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diff --git a/docs/index.html b/docs/index.html index 28915fb..2c6303f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,8 @@ <title>Chemical Entities as R Objects • chents</title> <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"> -<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"> -<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"> +<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"> +<link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"> <script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Chemical Entities as R Objects"> <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."> @@ -22,7 +22,7 @@ <a class="navbar-brand me-2" href="index.html">chents</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.3.6</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -49,21 +49,114 @@ <main id="main" class="col-md-9"><div class="section level1"> <div class="page-header"><h1 id="chents">chents<a class="anchor" aria-label="anchor" href="#chents"></a> </h1></div> -<p><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> +<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="features">Features<a class="anchor" aria-label="anchor" href="#features"></a> +<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></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> +<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="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a> +<h2 id="using-r6-classes">Using R6 classes<a class="anchor" aria-label="anchor" href="#using-r6-classes"></a> </h2> -<p>Some examples are available from the <a href="https://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>.</p> +<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> </div> </main><aside class="col-md-3"><div class="links"> @@ -91,7 +184,7 @@ <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> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> </ul> </div> @@ -106,7 +199,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer> |