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<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>depict • depict</title> <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> <!-- headroom.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="pkgdown.css" rel="stylesheet"> <script src="pkgdown.js"></script> <meta property="og:title" content="depict" /> <!-- 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]--> </head> <body> <div class="container template-title-body"> <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">depict</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="index.html"> <span class="fas fa fas fa-home fa-lg"></span> </a> </li> <li> <a href="reference/index.html">Reference</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header> <div class="row"> <div class="contents col-md-9"> <div class="page-header"> <h1>depict</h1> </div> <hr> <div id="output-github_document" class="section level2"> <h2 class="hasAnchor"> <a href="#output-github_document" class="anchor"></a>output: github_document</h2> <!-- README.md is generated from README.Rmd. Please edit that file --> </div> <div id="depict" class="section level1"> <p>depict is an R wrapper around the wonderful depiction api written by <a href="https://github.com/johnmay">John May</a>. The entire <a href="https://github.com/cdk">CDK</a> team, but especially John, have been steadily improving the visualization features of CDK. The depiction API is succinct and powerful and provides access to a vary large amount of the end-user desired functionality with a small number of composable functions. Because of the design of this API it is now relatively straightforward to design a simple streamlined interface to allow users to quickly and easily generate beautiful graphics.</p> <div id="installation" class="section level2"> <h2 class="hasAnchor"> <a href="#installation" class="anchor"></a>Installation</h2> <p>You can install depict from github with:</p> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="co"># install.packages("devtools")</span></span> <span id="cb1-2"><a href="#cb1-2"></a>devtools<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/devtools/man/remote-reexports.html">install_github</a></span>(<span class="st">"CDK-R/depict"</span>)</span></code></pre></div> </div> <div id="example" class="section level2"> <h2 class="hasAnchor"> <a href="#example" class="anchor"></a>Example</h2> </div> <div id="simple-depiciton" class="section level2"> <h2 class="hasAnchor"> <a href="#simple-depiciton" class="anchor"></a>Simple Depiciton</h2> <p>A simple wrapper around cdk’s excellent depict module.</p> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(depict)</span> <span id="cb2-2"><a href="#cb2-2"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(magrittr)</span> <span id="cb2-3"><a href="#cb2-3"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(grid)</span> <span id="cb2-4"><a href="#cb2-4"></a></span> <span id="cb2-5"><a href="#cb2-5"></a><span class="co"># you must supply java colors </span></span> <span id="cb2-6"><a href="#cb2-6"></a>color <-<span class="st"> </span><span class="kw">J</span>(<span class="st">"java.awt.Color"</span>)</span> <span id="cb2-7"><a href="#cb2-7"></a></span> <span id="cb2-8"><a href="#cb2-8"></a><span class="co"># load in penicillin</span></span> <span id="cb2-9"><a href="#cb2-9"></a>pen <-<span class="st"> </span><span class="kw"><a href="reference/parse_smiles.html">parse_smiles</a></span>(<span class="st">"CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)[O-])C penicillin"</span>)</span> <span id="cb2-10"><a href="#cb2-10"></a>cav <-<span class="st"> </span><span class="kw"><a href="reference/parse_smiles.html">parse_smiles</a></span>(<span class="st">"CN1C=NC2=C1C(=O)N(C(=O)N2C)C"</span>)</span> <span id="cb2-11"><a href="#cb2-11"></a></span> <span id="cb2-12"><a href="#cb2-12"></a><span class="co"># define the regions to highlight</span></span> <span id="cb2-13"><a href="#cb2-13"></a><span class="co"># either all atoms/bonds</span></span> <span id="cb2-14"><a href="#cb2-14"></a><span class="co"># or a SMARTS-defined subregion</span></span> <span id="cb2-15"><a href="#cb2-15"></a>atms <-<span class="st"> </span>pen<span class="op">$</span><span class="kw">atoms</span>()</span> <span id="cb2-16"><a href="#cb2-16"></a>bnds <-<span class="st"> </span>pen<span class="op">$</span><span class="kw">bonds</span>()</span> <span id="cb2-17"><a href="#cb2-17"></a>lactam <-<span class="st"> </span><span class="kw"><a href="reference/match_smarts.html">match_smarts</a></span>(<span class="st">"C1(=O)NCC1"</span>, pen)</span> <span id="cb2-18"><a href="#cb2-18"></a></span> <span id="cb2-19"><a href="#cb2-19"></a><span class="co"># use piping to change the behavior as desired</span></span> <span id="cb2-20"><a href="#cb2-20"></a><span class="kw"><a href="reference/depiction.html">depiction</a></span>() <span class="op">%>%</span></span> <span id="cb2-21"><a href="#cb2-21"></a><span class="st"> </span><span class="kw"><a href="reference/highlight_atoms.html">highlight_atoms</a></span>(atms, color<span class="op">$</span>LIGHT_GRAY) <span class="op">%>%</span></span> <span id="cb2-22"><a href="#cb2-22"></a><span class="st"> </span><span class="kw"><a href="reference/highlight_atoms.html">highlight_atoms</a></span>(bnds, color<span class="op">$</span>LIGHT_GRAY) <span class="op">%>%</span></span> <span id="cb2-23"><a href="#cb2-23"></a><span class="st"> </span><span class="kw"><a href="reference/highlight_atoms.html">highlight_atoms</a></span>(lactam, color<span class="op">$</span>RED) <span class="op">%>%</span></span> <span id="cb2-24"><a href="#cb2-24"></a><span class="st"> </span><span class="kw"><a href="reference/set_size.html">set_size</a></span>(<span class="dv">400</span>, <span class="dv">400</span>) <span class="op">%>%</span></span> <span id="cb2-25"><a href="#cb2-25"></a><span class="st"> </span><span class="kw"><a href="reference/set_zoom.html">set_zoom</a></span>(<span class="dv">3</span>) <span class="op">%>%</span></span> <span id="cb2-26"><a href="#cb2-26"></a><span class="st"> </span><span class="kw"><a href="reference/outerglow.html">outerglow</a></span>() <span class="op">%>%</span></span> <span id="cb2-27"><a href="#cb2-27"></a><span class="st"> </span><span class="kw"><a href="reference/add_title.html">add_title</a></span>() <span class="op">%>%</span></span> <span id="cb2-28"><a href="#cb2-28"></a><span class="st"> </span><span class="kw"><a href="reference/depict.html">depict</a></span>(pen) <span class="op">%>%</span></span> <span id="cb2-29"><a href="#cb2-29"></a><span class="st"> </span><span class="kw"><a href="reference/get_image.html">get_image</a></span>() <span class="op">%>%</span></span> <span id="cb2-30"><a href="#cb2-30"></a><span class="st"> </span>grid<span class="op">::</span><span class="kw"><a href="https://rdrr.io/r/grid/grid.raster.html">grid.raster</a></span>()</span></code></pre></div> <p><img src="man/figures/penicillin_highlight.png"></p> </div> <div id="a-larger-example" class="section level2"> <h2 class="hasAnchor"> <a href="#a-larger-example" class="anchor"></a>A Larger Example</h2> <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>insulinmol <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/system.file.html">system.file</a></span>(<span class="st">"molfiles/ChEBI_5931.mol"</span>, <span class="dt">package=</span><span class="st">"depict"</span>)</span> <span id="cb3-2"><a href="#cb3-2"></a>insulin <-<span class="st"> </span><span class="kw"><a href="reference/read_mol.html">read_mol</a></span>(insulinmol)</span> <span id="cb3-3"><a href="#cb3-3"></a></span> <span id="cb3-4"><a href="#cb3-4"></a>cysteine <-<span class="st"> </span><span class="kw"><a href="reference/match_smarts.html">match_smarts</a></span>(<span class="st">"C(=O)C(CS)N"</span>, insulin)</span> <span id="cb3-5"><a href="#cb3-5"></a>xlinks <-<span class="st"> </span><span class="kw"><a href="reference/match_smarts.html">match_smarts</a></span>(<span class="st">"SS"</span>, insulin)</span> <span id="cb3-6"><a href="#cb3-6"></a></span> <span id="cb3-7"><a href="#cb3-7"></a>dp <-<span class="st"> </span><span class="kw"><a href="reference/depiction.html">depiction</a></span>()<span class="op">%>%</span><span class="st"> </span></span> <span id="cb3-8"><a href="#cb3-8"></a><span class="st"> </span><span class="kw"><a href="reference/set_size.html">set_size</a></span>(<span class="dv">700</span>, <span class="dv">400</span>) <span class="op">%>%</span></span> <span id="cb3-9"><a href="#cb3-9"></a><span class="st"> </span><span class="kw"><a href="reference/set_zoom.html">set_zoom</a></span>(<span class="dv">10</span>) <span class="op">%>%</span></span> <span id="cb3-10"><a href="#cb3-10"></a><span class="st"> </span><span class="kw"><a href="reference/outerglow.html">outerglow</a></span>() <span class="op">%>%</span></span> <span id="cb3-11"><a href="#cb3-11"></a><span class="st"> </span><span class="kw"><a href="reference/highlight_atoms.html">highlight_atoms</a></span>(cysteine, color<span class="op">$</span>YELLOW) <span class="op">%>%</span></span> <span id="cb3-12"><a href="#cb3-12"></a><span class="st"> </span><span class="kw"><a href="reference/highlight_atoms.html">highlight_atoms</a></span>(xlinks, color<span class="op">$</span>YELLOW) <span class="op">%>%</span></span> <span id="cb3-13"><a href="#cb3-13"></a><span class="st"> </span><span class="kw"><a href="reference/depict.html">depict</a></span>(insulin) <span class="op">%>%</span></span> <span id="cb3-14"><a href="#cb3-14"></a><span class="st"> </span><span class="kw"><a href="reference/get_image.html">get_image</a></span>() <span class="op">%>%</span></span> <span id="cb3-15"><a href="#cb3-15"></a><span class="st"> </span>grid<span class="op">::</span><span class="kw"><a href="https://rdrr.io/r/grid/grid.raster.html">grid.raster</a></span>()</span></code></pre></div> <p><img src="man/figures/insulin.png"></p> </div> <div id="coding-notes" class="section level2"> <h2 class="hasAnchor"> <a href="#coding-notes" class="anchor"></a>Coding notes</h2> <p>A few notes about setup:</p> <ol> <li>Java can be touch on OSX in particular. When in doubt try <code>sudo R CMD javareconf</code> and reinstall rJava from source.</li> <li>Currently I am using the <code><a href="https://rdrr.io/r/base/Extract.html">$</a></code> operator in just about all of my functions. This makes it about a billion times easier and more succinct to code at the price of performance. If performance becomes an issue we can use low-level calls. If its important to you I’m happy to accept pull requests.</li> <li>The API is still in flux. I am currently happy with the design but there are a few areas where I’d like to kick the tires a bit more - especially in regards to selection.</li> <li>java.awt.colors are a bit tough to warp since there are many arities and classes accepted.. I think I will provide a number of colors.</li> <li>SMARTS selectors. common smarts selections for AminoAcids, Nucleic Acids, Sugars may be worth including as well.</li> <li> </ol> </div> </div> </div> </div> <footer> <div class="copyright"> <p>Developed by Zachary Charlop-Powers.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> </div> </body> </html>