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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://pkgdown.jrwb.de/chents/coverage/coverage.html"><img src="https://img.shields.io/badge/coverage-jrwb.de-blue.svg" alt="Code coverage"></a></p>
<p>When working with data on chemical substances, we often need a reliable link between the data and the chemical identity of the substances. The R package <strong>chents</strong> provides a way to define an R object corresponding to a chemically defined substances (“chemical entity”) and to collect related information.</p>
<p>When first defining a chemical entity, some chemical information is retrieved from the <a href="https://pubchem.ncbi.nlm.nih.gov/" class="external-link">PubChem</a> website using the <a href="https://docs.ropensci.org/webchem/" class="external-link">webchem</a> package.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/chents/">chents</a></span><span class="op">)</span></span>
<span><span class="va">caffeine</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Caffeine"</span><span class="op">)</span></span>
<span><span class="co">#> Querying PubChem for name Caffeine ...</span></span>
<span><span class="co">#> Get chemical information from RDKit using PubChem SMILES</span></span>
<span><span class="co">#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></span></code></pre></div>
<p>If Python and <a href="https://rdkit.org" class="external-link">RDKit</a> (> 2015.03) are installed and configured for use with the <a href="https://rstudio.github.io/reticulate/" class="external-link">reticulate</a> package, some additional chemical information including a 2D graph are computed.</p>
<p>The print method gives an overview of the information that was collected.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span>
<span><span class="co">#> <chent></span></span>
<span><span class="co">#> Identifier $identifier Caffeine </span></span>
<span><span class="co">#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span></span>
<span><span class="co">#> SMILES string $smiles:</span></span>
<span><span class="co">#> PubChem </span></span>
<span><span class="co">#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span></span>
<span><span class="co">#> Molecular weight $mw: 194.2 </span></span>
<span><span class="co">#> PubChem synonyms (up to 10):</span></span>
<span><span class="co">#> [1] "caffeine" "58-08-2" </span></span>
<span><span class="co">#> [3] "Guaranine" "1,3,7-Trimethylxanthine"</span></span>
<span><span class="co">#> [5] "Methyltheobromine" "Theine" </span></span>
<span><span class="co">#> [7] "Thein" "Cafeina" </span></span>
<span><span class="co">#> [9] "Caffein" "Cafipel"</span></span></code></pre></div>
<p>There is a very simple plotting method for the chemical structure.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></code></pre></div>
<p><img src="reference/figures/README-unnamed-chunk-4-1.png"><!-- --></p>
<p>If you have a so-called ISO common name of a pesticide active ingredient, you can use the ‘pai’ class derived from the ‘chent’ class, which starts with querying the <a href="http://www.bcpcpesticidecompendium.org/" class="external-link">BCPC compendium</a> first.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">delta</span> <span class="op"><-</span> <span class="va"><a href="reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Deltamethrin"</span><span class="op">)</span></span>
<span><span class="co">#> Querying BCPC for Deltamethrin ...</span></span>
<span><span class="co">#> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ...</span></span>
<span><span class="co">#> Get chemical information from RDKit using PubChem SMILES</span></span>
<span><span class="co">#> CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">delta</span><span class="op">)</span></span></code></pre></div>
<p><img src="reference/figures/README-unnamed-chunk-5-1.png"><!-- --></p>
<p>Additional information can be read from a local .yaml file. This information can be leveraged e.g. by the <a href="https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html" class="external-link">PEC_soil</a> function of the ‘pfm’ package. However, this functionality is to be superseded by a dedicated package, defining data for the environmental risk assessment on chemicals, in particular on active ingredients of plant protection products.</p>
<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>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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></div>
<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>
<div class="sourceCode" id="cb6"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="fu">sudo</span> apt install python3-rdkit</span></code></pre></div>
<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>
</div>
<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>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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></div>
</div>
<div class="section level2">
<h2 id="using-r6-classes">Using R6 classes<a class="anchor" aria-label="anchor" href="#using-r6-classes"></a>
</h2>
<p>Note that the <code>chent</code> objects defined by this package are <a href="https://r6.r-lib.org/articles/Introduction.html" class="external-link">R6</a> classes. Therefore, if you think you make a copy by assigning them to a new name, the objects will still be connected, because only the reference is copied. For example, you can create a molecule without retrieving data from PubChem</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">but</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Butane"</span>, smiles <span class="op">=</span> <span class="st">"CCCC"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co">#> Get chemical information from RDKit using user SMILES</span></span>
<span><span class="co">#> CCCC</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">but</span><span class="op">)</span></span>
<span><span class="co">#> <chent></span></span>
<span><span class="co">#> Identifier $identifier Butane </span></span>
<span><span class="co">#> InChI Key $inchikey NA </span></span>
<span><span class="co">#> SMILES string $smiles:</span></span>
<span><span class="co">#> user </span></span>
<span><span class="co">#> "CCCC" </span></span>
<span><span class="co">#> Molecular weight $mw: 58.1</span></span></code></pre></div>
<p>If you then assign a new name and add PubChem information to the object with the new name, the information will also be added to the original <code>chent</code> object:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">but_pubchem</span> <span class="op"><-</span> <span class="va">but</span></span>
<span><span class="va">but_pubchem</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#> Querying PubChem for name Butane ...</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">but</span><span class="op">)</span></span>
<span><span class="co">#> <chent></span></span>
<span><span class="co">#> Identifier $identifier Butane </span></span>
<span><span class="co">#> InChI Key $inchikey IJDNQMDRQITEOD-UHFFFAOYSA-N </span></span>
<span><span class="co">#> SMILES string $smiles:</span></span>
<span><span class="co">#> user PubChem </span></span>
<span><span class="co">#> "CCCC" "CCCC" </span></span>
<span><span class="co">#> Molecular weight $mw: 58.1 </span></span>
<span><span class="co">#> PubChem synonyms (up to 10):</span></span>
<span><span class="co">#> [1] "BUTANE" "n-Butane" "106-97-8" </span></span>
<span><span class="co">#> [4] "Diethyl" "Methylethylmethane" "Butanen" </span></span>
<span><span class="co">#> [7] "Butani" "Butyl hydride" "HC 600" </span></span>
<span><span class="co">#> [10] "A 21 (lowing agent)"</span></span></code></pre></div>
<p>You can create a derived, independent object using the <code>clone()</code> method that will not be affected by operations on the original object:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">but_new</span> <span class="op"><-</span> <span class="va"><a href="reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Butane"</span>, smiles <span class="op">=</span> <span class="st">"CCCC"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co">#> Get chemical information from RDKit using user SMILES</span></span>
<span><span class="co">#> CCCC</span></span>
<span><span class="va">but_clone</span> <span class="op"><-</span> <span class="va">but_new</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span><span class="op">)</span></span>
<span><span class="va">but_new</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#> Querying PubChem for name Butane ...</span></span>
<span><span class="va">but_clone</span></span>
<span><span class="co">#> <chent></span></span>
<span><span class="co">#> Identifier $identifier Butane </span></span>
<span><span class="co">#> InChI Key $inchikey NA </span></span>
<span><span class="co">#> SMILES string $smiles:</span></span>
<span><span class="co">#> user </span></span>
<span><span class="co">#> "CCCC" </span></span>
<span><span class="co">#> Molecular weight $mw: 58.1</span></span></code></pre></div>
</div>
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</main><aside class="col-md-3"><div class="links">
<h2 data-toc-skip>Links</h2>
<ul class="list-unstyled">
<li><a href="https://github.com/jranke/chents/" class="external-link">Browse source code</a></li>
</ul>
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<h2 data-toc-skip>License</h2>
<ul class="list-unstyled">
<li>GPL</li>
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<div class="citation">
<h2 data-toc-skip>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html#citation">Citing chents</a></li>
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<div class="developers">
<h2 data-toc-skip>Developers</h2>
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<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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