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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.</p>
</div>
<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="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
<p><div class="r6-fields"></p><dl>
<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</p></dd>
<dt><code>mol</code></dt><dd><p><rdkit.Chem.rdchem.Mol> object</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><p></div></p>
<h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
<ul>
<li><p><a href='#method-new'><code>chent$new()</code></a></p></li>
<li><p><a href='#method-try_pubchem'><code>chent$try_pubchem()</code></a></p></li>
<li><p><a href='#method-get_pubchem'><code>chent$get_pubchem()</code></a></p></li>
<li><p><a href='#method-get_rdkit'><code>chent$get_rdkit()</code></a></p></li>
<li><p><a href='#method-get_chyaml'><code>chent$get_chyaml()</code></a></p></li>
<li><p><a href='#method-add_p0'><code>chent$add_p0()</code></a></p></li>
<li><p><a href='#method-add_cwsat'><code>chent$add_cwsat()</code></a></p></li>
<li><p><a href='#method-add_PUF'><code>chent$add_PUF()</code></a></p></li>
<li><p><a href='#method-add_TP'><code>chent$add_TP()</code></a></p></li>
<li><p><a href='#method-add_transformation'><code>chent$add_transformation()</code></a></p></li>
<li><p><a href='#method-add_soil_degradation'><code>chent$add_soil_degradation()</code></a></p></li>
<li><p><a href='#method-add_soil_ff'><code>chent$add_soil_ff()</code></a></p></li>
<li><p><a href='#method-add_soil_sorption'><code>chent$add_soil_sorption()</code></a></p></li>
<li><p><a href='#method-pdf'><code>chent$pdf()</code></a></p></li>
<li><p><a href='#method-png'><code>chent$png()</code></a></p></li>
<li><p><a href='#method-emf'><code>chent$emf()</code></a></p></li>
<li><p><a href='#method-clone'><code>chent$clone()</code></a></p></li>
</ul>
<p><hr>
<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
<span class='va'>identifier</span>,
smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
pubchem_from <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"smiles"</span>, <span class='st'>"inchikey"</span><span class='op'>)</span>,
rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
template <span class='op'>=</span> <span class='cn'>NULL</span>,
chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-try_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>try_pubchem()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>try_pubchem</span><span class='op'>(</span><span class='va'>query</span>, from <span class='op'>=</span> <span class='st'>"name"</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-get_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_pubchem()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_pubchem</span><span class='op'>(</span><span class='va'>pubchem_cid</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-get_rdkit"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_rdkit()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_rdkit</span><span class='op'>(</span>template <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-get_chyaml"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_chyaml()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_chyaml</span><span class='op'>(</span>
repo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"wd"</span>, <span class='st'>"local"</span>, <span class='st'>"web"</span><span class='op'>)</span>,
chyaml <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/utils/URLencode.html'>URLencode</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".yaml"</span><span class='op'>)</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_p0"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_p0()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_p0</span><span class='op'>(</span><span class='va'>p0</span>, T <span class='op'>=</span> <span class='cn'>NA</span>, source <span class='op'>=</span> <span class='cn'>NA</span>, page <span class='op'>=</span> <span class='cn'>NA</span>, remark <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_cwsat"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_cwsat()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_cwsat</span><span class='op'>(</span><span class='va'>cwsat</span>, T <span class='op'>=</span> <span class='cn'>NA</span>, pH <span class='op'>=</span> <span class='cn'>NA</span>, source <span class='op'>=</span> <span class='cn'>NA</span>, page <span class='op'>=</span> <span class='cn'>NA</span>, remark <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_PUF"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_PUF()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_PUF</span><span class='op'>(</span>
PUF <span class='op'>=</span> <span class='fl'>0</span>,
source <span class='op'>=</span> <span class='st'>"focus_generic_gw_2014"</span>,
page <span class='op'>=</span> <span class='fl'>41</span>,
remark <span class='op'>=</span> <span class='st'>"Conservative default value"</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_TP"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_TP()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_TP</span><span class='op'>(</span><span class='va'>x</span>, smiles <span class='op'>=</span> <span class='cn'>NULL</span>, pubchem <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_transformation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_transformation()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_transformation</span><span class='op'>(</span>
<span class='va'>study_type</span>,
<span class='va'>TP_identifier</span>,
<span class='va'>max_occurrence</span>,
remark <span class='op'>=</span> <span class='st'>""</span>,
source <span class='op'>=</span> <span class='cn'>NA</span>,
pages <span class='op'>=</span> <span class='cn'>NA</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_soil_degradation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_degradation()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_degradation</span><span class='op'>(</span>
<span class='va'>soils</span>,
<span class='va'>DT50_mod</span>,
<span class='va'>DT50_mod_ref</span>,
type <span class='op'>=</span> <span class='cn'>NA</span>,
country <span class='op'>=</span> <span class='cn'>NA</span>,
pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
temperature <span class='op'>=</span> <span class='cn'>NA</span>,
moisture <span class='op'>=</span> <span class='cn'>NA</span>,
category <span class='op'>=</span> <span class='st'>"lab"</span>,
formulation <span class='op'>=</span> <span class='cn'>NA</span>,
model <span class='op'>=</span> <span class='cn'>NA</span>,
chi2 <span class='op'>=</span> <span class='cn'>NA</span>,
remark <span class='op'>=</span> <span class='st'>""</span>,
<span class='va'>source</span>,
page <span class='op'>=</span> <span class='cn'>NA</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_soil_ff"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_ff()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_ff</span><span class='op'>(</span><span class='va'>target</span>, <span class='va'>soils</span>, ff <span class='op'>=</span> <span class='fl'>1</span>, remark <span class='op'>=</span> <span class='st'>""</span>, <span class='va'>source</span>, page <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-add_soil_sorption"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_sorption()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_sorption</span><span class='op'>(</span>
<span class='va'>soils</span>,
<span class='va'>Kf</span>,
<span class='va'>Kfoc</span>,
<span class='va'>N</span>,
type <span class='op'>=</span> <span class='cn'>NA</span>,
pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
perc_clay <span class='op'>=</span> <span class='cn'>NA</span>,
CEC <span class='op'>=</span> <span class='cn'>NA</span>,
remark <span class='op'>=</span> <span class='st'>""</span>,
<span class='va'>source</span>,
page <span class='op'>=</span> <span class='cn'>NA</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-pdf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/pdf.html'>pdf()</a></code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>pdf</span><span class='op'>(</span>
file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".pdf"</span><span class='op'>)</span>,
dir <span class='op'>=</span> <span class='st'>"structures/pdf"</span>,
template <span class='op'>=</span> <span class='cn'>NULL</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-png"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/png.html'>png()</a></code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>png</span><span class='op'>(</span>
file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".png"</span><span class='op'>)</span>,
dir <span class='op'>=</span> <span class='st'>"structures/png"</span>,
antialias <span class='op'>=</span> <span class='st'>"gray"</span>
<span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-emf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>emf()</code></h3>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>emf</span><span class='op'>(</span>file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".emf"</span><span class='op'>)</span>, dir <span class='op'>=</span> <span class='st'>"structures/emf"</span><span class='op'>)</span></pre><p></div></p>
<p><hr>
<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
<p><div class="arguments"></p><dl>
<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
</dl><p></div></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='va'>oct</span> <span class='op'><-</span> <span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"1-octanol"</span>, smiles <span class='op'>=</span> <span class='st'>"CCCCCCCCO"</span><span class='op'>)</span>
</div><div class='output co'>#> <span class='message'>PubChem:</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'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</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 $mw: 130.2
#> PubChem synonyms (up to 10):
#> [1] "1-octanol" "Octan-1-ol" "octanol" "111-87-5"
#> [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "caprylic alcohol"
#> [9] "n-Octyl alcohol" "Heptyl carbinol" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</span>
<span class='op'>}</span>
</div><div class='input'>
<span class='va'>caffeine</span> <span class='op'><-</span> <span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"caffeine"</span><span class='op'>)</span>
</div><div class='output co'>#> <span class='message'>PubChem:</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://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</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 $mw: 194.2
#> PubChem synonyms (up to 10):
#> [1] "caffeine" "58-08-2"
#> [3] "1,3,7-Trimethylxanthine" "Guaranine"
#> [5] "Thein" "Methyltheobromine"
#> [7] "Cafeina" "Theine"
#> [9] "Koffein" "Mateina" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
<span class='op'>}</span>
</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre>
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