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<title>Chemical Entities as R Objects • chents</title>
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<meta name="description" content="Utilities for dealing with chemical entities and associated data as R objects. If Python and RDKit (> 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.">
<meta property="og:description" content="Utilities for dealing with chemical entities and associated data as R objects. If Python and RDKit (> 2015.03) are installed and configured for use with reticulate, some basic chemoinformatics functions like the calculation of molecular weight and plotting of chemical structures in R graphics are available.">
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<div class="page-header"><h1 id="chents">chents<a class="anchor" aria-label="anchor" href="#chents"></a>
</h1></div>
<p><a href="https://pkgdown.jrwb.de/chents/"><img src="https://img.shields.io/badge/docs-jrwb.de-blue.svg" alt="Online documentation"></a> <a href="https://jranke.r-universe.dev/chents" class="external-link"><img src="https://jranke.r-universe.dev/badges/chents" alt="R-Universe status"></a> <a href="https://app.travis-ci.com/jranke/chents" class="external-link"><img src="https://app.travis-ci.com/jranke/chents.svg?token=Sq9VuYWyRz2FbBLxu6DK&branch=main" alt="Build Status"></a> <a href="https://app.codecov.io/gh/jranke/chents" class="external-link"><img src="https://codecov.io/github/jranke/chents/branch/main/graphs/badge.svg" alt="codecov"></a></p>
<p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R.</p>
<div class="section level2">
<h2 id="features">Features<a class="anchor" aria-label="anchor" href="#features"></a>
</h2>
<ul>
<li>Some chemical information is retrieved from the PubChem website using the webchem package</li>
<li>If Python and RDKit (> 2015.03) are installed and configured for use with ‘reticulate’, some basic chemoinformatics functions some additional chemical information is computed and a 2D graph can be plotted</li>
<li>Additional information can be read from a local .yaml file</li>
</ul>
</div>
<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
<p>You can conveniently install chents from the repository kindly made available by the R-Universe project:</p>
<pre><code><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"chents"</span>,</span>
<span> repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"https://jranke.r-universe.dev"</span>, <span class="st">"https://cran.r-project.org"</span><span class="op">)</span><span class="op">)</span></span></code></pre>
<p>In order to profit from the chemoinformatics, you need to install RDKit and its python bindings. On a Debian type Linux distribution, just use</p>
<pre><code>sudo apt install python3-rdkit</code></pre>
<p>If you use this package on Windows or MacOS, I would be happy to include installation instructions here if you share them with me, e.g. via a Pull Request.</p>
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<div class="section level2">
<h2 id="configuration-of-the-python-version-to-use">Configuration of the Python version to use<a class="anchor" aria-label="anchor" href="#configuration-of-the-python-version-to-use"></a>
</h2>
<p>On Debian type Linux distributions, you can use the following line in your global or project specific <code>.Rprofile</code> file to tell the <code>reticulate</code> package to use the system Python version that will find the RDKit installed in the system location.</p>
<pre><code><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html" class="external-link">Sys.setenv</a></span><span class="op">(</span>RETICULATE_PYTHON<span class="op">=</span><span class="st">"/usr/bin/python3"</span><span class="op">)</span></span></code></pre>
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<div class="section level2">
<h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
</h2>
<p>Some examples are available from the <a href="https://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>. For example, in the <a href="https://pkgdown.jrwb.de/chents/reference/chent.html#ref-examples">example code section of the chent object docs</a> you can see how to generate an R object for caffeine, show some of the information retrieved from PubChem and plot it by virtue of RDKit.</p>
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<h2 data-toc-skip>Links</h2>
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<li><a href="https://github.com/jranke/chents/" class="external-link">Browse source code</a></li>
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<h2 data-toc-skip>License</h2>
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<li>GPL</li>
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<div class="citation">
<h2 data-toc-skip>Citation</h2>
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<li><a href="authors.html#citation">Citing chents</a></li>
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<div class="developers">
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
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<p>Developed by Johannes Ranke.</p>
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