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jbloom committed Jan 26, 2024
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6 changes: 3 additions & 3 deletions RBD_average.html
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<title>Averaging models &#8212; polyclonal 6.9 documentation</title>
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<title>Overview: module code &#8212; polyclonal 6.9 documentation</title>
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<title>polyclonal.pdb_utils &#8212; polyclonal 3.2 documentation</title>
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Expand Down Expand Up @@ -42,7 +40,6 @@ <h1>Source code for polyclonal.pdb_utils</h1><div class="highlight"><pre>

<span class="sd">&quot;&quot;&quot;</span>


<span class="kn">import</span> <span class="nn">collections</span> <span class="c1"># noqa: F401</span>
<span class="kn">import</span> <span class="nn">itertools</span>
<span class="kn">import</span> <span class="nn">os</span> <span class="c1"># noqa: F401</span>
Expand All @@ -58,12 +55,14 @@ <h1>Source code for polyclonal.pdb_utils</h1><div class="highlight"><pre>
<span class="kn">import</span> <span class="nn">requests</span> <span class="c1"># noqa: F401</span>


<div class="viewcode-block" id="inter_residue_distances"><a class="viewcode-back" href="../../polyclonal.pdb_utils.html#polyclonal.pdb_utils.inter_residue_distances">[docs]</a><span class="k">def</span> <span class="nf">inter_residue_distances</span><span class="p">(</span>
<div class="viewcode-block" id="inter_residue_distances">
<a class="viewcode-back" href="../../polyclonal.pdb_utils.html#polyclonal.pdb_utils.inter_residue_distances">[docs]</a>
<span class="k">def</span> <span class="nf">inter_residue_distances</span><span class="p">(</span>
<span class="n">input_pdbfile</span><span class="p">,</span>
<span class="n">target_chains</span><span class="p">,</span>
<span class="n">target_atom</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="p">):</span>
<span class="sa">r</span><span class="sd">&quot;&quot;&quot;Get inter-residue distances from a PDB file.</span>
<span class="w"> </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;Get inter-residue distances from a PDB file.</span>

<span class="sd"> If a residue number is present in multiple chains, gets the closest distance</span>
<span class="sd"> for each partner from all residues with that number. This is useful for</span>
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<span class="p">)</span></div>


<div class="viewcode-block" id="reassign_b_factor"><a class="viewcode-back" href="../../polyclonal.pdb_utils.html#polyclonal.pdb_utils.reassign_b_factor">[docs]</a><span class="k">def</span> <span class="nf">reassign_b_factor</span><span class="p">(</span>

<div class="viewcode-block" id="reassign_b_factor">
<a class="viewcode-back" href="../../polyclonal.pdb_utils.html#polyclonal.pdb_utils.reassign_b_factor">[docs]</a>
<span class="k">def</span> <span class="nf">reassign_b_factor</span><span class="p">(</span>
<span class="n">input_pdbfile</span><span class="p">,</span>
<span class="n">output_pdbfile</span><span class="p">,</span>
<span class="n">df</span><span class="p">,</span>
Expand All @@ -206,7 +208,7 @@ <h1>Source code for polyclonal.pdb_utils</h1><div class="highlight"><pre>
<span class="n">missing_metric</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="n">model_index</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="p">):</span>
<span class="sa">r</span><span class="sd">&quot;&quot;&quot;Reassign B factors in PDB file to some other metric.</span>
<span class="w"> </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;Reassign B factors in PDB file to some other metric.</span>

<span class="sd"> B-factor re-assignment is useful because PDB images can be colored</span>
<span class="sd"> by B factor using programs such as ``pymol`` using commands like::</span>
Expand Down Expand Up @@ -378,12 +380,15 @@ <h1>Source code for polyclonal.pdb_utils</h1><div class="highlight"><pre>
<span class="n">io</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">output_pdbfile</span><span class="p">)</span></div>


<div class="viewcode-block" id="extract_atom_locations"><a class="viewcode-back" href="../../polyclonal.pdb_utils.html#polyclonal.pdb_utils.extract_atom_locations">[docs]</a><span class="k">def</span> <span class="nf">extract_atom_locations</span><span class="p">(</span>

<div class="viewcode-block" id="extract_atom_locations">
<a class="viewcode-back" href="../../polyclonal.pdb_utils.html#polyclonal.pdb_utils.extract_atom_locations">[docs]</a>
<span class="k">def</span> <span class="nf">extract_atom_locations</span><span class="p">(</span>
<span class="n">input_pdbfile</span><span class="p">,</span>
<span class="n">target_chains</span><span class="p">,</span>
<span class="n">target_atom</span><span class="o">=</span><span class="s2">&quot;CA&quot;</span><span class="p">,</span>
<span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Extract atom locations from target chains of a PDB file.</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Extract atom locations from target chains of a PDB file.</span>

<span class="sd"> By default the locations of alpha carbons are extracted, but any atom</span>
<span class="sd"> can be specified. If a residue does not have the specified atom,</span>
Expand Down Expand Up @@ -507,6 +512,7 @@ <h1>Source code for polyclonal.pdb_utils</h1><div class="highlight"><pre>
<span class="k">return</span> <span class="n">output</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>



<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">doctest</span>

Expand Down Expand Up @@ -554,13 +560,12 @@ <h3>Navigation</h3>
<li class="toctree-l1"><a class="reference internal" href="../../visualize_RBD.html">Visualize antibody mix</a></li>
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Expand Down Expand Up @@ -588,7 +593,7 @@ <h3 id="searchlabel">Quick search</h3>
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