.html
@@ -1,23 +1,21 @@
+
+
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>pyKVFinder.grid &mdash; pyKVFinder 0.7.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
-      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
 
 
     <link rel="shortcut icon" href="../../_static/icon.ico"/>
-  <!--[if lt IE 9]>
-    <script src="../../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
-
-        <script src="../../_static/jquery.js?v=5d32c60e"></script>
-        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=6dfdf7c3"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="../../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../../_static/documentation_options.js?v=6dfdf7c3"></script>
+      <script src="../../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -35,9 +33,6 @@
             pyKVFinder
               <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
-              <div class="version">
-                0.7
-              </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
     <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />

diff --git a/docs/_modules/pyKVFinder/main.html b/docs/_modules/pyKVFinder/main.html
@@ -1,23 +1,21 @@
+
+
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>pyKVFinder.main &mdash; pyKVFinder 0.7.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
-      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
 
 
     <link rel="shortcut icon" href="../../_static/icon.ico"/>
-  <!--[if lt IE 9]>
-    <script src="../../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
-
-        <script src="../../_static/jquery.js?v=5d32c60e"></script>
-        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=6dfdf7c3"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="../../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../../_static/documentation_options.js?v=6dfdf7c3"></script>
+      <script src="../../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -35,9 +33,6 @@
             pyKVFinder
               <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
-              <div class="version">
-                0.7
-              </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
     <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />

diff --git a/docs/_modules/pyKVFinder/utils.html b/docs/_modules/pyKVFinder/utils.html
@@ -1,23 +1,21 @@
+
+
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>pyKVFinder.utils &mdash; pyKVFinder 0.7.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
-      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
 
 
     <link rel="shortcut icon" href="../../_static/icon.ico"/>
-  <!--[if lt IE 9]>
-    <script src="../../_static/js/html5shiv.min.js"></script>
-  <![endif]-->
-
-        <script src="../../_static/jquery.js?v=5d32c60e"></script>
-        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=6dfdf7c3"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+      <script src="../../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../../_static/documentation_options.js?v=6dfdf7c3"></script>
+      <script src="../../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -35,9 +33,6 @@
             pyKVFinder
               <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
-              <div class="version">
-                0.7
-              </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
     <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />

diff --git a/docs/_sources/package/tutorial/index.rst.txt b/docs/_sources/package/tutorial/index.rst.txt
@@ -630,7 +630,7 @@ A hydropathy characterization, that maps a target hydrophobicity scale on surfac
 
   * `pyKVFinder.hydropathy <../api_reference/hydropathy.html>`_
 
-1. Performing depth characterization
+8. Performing depth characterization
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.

diff --git a/docs/_static/css/badge_only.css b/docs/_static/css/badge_only.css
File	Stmts	Miss	Cover	Missing
pyKVFinder
grid.py	729	112	85%	918, 922, 2243–2263, 2400–2477, 2749–2766, 2867–2936
main.py	361	69	81%	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.py	312	6	98%	571, 603, 606–608, 630
TOTAL	1402	187	87%