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<h1>An R6 class for chemical entities with associated data</h1>
</div>
<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 and configured for use with PythonInR.</p>
<pre class="usage"><span class='no'>chent</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An <code>R6Class</code> generator object</p>
<h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
<dl class='dl-horizontal'>
<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd>
<dt><code>inchikey</code></dt><dd><p>InChI Key, with attribute 'source'</p></dd>
<dt><code>smiles</code></dt><dd><p>SMILES code, with attribute 'source'</p></dd>
<dt><code>mw</code></dt><dd><p>Molecular weight, with attribute 'source'</p></dd>
<dt><code>pubchem</code></dt><dd><p>List of information retreived from PubChem</p></dd>
<dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit, if installed and
configured for use with PythonInR</p></dd>
<dt><code>svg</code></dt><dd><p>SVG code</p></dd>
<dt><code>Picture</code></dt><dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
<dt><code>Pict_font_size</code></dt><dd><p>Font size as extracted from the intermediate PostScript file</p></dd>
<dt><code>pdf_height</code></dt><dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
<dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
<dt><code>degradation</code></dt><dd><p>List of degradation endpoints</p></dd>
</dl>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>oct</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'></span>
#> <span class='message'>Initialize Python Version 2.7.13 (default, Nov 24 2017, 17:33:09) </span>
#> <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
#> <span class='message'>CCCCCCCCO</span></div><div class='output co'>#> <span class='message'>Loading required namespace: grConvert</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#> <chent>
#> Identifier $identifier 1-octanol
#> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N
#> SMILES string $smiles:
#> user PubChem_Canonical
#> "CCCCCCCCO" "CCCCCCCCO"
#> Molecular weight $mw: 130.2
#> PubChem synonyms (up to 10):
#> [1] "957" "1-octanol" "Octan-1-ol" "octanol"
#> [5] "Octyl alcohol" "N-octanol" "111-87-5" "Capryl alcohol"
#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
#> <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>caffeine</span>)</div><div class='output co'>#> <chent>
#> Identifier $identifier caffeine
#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N
#> SMILES string $smiles:
#> PubChem_Canonical
#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
#> Molecular weight $mw: 194.2
#> PubChem synonyms (up to 10):
#> [1] "2519" "caffeine"
#> [3] "1,3,7-Trimethylxanthine" "58-08-2"
#> [5] "Guaranine" "Thein"
#> [7] "Cafeina" "Methyltheobromine"
#> [9] "Koffein" "Mateina" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#format">Format</a></li>
<li><a href="#fields">Fields</a></li>
<li><a href="#examples">Examples</a></li>
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