Update documentation

docs/_sources/plugins/pymol/index.rst.txt

@@ -9,19 +9,32 @@ Installation
 
 First, it is required to install Anaconda or Miniconda (Python 3.10 or later). If you do not have it installed, please refer to `Anaconda <https://www.anaconda.com/products/distribution>`_ or `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ websites.
 
-In the `Anaconda Prompt`, create a new environment and install PyMOL:
+In the `Anaconda Prompt`, create a new environment and activate it:
 
 .. code-block:: bash
 
     conda create -n pymol python=3.10
     conda activate pymol
-    # PyMOL v3.0
-    conda install -c conda-forge -c schrodinger pymol-bundle
-    # PyMOL v2.6
-    conda install -c conda-forge -c schrodinger pymol-bundle=2.6 
-    # PyMOL Open-Source
-    conda install -c conda-forge pymol-open-source
 
+Then, install **one** of the following versions of PyMOL:
+
+* PyMOL v3.0 (Schrodinger)
+
+    .. code-block:: bash
+
+        conda install -c conda-forge -c schrodinger pymol-bundle
+
+* PyMOL v2.6 (Schrodinger):
+
+    .. code-block:: bash
+
+        conda install -c conda-forge -c schrodinger pymol-bundle=2.6 
+
+* PyMOL Open-Source
+
+    .. code-block:: bash
+
+        conda install -c conda-forge pymol-open-source
 
 After installing one of the PyMOL versions (v3.0, v2.6 or Open-Source), you need to install the `pyKVFinder <https://pypi.org/project/pyKVFinder/>`_ package, if you have not done it yet:
 

docs/package/api_reference/calculate_frequencies.html

@@ -128,20 +128,20 @@
 <h1>pyKVFinder.calculate_frequencies<a class="headerlink" href="#pykvfinder-calculate-frequencies" title="Link to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="pyKVFinder.calculate_frequencies">
-<span class="sig-prename descclassname"><span class="pre">pyKVFinder.</span></span><span class="sig-name descname"><span class="pre">calculate_frequencies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">residues</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/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.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</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="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><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.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.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/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../../_modules/pyKVFinder/utils.html#calculate_frequencies"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyKVFinder.calculate_frequencies" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">pyKVFinder.</span></span><span class="sig-name descname"><span class="pre">calculate_frequencies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">residues</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/typing.html#typing.Dict" title="(in Python v3.13)"><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 v3.13)"><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.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</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 v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.13)"><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 v3.13)"><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.Dict" title="(in Python v3.13)"><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 v3.13)"><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.Dict" title="(in Python v3.13)"><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 v3.13)"><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/functions.html#int" title="(in Python v3.13)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../../_modules/pyKVFinder/utils.html#calculate_frequencies"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pyKVFinder.calculate_frequencies" title="Link to this definition"></a></dt>
 <dd><p>Calculate frequencies of residues and class of residues
 (R1, R2, R3, R4 and R5) for detected cavities.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>residues</strong> (<em>Dict</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>List</em><em>[</em><em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>]</em><em>]</em><em>]</em>) – A dictionary with a list of interface residues for each detected
+<dd class="field-odd"><p><strong>residues</strong> (<em>Dict</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em>, </em><em>List</em><em>[</em><em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><em>str</em></a><em>]</em><em>]</em><em>]</em>) – A dictionary with a list of interface residues for each detected
 cavity.</p>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p><strong>frequencies</strong> – A dictionary with frequencies of residues and class for
 residues of each detected cavity.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a>, Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a>, Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a>]]]</p>
+<dd class="field-odd"><p>Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a>, Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a>, Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)">str</a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.13)">int</a>]]]</p>
 </dd>
 </dl>
 <div class="admonition note">