Documentation build

TheoChem-VU · Feb 6, 2024 · e3c3bca · e3c3bca
1 parent 10ffff0
commit e3c3bca
Show file tree

Hide file tree

Showing 33 changed files with 2,800 additions and 47 deletions.
diff --git a/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree b/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree
diff --git a/docs/_build/doctrees/api/tcutility.data.doctree b/docs/_build/doctrees/api/tcutility.data.doctree
diff --git a/docs/_build/doctrees/api/tcutility.doctree b/docs/_build/doctrees/api/tcutility.doctree
diff --git a/docs/_build/doctrees/api/tcutility.job.doctree b/docs/_build/doctrees/api/tcutility.job.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -254,6 +254,9 @@ <h1>All modules for which code is available</h1>
 <li><a href="tcutility/analysis/vdd/manager.html">tcutility.analysis.vdd.manager</a></li>
 <li><a href="tcutility/analysis/vibration/ts_vibration.html">tcutility.analysis.vibration.ts_vibration</a></li>
 <li><a href="tcutility/cache.html">tcutility.cache</a></li>
+<li><a href="tcutility/data/atom.html">tcutility.data.atom</a></li>
+<li><a href="tcutility/data/functionals.html">tcutility.data.functionals</a></li>
+<li><a href="tcutility/data/molecules.html">tcutility.data.molecules</a></li>
 <li><a href="tcutility/formula.html">tcutility.formula</a></li>
 <li><a href="tcutility/geometry.html">tcutility.geometry</a></li>
 <li><a href="tcutility/job/adf.html">tcutility.job.adf</a></li>

diff --git a/docs/_build/html/_modules/tcutility.html b/docs/_build/html/_modules/tcutility.html
@@ -271,7 +271,7 @@ <h1>Source code for tcutility</h1><div class="highlight"><pre>
 
 
 
-<span class="kn">from</span> <span class="nn">tcutility</span> <span class="kn">import</span> <span class="n">constants</span><span class="p">,</span> <span class="n">formula</span><span class="p">,</span> <span class="n">geometry</span><span class="p">,</span> <span class="n">log</span><span class="p">,</span> <span class="n">molecule</span><span class="p">,</span> <span class="n">results</span><span class="p">,</span> <span class="n">slurm</span><span class="p">,</span> <span class="n">data</span>  <span class="c1"># noqa: F401, E402</span>
+<span class="kn">from</span> <span class="nn">tcutility</span> <span class="kn">import</span> <span class="n">constants</span><span class="p">,</span> <span class="n">formula</span><span class="p">,</span> <span class="n">geometry</span><span class="p">,</span> <span class="n">log</span><span class="p">,</span> <span class="n">molecule</span><span class="p">,</span> <span class="n">results</span><span class="p">,</span> <span class="n">slurm</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">analysis</span><span class="p">,</span> <span class="n">spell_check</span>  <span class="c1"># noqa: F401, E402</span>
 </pre></div>
 
                 </article>

diff --git a/docs/_build/html/_modules/tcutility/data/atom.html b/docs/_build/html/_modules/tcutility/data/atom.html
diff --git a/docs/_build/html/_modules/tcutility/data/functionals.html b/docs/_build/html/_modules/tcutility/data/functionals.html
diff --git a/docs/_build/html/_modules/tcutility/data/molecules.html b/docs/_build/html/_modules/tcutility/data/molecules.html
@@ -0,0 +1,365 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>tcutility.data.molecules &#8212; TCutility v0.8.5 documentation</title>
+
+
+
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
+  </script>
+
+  <!-- Loaded before other Sphinx assets -->
+  <link href="../../../_static/styles/theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+<link href="../../../_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+<link href="../../../_static/styles/pydata-sphinx-theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+
+
+  <link href="../../../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+  <link rel="preload" as="font" type="font/woff2" crossorigin href="../../../_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
+<link rel="preload" as="font" type="font/woff2" crossorigin href="../../../_static/vendor/fontawesome/6.5.1/webfonts/fa-brands-400.woff2" />
+<link rel="preload" as="font" type="font/woff2" crossorigin href="../../../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
+
+    <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
+    <link rel="stylesheet" type="text/css" href="../../../_static/tabs.css?v=a5c4661c" />
+
+  <!-- Pre-loaded scripts that we'll load fully later -->
+  <link rel="preload" as="script" href="../../../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae" />
+<link rel="preload" as="script" href="../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
+  <script src="../../../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
+
+    <script src="../../../_static/documentation_options.js?v=ebd327a5"></script>
+    <script src="../../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
+    <script src="../../../_static/copybutton.js?v=f281be69"></script>
+    <script src="../../../_static/tabs.js?v=3030b3cb"></script>
+    <script>DOCUMENTATION_OPTIONS.pagename = '_modules/tcutility/data/molecules';</script>
+    <link rel="icon" href="https://avatars.githubusercontent.com/u/119413491"/>
+    <link rel="index" title="Index" href="../../../genindex.html" />
+    <link rel="search" title="Search" href="../../../search.html" />
+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
+  <meta name="docsearch:language" content="en"/>
+  </head>
+
+
+  <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
+
+
+
+  <a id="pst-skip-link" class="skip-link" href="#main-content">Skip to main content</a>
+
+  <div id="pst-scroll-pixel-helper"></div>
+
+  <button type="button" class="btn rounded-pill" id="pst-back-to-top">
+    <i class="fa-solid fa-arrow-up"></i>
+    Back to top
+  </button>
+
+
+  <input type="checkbox"
+          class="sidebar-toggle"
+          name="__primary"
+          id="__primary"/>
+  <label class="overlay overlay-primary" for="__primary"></label>
+
+  <input type="checkbox"
+          class="sidebar-toggle"
+          name="__secondary"
+          id="__secondary"/>
+  <label class="overlay overlay-secondary" for="__secondary"></label>
+
+  <div class="search-button__wrapper">
+    <div class="search-button__overlay"></div>
+    <div class="search-button__search-container">
+<form class="bd-search d-flex align-items-center"
+      action="../../../search.html"
+      method="get">
+  <i class="fa-solid fa-magnifying-glass"></i>
+  <input type="search"
+         class="form-control"
+         name="q"
+         id="search-input"
+         placeholder="Search the docs ..."
+         aria-label="Search the docs ..."
+         autocomplete="off"
+         autocorrect="off"
+         autocapitalize="off"
+         spellcheck="false"/>
+  <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
+</form></div>
+  </div>
+
+    <header class="bd-header navbar navbar-expand-lg bd-navbar">
+<div class="bd-header__inner bd-page-width">
+  <label class="sidebar-toggle primary-toggle" for="__primary">
+    <span class="fa-solid fa-bars"></span>
+  </label>
+
+
+  <div class="col-lg-3 navbar-header-items__start">
+
+      <div class="navbar-item"><!-- _templates/logo.html -->
+<style>
+    .myDiv {
+      color: #323232;
+      font-size: 30px;
+      font-weight: 400;
+      line-height: : 33px;
+      text-decoration: none;
+    }
+</style>
+<div class="myDiv">
+    <a href="./index.html">
+        <img src="https://avatars.githubusercontent.com/u/119413491?s=60&v=4">
+        TCutility
+    </a>
+</div></div>
+
+  </div>
+
+  <div class="col-lg-9 navbar-header-items">
+
+
+    <div class="navbar-header-items__end">
+
+        <div class="navbar-item navbar-persistent--container">
+
+
+ <script>
+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass"></i>
+    <span class="search-button__default-text">Search</span>
+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+   </button>
+ `);
+ </script>
+        </div>
+
+
+        <div class="navbar-item"><!-- _templates/star.html -->
+<a href=https://github.com/TheoChem-VU><i class="fa-brands fa-github"></i> TheoCheM</a></div>
+
+    </div>
+
+  </div>
+
+
+    <div class="navbar-persistent--mobile">
+
+ <script>
+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass"></i>
+    <span class="search-button__default-text">Search</span>
+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+   </button>
+ `);
+ </script>
+    </div>
+
+
+
+</div>
+
+    </header>
+
+
+  <div class="bd-container">
+    <div class="bd-container__inner bd-page-width">
+
+
+
+
+
+      <div class="bd-sidebar-primary bd-sidebar hide-on-wide">
+
+
+
+  <div class="sidebar-header-items sidebar-primary__section">
+
+
+
+
+      <div class="sidebar-header-items__end">
+
+          <div class="navbar-item"><!-- _templates/star.html -->
+<a href=https://github.com/TheoChem-VU><i class="fa-brands fa-github"></i> TheoCheM</a></div>
+
+      </div>
+
+  </div>
+
+
+  <div class="sidebar-primary-items__end sidebar-primary__section">
+  </div>
+
+  <div id="rtd-footer-container"></div>
+
+
+      </div>
+
+      <main id="main-content" class="bd-main">
+
+
+          <div class="bd-content">
+            <div class="bd-article-container">
+
+              <div class="bd-header-article">
+<div class="header-article-items header-article__inner">
+
+    <div class="header-article-items__start">
+
+        <div class="header-article-item">
+
+
+
+<nav aria-label="Breadcrumb">
+  <ul class="bd-breadcrumbs">
+
+    <li class="breadcrumb-item breadcrumb-home">
+      <a href="../../../index.html" class="nav-link" aria-label="Home">
+        <i class="fa-solid fa-home"></i>
+      </a>
+    </li>
+
+    <li class="breadcrumb-item"><a href="../../index.html" class="nav-link">Module code</a></li>
+
+
+    <li class="breadcrumb-item"><a href="../../tcutility.html" class="nav-link">tcutility</a></li>
+
+    <li class="breadcrumb-item active" aria-current="page">tcutility.da...</li>
+  </ul>
+</nav>
+</div>
+
+    </div>
+
+
+</div>
+</div>
+
+
+
+
+<div id="searchbox"></div>
+                <article class="bd-article">
+
+  <h1>Source code for tcutility.data.molecules</h1><div class="highlight"><pre>
+<span></span><span class="kn">from</span> <span class="nn">tcutility</span> <span class="kn">import</span> <span class="n">molecule</span>
+<span class="kn">import</span> <span class="nn">os</span>
+
+
+<span class="n">j</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span>
+
+<span class="n">root_dir</span> <span class="o">=</span> <span class="n">j</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;molecules&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="get">
+<a class="viewcode-back" href="../../../api/tcutility.data.html#tcutility.data.molecules.get">[docs]</a>
+<span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+    <span class="n">p</span> <span class="o">=</span> <span class="n">j</span><span class="p">(</span><span class="n">root_dir</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">name</span><span class="o">.</span><span class="n">removesuffix</span><span class="p">(</span><span class="s2">&quot;.xyz&quot;</span><span class="p">)</span><span class="si">}</span><span class="s1">.xyz&#39;</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">molecule</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">p</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_molecules">
+<a class="viewcode-back" href="../../../api/tcutility.data.html#tcutility.data.molecules.get_molecules">[docs]</a>
+<span class="k">def</span> <span class="nf">get_molecules</span><span class="p">(</span><span class="n">tags</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">root_dir</span><span class="p">):</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">f</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.xyz&#39;</span><span class="p">):</span>
+            <span class="k">continue</span>
+
+        <span class="n">mol</span> <span class="o">=</span> <span class="n">get</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">tags</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">any</span><span class="p">(</span><span class="n">tag</span> <span class="ow">in</span> <span class="n">mol</span><span class="o">.</span><span class="n">flags</span><span class="o">.</span><span class="n">tags</span> <span class="k">for</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">tags</span><span class="p">):</span>
+            <span class="k">yield</span> <span class="n">mol</span></div>
+
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
+    <span class="k">for</span> <span class="n">mol</span> <span class="ow">in</span> <span class="n">get_molecules</span><span class="p">():</span>
+        <span class="nb">print</span><span class="p">(</span><span class="n">mol</span><span class="p">,</span> <span class="n">mol</span><span class="o">.</span><span class="n">flags</span><span class="p">)</span>
+</pre></div>
+
+                </article>
+
+
+
+
+
+                <footer class="prev-next-footer">
+
+<div class="prev-next-area">
+</div>
+                </footer>
+
+            </div>
+
+
+
+                <div class="bd-sidebar-secondary bd-toc"></div>
+
+
+          </div>
+          <footer class="bd-footer-content">
+
+          </footer>
+
+      </main>
+    </div>
+  </div>
+
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
+  <script src="../../../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae"></script>
+<script src="../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae"></script>
+
+  <footer class="bd-footer">
+<div class="bd-footer__inner bd-page-width">
+
+    <div class="footer-items__start">
+
+        <div class="footer-item">
+
+  <p class="copyright">
+
+      © Copyright 2024, TheoCheM VU Amsterdam.
+      <br/>
+
+  </p>
+</div>
+
+        <div class="footer-item">
+
+  <p class="sphinx-version">
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
+    <br/>
+  </p>
+</div>
+
+    </div>
+
+
+
+    <div class="footer-items__end">
+
+        <div class="footer-item">
+<p class="theme-version">
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.15.2.
+</p></div>
+
+    </div>
+
+</div>
+
+  </footer>
+  </body>
+</html>