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<h1>An R6 class for chemical entities with associated data</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
<div class="hidden name"><code>chent.Rd</code></div>
</div>
<div class="ref-description">
<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>
</div>
<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>p0</code></dt><dd><p>Vapour pressure in Pa</p></dd>
<dt><code>cwsat</code></dt><dd><p>Water solubility in mg/L</p></dd>
<dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
<dt><code>soil_degradation</code></dt><dd><p>Dataframe of modelling DT50 values</p></dd>
<dt><code>soil_ff</code></dt><dd><p>Dataframe of formation fractions</p></dd>
<dt><code>soil_sorption</code></dt><dd><p>Dataframe of soil sorption data</p></dd>
<dt><code>PUF</code></dt><dd><p>Plant uptake factor</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, Sep 26 2018, 18:42:22) </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'>Lade nötigen Namensraum: 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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></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 $mw: 130.2
#> PubChem synonyms (up to 10):
#> [1] "957" "1-octanol" "Octan-1-ol" "octanol"
#> [5] "111-87-5" "N-octanol" "Capryl alcohol" "Octyl alcohol"
#> [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>caffeine</span>$<span class='no'>Picture</span>)) {
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>oct</span>)
}</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'caffeine' nicht gefunden</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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></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 $mw: 194.2
#> PubChem synonyms (up to 10):
#> [1] "2519" "caffeine"
#> [3] "58-08-2" "Guaranine"
#> [5] "1,3,7-Trimethylxanthine" "Thein"
#> [7] "Cafeina" "Methyltheobromine"
#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> (!<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/NULL'>is.null</a></span>(<span class='no'>caffeine</span>$<span class='no'>Picture</span>)) {
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>caffeine</span>)
}</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></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>
</ul>
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