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diff --git a/inst/web/chent.html b/inst/web/chent.html new file mode 100644 index 0000000..f2adb6b --- /dev/null +++ b/inst/web/chent.html @@ -0,0 +1,156 @@ +<!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"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <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 <- chent$new("1-octanol", smiles = "CCCCCCCCO") +oct$try_pubchem() +</div> +<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&db=pccompound&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&db=pccompound&ID=957</strong> +<div class='input'>print(oct) +</div> +<div class='output'><chent> +Identifier $identifier 1-octanol +InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N +SMILES string $smiles CCCCCCCCO +Molecular weight $mw: 130.2 +PubChem synonyms (first 10): + [1] "1-octanol" "Octan-1-ol" "octanol" "N-octanol" "Capryl alcohol" "Octyl alcohol" + [7] "n-Octyl alcohol" "caprylic alcohol" "Heptyl carbinol" "1-Hydroxyoctane" +</div> +<div class='input'>plot(oct) +</div> +<div class='input'>caffeine <- chent$new("caffeine", source = "pubchem") +</div> +<strong class='message'>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&db=pccompound&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&db=pccompound&ID=1188</strong> +<div class='input'>print(caffeine) +</div> +<div class='output'><chent> +Identifier $identifier caffeine +InChI Key $inchikey LRFVTYWOQMYALW-UHFFFAOYSA-N +SMILES string $smiles C1=NC2=C(N1)C(=O)NC(=O)N2 +Molecular weight $mw: 152.1 +PubChem synonyms (first 10): + [1] "xanthine" "2,6-Dihydroxypurine" "69-89-6" "Xanthin" "2,6-dioxopurine" + [6] "Pseudoxanthine" "Isoxanthine" "Xanthic oxide" "1H-Purine-2,6-diol" "Purine-2,6-diol" +</div> +<div class='input'>caffeine$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> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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