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| -rw-r--r-- | docs/index.html | 16 |
1 files changed, 10 insertions, 6 deletions
diff --git a/docs/index.html b/docs/index.html index 2c6303f..5d7693c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -11,8 +11,8 @@ <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."> +<meta name="description" content="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 chents provides a way to define an R object corresponding to a chemically defined substances, i.e. a chemical entity and to collect related information. 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="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 chents provides a way to define an R object corresponding to a chemically defined substances, i.e. a chemical entity and to collect related information. 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."> </head> <body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -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="">0.4.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.2</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"> @@ -50,7 +50,10 @@ <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 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 ‘chents’ provides a way to define an R object corresponding to a chemically defined substances, i.e. a chemical entity and to collect related information. 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.</p> +<div class="section level2"> +<h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a> +</h2> <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> @@ -78,7 +81,7 @@ <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><img src="reference/figures/README-unnamed-chunk-5-1.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> @@ -87,8 +90,9 @@ <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><img src="reference/figures/README-unnamed-chunk-6-1.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> <div class="section level2"> <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> </h2> |