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If Python and RDKit (> 2015.03) are installed and - configured for use with 'PythonInR', some basic chemoinformatics functions - like the calculation of molecular weight and plotting of chemical - structures in R graphics are available. For plotting, you need - grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN."> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<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/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."> </head> <body> - <div class="container template-home"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="index.html">chents</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.7</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> -<li> - <a href="index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="reference/index.html">Reference</a> -</li> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container"> + + <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="">0.3.7</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"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"> +<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li> </ul> -<ul class="nav navbar-nav navbar-right"> -<li> - <a href="https://github.com/jranke/chents"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/chents/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul> </div> -<!--/.nav-collapse --> - </div> -<!--/.container --> -</div> -<!--/.navbar --> - - </header><div class="row"> - <div class="contents col-md-9"> -<div id="chents" class="section level1"> -<div class="page-header"><h1 class="hasAnchor"> -<a href="#chents" class="anchor"></a>chents</h1></div> + </div> +</nav><div class="container template-home"> +<div class="row"> + <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://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 id="features" class="section level2"> -<h2 class="hasAnchor"> -<a href="#features" class="anchor"></a>Features</h2> +<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 PythonInR is installed and configured, and RDKit is available via PythonInR, some additional chemical information is computed and a 2D graph can be plotted</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 id="examples" class="section level2"> -<h2 class="hasAnchor"> -<a href="#examples" class="anchor"></a>Examples</h2> -<p>Some examples are available from the <a href="http://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>.</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> +<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> </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> +<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> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <div class="links"> -<h2>Links</h2> +<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> +</div> +</div> + </main><aside class="col-md-3"><div class="links"> +<h2 data-toc-skip>Links</h2> <ul class="list-unstyled"> -<li>Browse source code at <br><a href="https://github.com/jranke/chents">https://github.com/jranke/chents</a> -</li> +<li><a href="https://github.com/jranke/chents/" class="external-link">Browse source code</a></li> </ul> </div> + <div class="license"> -<h2>License</h2> +<h2 data-toc-skip>License</h2> <ul class="list-unstyled"> <li>GPL</li> </ul> </div> -<div class="developers"> -<h2>Developers</h2> + + +<div class="citation"> +<h2 data-toc-skip>Citation</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +<li><a href="authors.html#citation">Citing chents</a></li> </ul> </div> - <div class="dev-status"> -<h2>Dev status</h2> +<div class="developers"> +<h2 data-toc-skip>Developers</h2> <ul class="list-unstyled"> -<li><a href="https://travis-ci.com/jranke/chents"><img src="https://travis-ci.com/jranke/chents.svg?branch=master" alt="Build Status"></a></li> -<li><a href="https://codecov.io/github/jranke/chents"><img src="https://codecov.io/github/jranke/chents/branch/master/graphs/badge.svg" alt="codecov"></a></li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> </ul> </div> -</div> + + + + </aside> </div> - <footer><div class="copyright"> + + <footer><div class="pkgdown-footer-left"> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> +<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> </div> - </footer> + + </footer> </div> - + + + </body> </html> |