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<h1>An R6 class for chemical entities with associated data</h1>
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<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>
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