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<h1>API Reference</h1><section id="serd-detect">
<h1>SERD.detect<a class="headerlink" href="#serd-detect" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.detect">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">detect</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</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.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surface_representation</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.Literal" title="(in Python v3.10)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'VDW'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'SES'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'SAS'</span></span><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">'SES'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">0.6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">probe</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">1.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vdw</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.Optional" title="(in Python v3.10)"><span class="pre">Optional</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</span></a><span class="p"><span class="pre">]</span></span><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">ignore_backbone</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 v3.10)"><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">True</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/typing.html#typing.Optional" title="(in Python v3.10)"><span class="pre">Optional</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</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">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 v3.10)"><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/SERD/SERD.html#detect"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.detect" title="Permalink to this definition"></a></dt>
<dd><p>Detect solvent-exposed residues of a target biomolecule.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em>) – A path to PDB or XYZ file of a target biomolecular structure.</p></li>
<li><p><strong>surface_representation</strong> (<em>Literal</em><em>[</em><em>"VDW"</em><em>, </em><em>"SES"</em><em>, </em><em>"SAS"</em><em>]</em><em>, </em><em>optional</em>) – Surface representation. Keywords options are VDW (van der Waals), SES (Solvent Excluded Surface)
or SAS (Solvent Accessible Surface), by default “SES”.</p></li>
<li><p><strong>step</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Grid spacing (A), by default 0.6.</p></li>
<li><p><strong>probe</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Probe size (A) to define SES and SAS representations, by default 1.4.</p></li>
<li><p><strong>vdw</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em><em>]</em><em>, </em><em>optional</em>) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der
Waals radii file: <cite>vdw.dat</cite>.</p></li>
<li><p><strong>ignore_backbone</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface residues, by default True.</p></li>
<li><p><strong>nthreads</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Number of threads, by default None. If None, the number of threads is
<cite>os.cpu_count() - 1</cite>.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Print extra information to standard output, by default False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>residues</strong> – A list of solvent-exposed residues.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>List[List[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)">str</a>]]</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>target</cite> must be a string or a pathlib.Path.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>surface_representation</cite> must be a <cite>VDW</cite>, <cite>SES</cite> or <cite>SAS</cite>.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>step</cite> must be a positive real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>step</cite> must be a positive real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>probe</cite> must be a non-negative real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>probe</cite> must be a non-negative real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>vdw</cite> must be a string or a pathlib.Path.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>nthreads</cite> must be a positive integer.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>nthreads</cite> must be a positive integer.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>verbose</cite> must be a boolean.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>probe</cite> must be a positive real number, when SES or SAS is set.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>target</cite> must be .pdb or .xyz.</p></li>
</ul>
</dd>
</dl>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The van der Waals radii file defines the radius values for each
atom by residue and when not defined, it uses a generic value
based on the atom type (see pyKVFinder package).</p>
</div>
</dd></dl>
</section>
<section id="serd-g2pdb">
<h1>SERD.g2pdb<a class="headerlink" href="#serd-g2pdb" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.g2pdb">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">g2pdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atomic</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <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.List" title="(in Python v3.10)"><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 v3.10)"><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 v3.10)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fn</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.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</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">'graph.pdb'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/SERD/SERD.html#g2pdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.g2pdb" title="Permalink to this definition"></a></dt>
<dd><p>Save a graph to a PDB-formatted file. Each node are represented by the
CA atom of the residue and edges are represented by CONECT record.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>graph</strong> (<em>networkx.classes.graph.Graph</em>) – A graph of solvent-exposed residues with edges defined by a distance smaller than the cutoff.</p></li>
<li><p><strong>atomic</strong> (<em>numpy.ndarray</em>) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
and radius) for each atom.</p></li>
<li><p><strong>residues</strong> (<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 v3.10)"><em>str</em></a><em>]</em><em>]</em>) – A list of solvent-exposed residues.</p></li>
<li><p><strong>fn</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em><em>, </em><em>optional</em>) – A path to a PDB file, by default “graph.pdb”.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="serd-get-vertices">
<h1>SERD.get_vertices<a class="headerlink" href="#serd-get-vertices" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.get_vertices">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">get_vertices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atomic</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">probe</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">1.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">0.6</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/SERD/SERD.html#get_vertices"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.get_vertices" title="Permalink to this definition"></a></dt>
<dd><p>Gets 3D grid vertices.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>atomic</strong> (<em>numpy.ndarray</em>) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
and radius) for each atom.</p></li>
<li><p><strong>probe</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Probe size (A), by default 4.0.</p></li>
<li><p><strong>step</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Grid spacing (A), by default 0.6.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>vertices</strong> – A numpy.ndarray with xyz vertices coordinates
(origin, X-axis, Y-axis, Z-axis).</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="serd-interface">
<h1>SERD.interface<a class="headerlink" href="#serd-interface" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.interface">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">interface</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">surface</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atomic</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_backbone</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 v3.10)"><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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">0.6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">probe</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">1.4</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/typing.html#typing.Optional" title="(in Python v3.10)"><span class="pre">Optional</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</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">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 v3.10)"><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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.10)"><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 v3.10)"><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 v3.10)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/SERD/SERD.html#interface"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.interface" title="Permalink to this definition"></a></dt>
<dd><p>Identifies the solvent-exposed residues based on a target solvent-exposed surface
and atomic information of a biomolecule (residue number, chain identifier, residue
name, xyz coordinates, radius).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>surface</strong> (<em>numpy.ndarray</em>) – <p>Surface points in the 3D grid (surface[nx, ny, nz]).
Surface array has integer labels in each positions, that are:</p>
<blockquote>
<div><ul>
<li><p>-1: solvent points;</p></li>
<li><p>0: biomolecule points;</p></li>
<li><p>1: solvent-exposed surface points.</p></li>
</ul>
<p>Enclosed regions are considered biomolecule points.</p>
</div></blockquote>
</p></li>
<li><p><strong>atomic</strong> (<em>numpy.ndarray</em>) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
and radius) for each atom.</p></li>
<li><p><strong>ignore_backbone</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface residues, by default True.</p></li>
<li><p><strong>step</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Grid spacing (A), by default 0.6.</p></li>
<li><p><strong>probe</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Probe size (A) to define SES and SAS representations, by default 1.4.</p></li>
<li><p><strong>nthreads</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Number of threads, by default None. If None, the number of threads is
<cite>os.cpu_count() - 1</cite>.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Print extra information to standard output, by default False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>residues</strong> – A list of solvent-exposed residues.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>List[List[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)">str</a>]]</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>surface</cite> must be a numpy.ndarray.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>surface</cite> has the incorrect shape. It must be (nx, ny, nz).</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>atomic</cite> must be a numpy.ndarray.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>atomic</cite> has incorrect shape. It must be (n, 8).</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>ignore_backbone</cite> must be a boolean.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>step</cite> must be a positive real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>probe</cite> must be a non-negative real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>probe</cite> must be a non-negative real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>nthreads</cite> must be a positive integer.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>nthreads</cite> must be a positive integer.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>verbose</cite> must be a boolean.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="serd-r2g">
<h1>SERD.r2g<a class="headerlink" href="#serd-r2g" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.r2g">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">r2g</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.List" title="(in Python v3.10)"><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 v3.10)"><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 v3.10)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atomic</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selection</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.Literal" title="(in Python v3.10)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'CA'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'CB'</span></span><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">'CB'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</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.Optional" title="(in Python v3.10)"><span class="pre">Optional</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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">intraresidual</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 v3.10)"><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>, <em class="sig-param"><span class="n"><span class="pre">weighted_edges</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 v3.10)"><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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Graph</span></span></span><a class="reference internal" href="../_modules/SERD/SERD.html#r2g"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.r2g" title="Permalink to this definition"></a></dt>
<dd><p>Create a graph from a list of solvent-exposed residues.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>residues</strong> (<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 v3.10)"><em>str</em></a><em>]</em><em>]</em>) – A list of solvent-exposed residues.</p></li>
<li><p><strong>atomic</strong> (<em>numpy.ndarray</em>) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
and radius) for each atom.</p></li>
<li><p><strong>selection</strong> (<em>{"CA"</em><em>, </em><em>"CB"</em><em>, </em><em>"all"}</em><em>, </em><em>optional</em>) – <p>Atomic selection, by default “CB”. Keywords options are:</p>
<blockquote>
<div><ul>
<li><p>’CA’: Select alfa-carbon;</p></li>
<li><p>’CB’: Select beta-carbon, except for glycine which selects the alfa-carbon;</p></li>
<li><p>’all’: Select all atoms, distance between residues are the smallest distance between the atoms of these residues.</p></li>
</ul>
</div></blockquote>
</p></li>
<li><p><strong>cutoff</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>]</em><em>, </em><em>optional</em>) – A limit of distance to define an edge between two solvent-exposed residues, by default None.
If None, cutoff depends on selection argument. If “CA”, cutoff is 10.0. If “CB”, cutoff is 8.0.</p></li>
<li><p><strong>intraresidual</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to consider intraresidual contacts to create adjacency matrix, by default False.</p></li>
<li><p><strong>weighted_edges</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to include the distances as weight of the edges.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A graph of solvent-exposed residues with edges defined by a distance smaller than the cutoff.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>networkx.classes.graph.Graph</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>selection</cite> must be <cite>CA</cite>, <cite>CB</cite>, or <cite>all</cite>.</p>
</dd>
</dl>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Cutoff for beta-carbon is based on CAPRI round 28. For more details, refer to
<a class="reference external" href="https://www.ebi.ac.uk/msd-srv/capri/round28/round28.html">https://www.ebi.ac.uk/msd-srv/capri/round28/round28.html</a>.</p>
</div>
</dd></dl>
</section>
<section id="serd-read-vdw">
<h1>SERD.read_vdw<a class="headerlink" href="#serd-read-vdw" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.read_vdw">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">read_vdw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fn</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.Optional" title="(in Python v3.10)"><span class="pre">Optional</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</span></a><span class="p"><span class="pre">]</span></span><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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.10)"><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 v3.10)"><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 v3.10)"><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 v3.10)"><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#float" title="(in Python v3.10)"><span class="pre">float</span></a><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#read_vdw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.read_vdw" title="Permalink to this definition"></a></dt>
<dd><p>Reads van der Waals radii from .dat file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>fn</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em><em>]</em><em>, </em><em>optional</em>) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der
Waals radii file: <cite>vdw.dat</cite>.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>vdw</strong> – A dictionary containing radii values.</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 v3.10)">str</a>, Dict[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)">str</a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)">float</a>]]</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>fn</cite> must be a string or a pathlib.Path.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – A line in <cite>vdw</cite> has incorrect format. The values must be double
tab-separated.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – A line in <cite>vdw</cite> has an incorrect radius type for an atom.</p></li>
</ul>
</dd>
</dl>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The van der Waals radii file defines the radius values for each
atom by residue and when not defined, it uses a generic value
based on the atom type (see <cite>van der Waals file template</cite>).
The package contains a built-in van der Waals radii file: <cite>vdw.dat</cite>.</p>
</div>
</dd></dl>
</section>
<section id="serd-read-pdb">
<h1>SERD.read_pdb<a class="headerlink" href="#serd-read-pdb" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.read_pdb">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">read_pdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fn</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.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vdw</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.Optional" title="(in Python v3.10)"><span class="pre">Optional</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.10)"><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 v3.10)"><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 v3.10)"><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 v3.10)"><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#float" title="(in Python v3.10)"><span class="pre">float</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 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><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/SERD/SERD.html#read_pdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.read_pdb" title="Permalink to this definition"></a></dt>
<dd><p>Reads PDB file into numpy.ndarrays.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>fn</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em>) – A path to PDB file.</p></li>
<li><p><strong>vdw</strong> (<em>Dict</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><em>Dict</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>]</em><em>]</em><em>, </em><em>optional</em>) – A dictionary containing radii values, by default None. If None, use output of <cite>pyKVFinder.read_vdw()</cite>.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>atomic</strong> – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
and radius) for each atom.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>fn</cite> must be a string or a pathlib.Path.</p>
</dd>
</dl>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The van der Waals radii file defines the radius values for each atom
by residue and when not defined, it uses a generic value based on the
atom type. The function by default loads the built-in van der Waals radii
file: <cite>vdw.dat</cite>.</p>
</div>
</dd></dl>
</section>
<section id="serd-save">
<h1>SERD.save<a class="headerlink" href="#serd-save" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.save">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">save</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.List" title="(in Python v3.10)"><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 v3.10)"><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 v3.10)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fn</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.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</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">'residues.pickle'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/SERD/SERD.html#save"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.save" title="Permalink to this definition"></a></dt>
<dd><p>Save list of solvent-exposed residues to binary pickle file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>residues</strong> (<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 v3.10)"><em>str</em></a><em>]</em><em>]</em>) – A list of solvent-exposed residues.</p></li>
<li><p><strong>fn</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em><em>, </em><em>optional</em>) – A path to pickle file, by default “residues.pickle”</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="serd-save-session">
<h1>SERD.save_session<a class="headerlink" href="#serd-save-session" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.save_session">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">save_session</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</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.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</span></a><span class="p"><span class="pre">]</span></span></span></em>, <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.List" title="(in Python v3.10)"><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 v3.10)"><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 v3.10)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fn</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.Union" title="(in Python v3.10)"><span class="pre">Union</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 v3.10)"><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/pathlib.html#pathlib.Path" title="(in Python v3.10)"><span class="pre">Path</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">'residues.pse'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/SERD/SERD.html#save_session"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.save_session" title="Permalink to this definition"></a></dt>
<dd><p>Save a PyMOL session with the solvent-exposed residues (shown as red sticks) and
the target biomolecular structure (shown as cartoon).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em>) – A path to PDB or XYZ file of a target biomolecular structure.</p></li>
<li><p><strong>residues</strong> (<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 v3.10)"><em>str</em></a><em>]</em><em>]</em>) – A list of solvent-exposed residues.</p></li>
<li><p><strong>fn</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.10)"><em>pathlib.Path</em></a><em>]</em><em>, </em><em>optional</em>) – A path to a PyMOL session file, by default “residues.pse”.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="serd-surface">
<h1>SERD.surface<a class="headerlink" href="#serd-surface" title="Permalink to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="SERD.surface">
<span class="sig-prename descclassname"><span class="pre">SERD.</span></span><span class="sig-name descname"><span class="pre">surface</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atomic</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surface_representation</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.Literal" title="(in Python v3.10)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'VDW'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'SES'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'SAS'</span></span><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">'SES'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">0.6</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">probe</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.Union" title="(in Python v3.10)"><span class="pre">Union</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><span class="pre">float</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 v3.10)"><span class="pre">int</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">1.4</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/typing.html#typing.Optional" title="(in Python v3.10)"><span class="pre">Optional</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</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">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 v3.10)"><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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference internal" href="../_modules/SERD/SERD.html#surface"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#SERD.surface" title="Permalink to this definition"></a></dt>
<dd><p>Defines the solvent-exposed surface of a target biomolecule in a 3D grid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>atomic</strong> (<em>numpy.ndarray</em>) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
and radius) for each atom.</p></li>
<li><p><strong>surface_representation</strong> (<em>Literal</em><em>[</em><em>"VDW"</em><em>, </em><em>"SES"</em><em>, </em><em>"SAS"</em><em>]</em><em>, </em><em>optional</em>) – Surface representation. Keywords options are VDW (van der Waals surface), SES (Solvent Excluded Surface)
or SAS (Solvent Accessible Surface), by default “SES”.</p></li>
<li><p><strong>step</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Grid spacing (A), by default 0.6.</p></li>
<li><p><strong>probe</strong> (<em>Union</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.10)"><em>float</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Probe size (A) to define SES and SAS representations, by default 1.4.</p></li>
<li><p><strong>nthreads</strong> (<em>Optional</em><em>[</em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a><em>]</em><em>, </em><em>optional</em>) – Number of threads, by default None. If None, the number of threads is
<cite>os.cpu_count() - 1</cite>.</p></li>
<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.10)"><em>bool</em></a><em>, </em><em>optional</em>) – Print extra information to standard output, by default False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p><strong>surface</strong> – Surface points in the 3D grid (surface[nx, ny, nz]).
Surface array has integer labels in each positions, that are:</p>
<blockquote>
<div><ul class="simple">
<li><p>-1: solvent points;</p></li>
<li><p>0: biomolecule points;</p></li>
<li><p>1: solvent-exposed surface points.</p></li>
</ul>
<p>Enclosed regions are considered biomolecule points.</p>
</div></blockquote>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>atomic</cite> must be a numpy.ndarray.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>atomic</cite> has incorrect shape. It must be (n, 8).</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>surface_representation</cite> must be a <cite>VDW</cite>, <cite>SES</cite> or <cite>SAS</cite>.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>step</cite> must be a positive real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>step</cite> must be a positive real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>probe</cite> must be a non-negative real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>probe</cite> must be a non-negative real number.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>nthreads</cite> must be a positive integer.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>nthreads</cite> must be a positive integer.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#TypeError" title="(in Python v3.10)"><strong>TypeError</strong></a> – <cite>verbose</cite> must be a boolean.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.10)"><strong>ValueError</strong></a> – <cite>probe</cite> must be a positive real number, when SES or SAS is set.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
</div>
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