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FanwangM committed Dec 26, 2024
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2 changes: 1 addition & 1 deletion .buildinfo
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# Sphinx build info version 1
# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 4f63c4033d8983dda5374d629656659f
config: 8d2e88a9e33b749590ad32e11c039989
tags: 645f666f9bcd5a90fca523b33c5a78b7
2 changes: 1 addition & 1 deletion _modules/procrustes/permutation.html
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Expand Up @@ -242,7 +242,7 @@ <h1>Source code for procrustes.permutation</h1><div class="highlight"><pre>
<span class="n">a</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">b</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">single</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
<span class="n">method</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;kopt&quot;</span><span class="p">,</span>
<span class="n">method</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;k-opt&quot;</span><span class="p">,</span>
<span class="n">guess_p1</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">guess_p2</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
<span class="n">pad</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
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10 changes: 7 additions & 3 deletions _static/js/versions.js
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const themeFlyoutDisplay = "hidden";
const themeVersionSelector = "True";
const themeLanguageSelector = "True";
const themeVersionSelector = true;
const themeLanguageSelector = true;

if (themeFlyoutDisplay === "attached") {
function renderLanguages(config) {
if (!config.projects.translations.length) {
return "";
}

// Insert the current language to the options on the selector
let languages = config.projects.translations.concat(config.projects.current);
languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name));

const languagesHTML = `
<dl>
<dt>Languages</dt>
${config.projects.translations
${languages
.map(
(translation) => `
<dd ${translation.slug == config.projects.current.slug ? 'class="rtd-current-item"' : ""}>
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2 changes: 1 addition & 1 deletion api/permutation.html
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Expand Up @@ -175,7 +175,7 @@

<dl class="py function">
<dt class="sig sig-object py" id="procrustes.permutation.permutation_2sided">
<span class="sig-prename descclassname"><span class="pre">procrustes.permutation.</span></span><span class="sig-name descname"><span class="pre">permutation_2sided</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a</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">b</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">single</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'kopt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">guess_p1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">guess_p2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">pad</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unpad_col</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unpad_row</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_finite</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">weight</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">lapack_driver</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'gesvd'</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 internal" href="utils.html#procrustes.utils.ProcrustesResult" title="procrustes.utils.ProcrustesResult"><span class="pre">ProcrustesResult</span></a></span></span><a class="reference internal" href="../_modules/procrustes/permutation.html#permutation_2sided"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#procrustes.permutation.permutation_2sided" title="Link to this definition"></a></dt>
<span class="sig-prename descclassname"><span class="pre">procrustes.permutation.</span></span><span class="sig-name descname"><span class="pre">permutation_2sided</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a</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">b</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">single</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'k-opt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">guess_p1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">guess_p2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">pad</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unpad_col</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unpad_row</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_finite</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</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">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">options</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">weight</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">lapack_driver</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</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">'gesvd'</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 internal" href="utils.html#procrustes.utils.ProcrustesResult" title="procrustes.utils.ProcrustesResult"><span class="pre">ProcrustesResult</span></a></span></span><a class="reference internal" href="../_modules/procrustes/permutation.html#permutation_2sided"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#procrustes.permutation.permutation_2sided" title="Link to this definition"></a></dt>
<dd><p>Perform two-sided permutation Procrustes.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
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2 changes: 1 addition & 1 deletion notebooks/Atom_Atom_Mapping.html
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Expand Up @@ -113,7 +113,7 @@ <h1>Atom-Atom Mapping<a class="headerlink" href="#Atom-Atom-Mapping" title="Link
same shape as matrix <span class="math notranslate nohighlight">\(\mathbf{B}\)</span>.</p></li>
<li><p><strong>Fig. (iii):</strong> The mapping between atoms can be also directly deduced from the optimal permutation matrix <span class="math notranslate nohighlight">\(\mathbf{P}\)</span>. Specifically, the transformed matrix <span class="math notranslate nohighlight">\(\mathbf{P^{\top}AP}\)</span> should be compared to matrix <span class="math notranslate nohighlight">\(\mathbf{B}\)</span> to identify the matching atoms; the zero rows/columns in <span class="math notranslate nohighlight">\(\mathbf{A}\)</span> (colored in blue) correspond to atoms in <span class="math notranslate nohighlight">\(\mathbf{B}\)</span> for which there are no corresponding atoms.</p></li>
</ul>
<p><img alt="Fig. 1. Atom-atom Mapping with Two-sided Permutation Procrustes" src="../_images/atom_atom_mapping.png" /></p>
<img alt="Fig. 1. Atom-atom Mapping with Two-sided Permutation Procrustes" src="../_images/atom_atom_mapping.png" />
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
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2 changes: 1 addition & 1 deletion notebooks/Chemical_Structure_Alignment.html
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Expand Up @@ -112,7 +112,7 @@ <h1>Chemical Structure Alignment<a class="headerlink" href="#Chemical-Structure-
</div></blockquote>
<p>In the code block below, we use the <code class="docutils literal notranslate"><span class="pre">procrustes</span></code> library for protein structure alignment. We use the 2HHB, which has cyclic-<span class="math notranslate nohighlight">\(C_2\)</span> global symmetry, and load its PDB file using <a class="reference external" href="https://github.com/theochem/iodata">IOData library</a> to obtain the 3D-Cartesian coordinates atoms. In 2HHB, the A and C (or B and D) are hemoglobin deoxy-alpha (beta) chains shown in <strong>Fig. (i)</strong>, and their <span class="math notranslate nohighlight">\(C_{\alpha}\)</span> atoms in <strong>Fig. (ii)</strong> are aligned in <strong>Fig. (iii)</strong> to show that they are homologous.
The results in <strong>Fig. (iii)</strong> are obtained with orthogonal Procrustes which implements the <em>Kabsch</em> algorithm. The root-mean-square deviation (RMSD) is used to assess the discrepancy between structures before and after the translation-rotation transformation.</p>
<p><img alt="Fig. 1. protein structure alignment with rotational Procrustes." src="../_images/protein_alignment.png" /></p>
<img alt="Fig. 1. protein structure alignment with rotational Procrustes." src="../_images/protein_alignment.png" />
<section id="Download-IOData-&amp;-Matplotlib-Libraries-&amp;-Example-Files">
<h2>Download IOData &amp; Matplotlib Libraries &amp; Example Files<a class="headerlink" href="#Download-IOData-&-Matplotlib-Libraries-&-Example-Files" title="Link to this heading"></a></h2>
<ul class="simple">
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