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<img src="" class="logo" alt=""><h1>An R6 class for chemical entities with associated data</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
<div class="d-none name"><code>chent.Rd</code></div>
</div>
<div class="ref-description section level2">
<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="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>An <code>R6Class</code> generator object</p>
</div>
<div class="section level2">
<h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
<p></p><div class="r6-fields"><dl><dt><code>identifier</code></dt>
<dd><p>(<code>character(1)</code>)<br>
The identifier that was used to initiate the object, with attribute 'source'</p></dd>
<dt><code>inchikey</code></dt>
<dd><p>(<code>character(1)</code>)<br>
InChI Key, with attribute 'source'</p></dd>
<dt><code>smiles</code></dt>
<dd><p>(<code><a href="https://rdrr.io/r/base/character.html" class="external-link">character()</a></code>)<br>
SMILES code(s), with attribute 'source'</p></dd>
<dt><code>mw</code></dt>
<dd><p>(<code>numeric(1)</code>)<br>
Molecular weight, with attribute 'source'</p></dd>
<dt><code>pubchem</code></dt>
<dd><p>(<code><a href="https://rdrr.io/r/base/list.html" class="external-link">list()</a></code>)<br>
List of information retrieved 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>PUF</code></dt>
<dd><p>Plant uptake factor</p></dd>
<dt><code>chyaml</code></dt>
<dd><p>List of information obtained from a YAML file</p></dd>
<dt><code>TPs</code></dt>
<dd><p>List of transformation products as chent objects
Add a transformation product to the internal list</p></dd>
<dt><code>transformations</code></dt>
<dd><p>Data frame of observed transformations
Add a line in the internal dataframe holding observed transformations</p></dd>
<dt><code>soil_degradation</code></dt>
<dd><p>Dataframe of modelling DT50 values
Add a line in the internal dataframe holding 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
Add soil sorption data</p></dd>
</dl><p></p></div>
</div>
<div class="section level2">
<h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
<div class="section">
<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
<ul><li><p><a href="#method-chent-new"><code>chent$new()</code></a></p></li>
<li><p><a href="#method-chent-try_pubchem"><code>chent$try_pubchem()</code></a></p></li>
<li><p><a href="#method-chent-get_pubchem"><code>chent$get_pubchem()</code></a></p></li>
<li><p><a href="#method-chent-get_rdkit"><code>chent$get_rdkit()</code></a></p></li>
<li><p><a href="#method-chent-get_chyaml"><code>chent$get_chyaml()</code></a></p></li>
<li><p><a href="#method-chent-add_p0"><code>chent$add_p0()</code></a></p></li>
<li><p><a href="#method-chent-add_cwsat"><code>chent$add_cwsat()</code></a></p></li>
<li><p><a href="#method-chent-add_PUF"><code>chent$add_PUF()</code></a></p></li>
<li><p><a href="#method-chent-add_TP"><code>chent$add_TP()</code></a></p></li>
<li><p><a href="#method-chent-add_transformation"><code>chent$add_transformation()</code></a></p></li>
<li><p><a href="#method-chent-add_soil_degradation"><code>chent$add_soil_degradation()</code></a></p></li>
<li><p><a href="#method-chent-add_soil_ff"><code>chent$add_soil_ff()</code></a></p></li>
<li><p><a href="#method-chent-add_soil_sorption"><code>chent$add_soil_sorption()</code></a></p></li>
<li><p><a href="#method-chent-pdf"><code>chent$pdf()</code></a></p></li>
<li><p><a href="#method-chent-png"><code>chent$png()</code></a></p></li>
<li><p><a href="#method-chent-emf"><code>chent$emf()</code></a></p></li>
<li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li>
</ul></div><p></p><hr><a id="method-chent-new"></a><div class="section">
<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section">
<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
<span> <span class="va">identifier</span>,</span>
<span> smiles <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> pubchem_from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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>,</span>
<span> rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> template <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> chyaml <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
<p></p><div class="arguments"><dl><dt><code>identifier</code></dt>
<dd><p>Identifier to be stored in the object</p></dd>
<dt><code>smiles</code></dt>
<dd><p>Optional user provided SMILES code</p></dd>
<dt><code>inchikey</code></dt>
<dd><p>Optional user provided InChI Key</p></dd>
<dt><code>pubchem</code></dt>
<dd><p>Should an attempt be made to retrieve chemical
information from PubChem via the webchem package?</p></dd>
<dt><code>pubchem_from</code></dt>
<dd><p>Possibility to select the argument
that is used to query pubchem</p></dd>
<dt><code>rdkit</code></dt>
<dd><p>Should an attempt be made to retrieve chemical
information from a local rdkit installation via python
and the reticulate package?</p></dd>
<dt><code>template</code></dt>
<dd><p>An optional SMILES code to be used as template for RDKit</p></dd>
<dt><code>chyaml</code></dt>
<dd><p>Should we look for a identifier.yaml file in the working
directory?
Try to get chemical information from PubChem</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-try_pubchem"></a><div class="section">
<h3 id="method-try-pubchem-">Method <code>try_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-try-pubchem-"></a></h3>
<div class="section">
<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
<p></p><div class="arguments"><dl><dt><code>query</code></dt>
<dd><p>Query string to be passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd>
<dt><code>from</code></dt>
<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a>
Get chemical information from PubChem for a known PubChem CID</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section">
<h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3>
<div class="section">
<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_pubchem</span><span class="op">(</span><span class="va">pubchem_cid</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
<p></p><div class="arguments"><dl><dt><code>pubchem_cid</code></dt>
<dd><p>CID
Get chemical information from RDKit if available</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-get_rdkit"></a><div class="section">
<h3 id="method-get-rdkit-">Method <code>get_rdkit()</code><a class="anchor" aria-label="anchor" href="#method-get-rdkit-"></a></h3>
<div class="section">
<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
<p></p><div class="arguments"><dl><dt><code>template</code></dt>
<dd><p>Optional template specified as a SMILES code
Obtain information from a YAML file</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section">
<h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3>
<div class="section">
<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_chyaml</span><span class="op">(</span></span>
<span> repo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">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>,</span>
<span> chyaml <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/URLencode.html" class="external-link">URLencode</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".yaml"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-4">Arguments<a class="anchor" aria-label="anchor" href="#arguments-4"></a></h4>
<p></p><div class="arguments"><dl><dt><code>repo</code></dt>
<dd><p>Should the file be looked for in the current working
directory, a local git repository under <code>~/git/chyaml</code>, or from
the web (not implemented).</p></dd>
<dt><code>chyaml</code></dt>
<dd><p>The filename to be looked for
Add a vapour pressure</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_p0"></a><div class="section">
<h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3>
<div class="section">
<h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4>
<p></p><div class="arguments"><dl><dt><code>p0</code></dt>
<dd><p>The vapour pressure in Pa</p></dd>
<dt><code>T</code></dt>
<dd><p>Temperature</p></dd>
<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>
<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>
<dt><code>remark</code></dt>
<dd><p>A remark
Add a water solubility</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_cwsat"></a><div class="section">
<h3 id="method-add-cwsat-">Method <code>add_cwsat()</code><a class="anchor" aria-label="anchor" href="#method-add-cwsat-"></a></h3>
<div class="section">
<h4 id="usage-6">Usage<a class="anchor" aria-label="anchor" href="#usage-6"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4>
<p></p><div class="arguments"><dl><dt><code>cwsat</code></dt>
<dd><p>The water solubility in mg/L</p></dd>
<dt><code>T</code></dt>
<dd><p>Temperature</p></dd>
<dt><code>pH</code></dt>
<dd><p>The pH value</p></dd>
<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>
<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>
<dt><code>remark</code></dt>
<dd><p>A remark
Add a plant uptake factor</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section">
<h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3>
<div class="section">
<h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span>
<span> PUF <span class="op">=</span> <span class="fl">0</span>,</span>
<span> source <span class="op">=</span> <span class="st">"focus_generic_gw_2014"</span>,</span>
<span> page <span class="op">=</span> <span class="fl">41</span>,</span>
<span> remark <span class="op">=</span> <span class="st">"Conservative default value"</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-7">Arguments<a class="anchor" aria-label="anchor" href="#arguments-7"></a></h4>
<p></p><div class="arguments"><dl><dt><code>PUF</code></dt>
<dd><p>The plant uptake factor, a number between 0 and 1</p></dd>
<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>
<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>
<dt><code>remark</code></dt>
<dd><p>A remark</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_TP"></a><div class="section">
<h3 id="method-add-tp-">Method <code>add_TP()</code><a class="anchor" aria-label="anchor" href="#method-add-tp-"></a></h3>
<div class="section">
<h4 id="usage-8">Usage<a class="anchor" aria-label="anchor" href="#usage-8"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-8">Arguments<a class="anchor" aria-label="anchor" href="#arguments-8"></a></h4>
<p></p><div class="arguments"><dl><dt><code>x</code></dt>
<dd><p>A chent object, or an identifier to generate a chent object</p></dd>
<dt><code>smiles</code></dt>
<dd><p>A SMILES code for defining a chent object</p></dd>
<dt><code>pubchem</code></dt>
<dd><p>Should chemical information be obtained from PubChem?</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section">
<h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3>
<div class="section">
<h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span>
<span> <span class="va">study_type</span>,</span>
<span> <span class="va">TP_identifier</span>,</span>
<span> <span class="va">max_occurrence</span>,</span>
<span> remark <span class="op">=</span> <span class="st">""</span>,</span>
<span> source <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> pages <span class="op">=</span> <span class="cn">NA</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-9">Arguments<a class="anchor" aria-label="anchor" href="#arguments-9"></a></h4>
<p></p><div class="arguments"><dl><dt><code>study_type</code></dt>
<dd><p>A characterisation of the study type</p></dd>
<dt><code>TP_identifier</code></dt>
<dd><p>An identifier of one of the transformation products
in <code>self$TPs</code></p></dd>
<dt><code>max_occurrence</code></dt>
<dd><p>The maximum observed occurrence of the
transformation product, expressed as a fraction of the amount that would
result from stochiometric transformation</p></dd>
<dt><code>remark</code></dt>
<dd><p>A remark</p></dd>
<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>
<dt><code>pages</code></dt>
<dd><p>The page from which the information was taken</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section">
<h3 id="method-add-soil-degradation-">Method <code>add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-degradation-"></a></h3>
<div class="section">
<h4 id="usage-10">Usage<a class="anchor" aria-label="anchor" href="#usage-10"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span>
<span> <span class="va">soils</span>,</span>
<span> <span class="va">DT50_mod</span>,</span>
<span> <span class="va">DT50_mod_ref</span>,</span>
<span> type <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> country <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> temperature <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> moisture <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> category <span class="op">=</span> <span class="st">"lab"</span>,</span>
<span> formulation <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> model <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> chi2 <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> remark <span class="op">=</span> <span class="st">""</span>,</span>
<span> <span class="va">source</span>,</span>
<span> page <span class="op">=</span> <span class="cn">NA</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-10">Arguments<a class="anchor" aria-label="anchor" href="#arguments-10"></a></h4>
<p></p><div class="arguments"><dl><dt><code>soils</code></dt>
<dd><p>Names of the soils</p></dd>
<dt><code>DT50_mod</code></dt>
<dd><p>The modelling DT50 in the sense of regulatory pesticide
fate modelling</p></dd>
<dt><code>DT50_mod_ref</code></dt>
<dd><p>The normalised modelling DT50 in the sense of
regulatory pesticide fate modelling</p></dd>
<dt><code>type</code></dt>
<dd><p>The soil type</p></dd>
<dt><code>country</code></dt>
<dd><p>The country (mainly for field studies)</p></dd>
<dt><code>pH_orig</code></dt>
<dd><p>The pH stated in the study</p></dd>
<dt><code>pH_medium</code></dt>
<dd><p>The medium in which this pH was measured</p></dd>
<dt><code>pH_H2O</code></dt>
<dd><p>The pH extrapolated to pure water</p></dd>
<dt><code>perc_OC</code></dt>
<dd><p>The percentage of organic carbon in the soil</p></dd>
<dt><code>temperature</code></dt>
<dd><p>The temperature during the study in degrees Celsius</p></dd>
<dt><code>moisture</code></dt>
<dd><p>The moisture during the study</p></dd>
<dt><code>category</code></dt>
<dd><p>Is it a laboratory ('lab') or field study ('field')</p></dd>
<dt><code>formulation</code></dt>
<dd><p>Name of the formulation applied, if it was not
the technical active ingredient</p></dd>
<dt><code>model</code></dt>
<dd><p>The degradation model used for deriving <code>DT50_mod</code></p></dd>
<dt><code>chi2</code></dt>
<dd><p>The relative error as defined in FOCUS kinetics</p></dd>
<dt><code>remark</code></dt>
<dd><p>A remark</p></dd>
<dt><code>source</code></dt>
<dd><p>An acronym specifying the source of the information</p></dd>
<dt><code>page</code></dt>
<dd><p>The page from which the information was taken</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section">
<h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3>
<div class="section">
<h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_ff</span><span class="op">(</span><span class="va">target</span>, <span class="va">soils</span>, ff <span class="op">=</span> <span class="fl">1</span>, remark <span class="op">=</span> <span class="st">""</span>, <span class="va">source</span>, page <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-11">Arguments<a class="anchor" aria-label="anchor" href="#arguments-11"></a></h4>
<p></p><div class="arguments"><dl><dt><code>target</code></dt>
<dd><p>The identifier(s) of the transformation product</p></dd>
<dt><code>soils</code></dt>
<dd><p>The soil name(s) in which the transformation was observed</p></dd>
<dt><code>ff</code></dt>
<dd><p>The formation fraction(s)</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section">
<h3 id="method-add-soil-sorption-">Method <code>add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-sorption-"></a></h3>
<div class="section">
<h4 id="usage-12">Usage<a class="anchor" aria-label="anchor" href="#usage-12"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span>
<span> <span class="va">soils</span>,</span>
<span> <span class="va">Kf</span>,</span>
<span> <span class="va">Kfoc</span>,</span>
<span> <span class="va">N</span>,</span>
<span> type <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> perc_clay <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> CEC <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> remark <span class="op">=</span> <span class="st">""</span>,</span>
<span> <span class="va">source</span>,</span>
<span> page <span class="op">=</span> <span class="cn">NA</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-12">Arguments<a class="anchor" aria-label="anchor" href="#arguments-12"></a></h4>
<p></p><div class="arguments"><dl><dt><code>Kf</code></dt>
<dd><p>The sorption constant in L/kg, either linear (then <code>N</code> is 1)
or according to Freundlich</p></dd>
<dt><code>Kfoc</code></dt>
<dd><p>The constant from above, normalised to soil organic carbon</p></dd>
<dt><code>N</code></dt>
<dd><p>The Freundlich exponent</p></dd>
<dt><code>perc_clay</code></dt>
<dd><p>The percentage of clay in the soil</p></dd>
<dt><code>CEC</code></dt>
<dd><p>The cation exchange capacity
Write a PDF image of the structure</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-pdf"></a><div class="section">
<h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3>
<div class="section">
<h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span>
<span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span>
<span> dir <span class="op">=</span> <span class="st">"structures/pdf"</span>,</span>
<span> template <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-13">Arguments<a class="anchor" aria-label="anchor" href="#arguments-13"></a></h4>
<p></p><div class="arguments"><dl><dt><code>file</code></dt>
<dd><p>The file to write to</p></dd>
<dt><code>dir</code></dt>
<dd><p>The directory to write the file to</p></dd>
<dt><code>template</code></dt>
<dd><p>A template expressed as SMILES to use in RDKit
Write a PNG image of the structure</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-png"></a><div class="section">
<h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3>
<div class="section">
<h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">png</span><span class="op">(</span></span>
<span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span>
<span> dir <span class="op">=</span> <span class="st">"structures/png"</span>,</span>
<span> antialias <span class="op">=</span> <span class="st">"gray"</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-14">Arguments<a class="anchor" aria-label="anchor" href="#arguments-14"></a></h4>
<p></p><div class="arguments"><dl><dt><code>antialias</code></dt>
<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a>
Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-emf"></a><div class="section">
<h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3>
<div class="section">
<h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">emf</span><span class="op">(</span>file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</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></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-15">Arguments<a class="anchor" aria-label="anchor" href="#arguments-15"></a></h4>
<p></p><div class="arguments"><dl><dt><code>file</code></dt>
<dd><p>The file to write to</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-chent-clone"></a><div class="section">
<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
<p>The objects of this class are cloneable with this method.</p><div class="section">
<h4 id="usage-16">Usage<a class="anchor" aria-label="anchor" href="#usage-16"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-16">Arguments<a class="anchor" aria-label="anchor" href="#arguments-16"></a></h4>
<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd>
</dl><p></p></div>
</div>
</div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</span> <span class="op"><-</span> <span class="va">chent</span><span class="op">$</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>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using user SMILES</span>
<span class="r-msg co"><span class="r-pr">#></span> CCCCCCCCO</span>
<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./1-octanol.yaml</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> <chent></span>
<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier 1-octanol </span>
<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey </span>
<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span>
<span class="r-out co"><span class="r-pr">#></span> user </span>
<span class="r-out co"><span class="r-pr">#></span> "CCCCCCCCO" </span>
<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 130.2 </span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">oct</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">oct</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><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></span></span>
<span class="r-msg co"><span class="r-pr">#></span> PubChem:</span>
<span class="r-msg co"><span class="r-pr">#></span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
<span class="r-msg co"><span class="r-pr">#></span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span>
<span class="r-msg co"><span class="r-pr">#></span> Did not find chyaml file ./caffeine.yaml</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> <chent></span>
<span class="r-out co"><span class="r-pr">#></span> Identifier $identifier caffeine </span>
<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span>
<span class="r-out co"><span class="r-pr">#></span> SMILES string $smiles:</span>
<span class="r-out co"><span class="r-pr">#></span> PubChem_Canonical </span>
<span class="r-out co"><span class="r-pr">#></span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span>
<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 194.2 </span>
<span class="r-out co"><span class="r-pr">#></span> PubChem synonyms (up to 10):</span>
<span class="r-out co"><span class="r-pr">#></span> [1] "caffeine" "58-08-2" </span>
<span class="r-out co"><span class="r-pr">#></span> [3] "Guaranine" "1,3,7-Trimethylxanthine"</span>
<span class="r-out co"><span class="r-pr">#></span> [5] "Methyltheobromine" "Theine" </span>
<span class="r-out co"><span class="r-pr">#></span> [7] "Thein" "Cafeina" </span>
<span class="r-out co"><span class="r-pr">#></span> [9] "Koffein" "Mateina" </span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="chent-1.png" alt="" width="700" height="433"></span>
</code></pre></div>
</div>
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