Add video tutorial for cavity detection in supramolecular cages

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ff86b850e3cd6fe0e32862d27a6322e8
+config: 6ec846394577230687d4342f1b5d6c47
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_sources/plugins/pymol/tutorial/cage-cavity-detection.rst.txt

@@ -127,3 +127,14 @@ We can select cavities in the **Average Depth** or **Maximum Depth** lists to hi
     The cavity points are colored using a gradient from blue to red to represent the depth of each point. The blue points correspond to the shallowest points on the cavity-bulk boundary, while the red points correspond to the deepest points. The depth scale ranges from 0.0 to the maximum depth of all cavities
 
 These characterizations can also serve as a quality control for cavity detection. For instance, if the cavity is poorly detected, the depth points will not be well-distributed, and the surface points will not be well-defined. In such cases, you can adjust the parameters and run pyKVFinder again to improve the results.
+
+Video tutorial
+--------------
+
+A video tutorial is available to guide you through the steps of this tutorial. 
+
+.. video:: pykvfinder_quick_video_tutorial.mp4
+    :width: 700
+    :poster: pykvfinder_video_poster.png
+
+|

docs/package/api_reference/Molecule.html

@@ -112,7 +112,7 @@
 <h1>pyKVFinder.Molecule<a class="headerlink" href="#pykvfinder-molecule" title="Link to this heading"></a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="pyKVFinder.Molecule">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pyKVFinder.</span></span><span class="sig-name descname"><span class="pre">Molecule</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">radii</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nthreads</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/pyKVFinder/main.html#Molecule"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyKVFinder.Molecule" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pyKVFinder.</span></span><span class="sig-name descname"><span class="pre">Molecule</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">radii</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nthreads</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/pyKVFinder/main.html#Molecule"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyKVFinder.Molecule" title="Link to this definition"></a></dt>
 <dd><p>A class for representing molecular structures.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

docs/plugins/pymol/tutorial/cage-cavity-detection.html

@@ -64,7 +64,10 @@
 <li class="toctree-l2"><a class="reference internal" href="../index.html#installation">Installation</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="../index.html#tutorial">Tutorial</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="biomolecular-cavity-detection.html">Biomolecular cavity detection</a></li>
-<li class="toctree-l3 current"><a class="current reference internal" href="#">Supramolecular cage cavity detection</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">Supramolecular cage cavity detection</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#video-tutorial">Video tutorial</a></li>
+</ul>
+</li>
 </ul>
 </li>
 </ul>
@@ -195,6 +198,13 @@ <h1>Supramolecular cage cavity detection<a class="headerlink" href="#supramolecu
 <p>The cavity points are colored using a gradient from blue to red to represent the depth of each point. The blue points correspond to the shallowest points on the cavity-bulk boundary, while the red points correspond to the deepest points. The depth scale ranges from 0.0 to the maximum depth of all cavities</p>
 </div>
 <p>These characterizations can also serve as a quality control for cavity detection. For instance, if the cavity is poorly detected, the depth points will not be well-distributed, and the surface points will not be well-defined. In such cases, you can adjust the parameters and run pyKVFinder again to improve the results.</p>
+<section id="video-tutorial">
+<h2>Video tutorial<a class="headerlink" href="#video-tutorial" title="Link to this heading"></a></h2>
+<p>A video tutorial is available to guide you through the steps of this tutorial.</p>
+<video controls="True" poster="pykvfinder_video_poster.png" preload="auto" width="700"><source src="../../../_images/pykvfinder_quick_video_tutorial.mp4" type="video/mp4"></video><div class="line-block">
+<div class="line"><br /></div>
+</div>
+</section>
 </section>
 
 

docs/source/conf.py

@@ -50,6 +50,7 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.viewcode",
     "sphinx.ext.githubpages",
+    "sphinxcontrib.video"
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/source/plugins/pymol/tutorial/cage-cavity-detection.rst

@@ -127,3 +127,14 @@ We can select cavities in the **Average Depth** or **Maximum Depth** lists to hi
     The cavity points are colored using a gradient from blue to red to represent the depth of each point. The blue points correspond to the shallowest points on the cavity-bulk boundary, while the red points correspond to the deepest points. The depth scale ranges from 0.0 to the maximum depth of all cavities
 
 These characterizations can also serve as a quality control for cavity detection. For instance, if the cavity is poorly detected, the depth points will not be well-distributed, and the surface points will not be well-defined. In such cases, you can adjust the parameters and run pyKVFinder again to improve the results.
+
+Video tutorial
+--------------
+
+A video tutorial is available to guide you through the steps of this tutorial. 
+
+.. video:: pykvfinder_quick_video_tutorial.mp4
+    :width: 700
+    :poster: pykvfinder_video_poster.png
+
+|