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authorJohannes Ranke <jranke@uni-bremen.de>2015-09-28 21:34:23 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-09-28 22:10:56 +0200
commitf908377f1de2e04ca3720d10084169c46a477ce2 (patch)
tree439bd00dec3a988f76ff74fd5ee652f55b17d061 /inst/web/chent.html
parent1df33dbb3d310f94ccddbf57906e12bd6fa93c3f (diff)
Several changes heading for a release to the public
- Add tests - Add staticdocs - Documentation improvements - Several small code improvements
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+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<title>chent. chents 0.2-1</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<meta name="author" content="">
+
+<link href="css/bootstrap.css" rel="stylesheet">
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+ <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
+<![endif]-->
+
+<script type="text/x-mathjax-config">
+ MathJax.Hub.Config({
+ tex2jax: {
+ inlineMath: [ ['$','$'], ["\\(","\\)"] ],
+ processEscapes: true
+ }
+ });
+</script>
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+ </head>
+
+ <body>
+ <div class="navbar">
+ <div class="navbar-inner">
+ <div class="container">
+ <a class="brand" href="#">chents 0.2-1</a>
+ <div class="nav">
+ <ul class="nav">
+ <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+</div>
+
+ <div class="container">
+ <header>
+
+ </header>
+
+ <h1>An R6 class for chemical entities with associated data</h1>
+
+<div class="row">
+ <div class="span8">
+ <h2>Usage</h2>
+ <pre><div>chent</div></pre>
+
+ <div class="Format">
+ <h2>Format</h2>
+
+ <p>An <code><a href='http://www.inside-r.org/packages/cran/R6/docs/R6Class'>R6Class</a></code> generator object</p>
+
+ </div>
+
+ <div class="Description">
+ <h2>Description</h2>
+
+ <p>The class is initialised with an identifier. Chemical information is retrieved from
+the internet. Additionally, it can be generated using RDKit if RDKit and its
+python bindings are installed.</p>
+
+ </div>
+
+ <div class="Fields">
+ <h2>Fields</h2>
+
+ <p></p>
+
+ <p><dl>
+<dt><code>identifier</code></dt><dd>The identifier that was used to initiate the object, with attribute 'source'</dd></p>
+
+ <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute 'source'</dd></p>
+
+ <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute 'source'</dd></p>
+
+ <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute 'source'</dd></p>
+
+ <p><dt><code>pubchem</code></dt><dd>List of information retreived from PubChem</dd></p>
+
+ <p><dt><code>rdkit</code></dt><dd>List of information obtained with RDKit</dd></p>
+
+ <p><dt><code>Picture</code></dt><dd>Graph as a <code><a href='http://www.inside-r.org/packages/cran/grImport/docs/picture'>picture</a></code> object obtained using grImport</dd></p>
+
+ <p></dl></p>
+
+ </div>
+
+ <h2 id="examples">Examples</h2>
+ <pre class="examples"><div class='input'>oct &lt;- chent$new(&quot;1-octanol&quot;, smiles = &quot;CCCCCCCCO&quot;)
+oct$try_pubchem()
+</div>
+<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&amp;db=pccompound&amp;term=1-octanol</strong>
+<strong class='message'>Found 1 entries in PubChem, using the first one.</strong>
+<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&amp;db=pccompound&amp;ID=957</strong>
+<div class='input'>print(oct)
+</div>
+<div class='output'>&lt;chent&gt;
+Identifier $identifier 1-octanol
+InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N
+SMILES string $smiles CCCCCCCCO
+Molecular weight $mw: 130.2
+PubChem synonyms (first 10):
+ [1] &quot;1-octanol&quot; &quot;Octan-1-ol&quot; &quot;octanol&quot; &quot;N-octanol&quot; &quot;Capryl alcohol&quot; &quot;Octyl alcohol&quot;
+ [7] &quot;n-Octyl alcohol&quot; &quot;caprylic alcohol&quot; &quot;Heptyl carbinol&quot; &quot;1-Hydroxyoctane&quot;
+</div>
+<div class='input'>plot(oct)
+</div>
+<div class='input'>caffeine &lt;- chent$new(&quot;caffeine&quot;, source = &quot;pubchem&quot;)
+</div>
+<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&amp;db=pccompound&amp;term=caffeine</strong>
+<strong class='message'>Found 217 entries in PubChem, using the first one.</strong>
+<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&amp;db=pccompound&amp;ID=1188</strong>
+<div class='input'>print(caffeine)
+</div>
+<div class='output'>&lt;chent&gt;
+Identifier $identifier caffeine
+InChI Key $inchikey LRFVTYWOQMYALW-UHFFFAOYSA-N
+SMILES string $smiles C1=NC2=C(N1)C(=O)NC(=O)N2
+Molecular weight $mw: 152.1
+PubChem synonyms (first 10):
+ [1] &quot;xanthine&quot; &quot;2,6-Dihydroxypurine&quot; &quot;69-89-6&quot; &quot;Xanthin&quot; &quot;2,6-dioxopurine&quot;
+ [6] &quot;Pseudoxanthine&quot; &quot;Isoxanthine&quot; &quot;Xanthic oxide&quot; &quot;1H-Purine-2,6-diol&quot; &quot;Purine-2,6-diol&quot;
+</div>
+<div class='input'>caffeine$get_rdkit()
+plot(caffeine)
+</div>
+<p><img src='chent-15.png' alt='' width='540' height='400' /></p></pre>
+ </div>
+ <div class="span4">
+ <!-- <ul>
+ <li>chent</li>
+ </ul>
+ <ul>
+ <li>data</li>
+ </ul> -->
+
+
+ </div>
+</div>
+
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