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to create a chent from the ISO common name of a pesticide active
ingredient, and additionally stores the ISO name as well as
the complete result of querying the BCPC compendium using
bcpc_query."><meta property="og:description" content="This class is derived from chent. It makes it easy
to create a chent from the ISO common name of a pesticide active
ingredient, and additionally stores the ISO name as well as
the complete result of querying the BCPC compendium using
bcpc_query."></head><body>
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<h1>An R6 class for pesticidal active ingredients and 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>pai.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>This class is derived from <a href="chent.html">chent</a>. It makes it easy
to create a <a href="chent.html">chent</a> from the ISO common name of a pesticide active
ingredient, and additionally stores the ISO name as well as
the complete result of querying the BCPC compendium using
<a href="https://docs.ropensci.org/webchem/reference/bcpc_query.html" class="external-link">bcpc_query</a>.</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="super-class">Super class<a class="anchor" aria-label="anchor" href="#super-class"></a></h2>
<p><code><a href="chent.html">chents::chent</a></code> -> <code>pai</code></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>iso</code></dt>
<dd><p>ISO common name of the active ingredient according to ISO 1750</p></dd>
<dt><code>bcpc</code></dt>
<dd><p>Information retrieved from the BCPC compendium available online
at <pesticidecompendium.bcpc.org></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-pai-new"><code>pai$new()</code></a></p></li>
<li><p><a href="#method-pai-clone"><code>pai$clone()</code></a></p></li>
</ul></div><p><details><summary>Inherited methods</summary><ul><li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href="chent.html#method-add_PUF"><code>chents::chent$add_PUF()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chents::chent$add_TP()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href="chent.html#method-add_cwsat"><code>chents::chent$add_cwsat()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chents::chent$add_p0()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href="chent.html#method-add_soil_degradation"><code>chents::chent$add_soil_degradation()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chents::chent$add_soil_ff()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href="chent.html#method-add_soil_sorption"><code>chents::chent$add_soil_sorption()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chents::chent$add_transformation()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href="chent.html#method-emf"><code>chents::chent$emf()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chents::chent$get_chyaml()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href="chent.html#method-get_pubchem"><code>chents::chent$get_pubchem()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chents::chent$get_rdkit()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href="chent.html#method-pdf"><code>chents::chent$pdf()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chents::chent$png()</code></a></span></li>
<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li>
</ul></details></p><hr><a id="method-pai-new"></a><div class="section">
<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
<p>Create a new pai object</p><div class="section">
<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
<span> <span class="va">iso</span>,</span>
<span> identifier <span class="op">=</span> <span class="va">iso</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> bcpc <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> pubchem_from <span class="op">=</span> <span class="st">"auto"</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">FALSE</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>iso</code></dt>
<dd><p>The ISO common name to be used in the query of the
BCPC compendium</p></dd>
<dt><code>identifier</code></dt>
<dd><p>Alternative identifier used for querying pubchem</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>bcpc</code></dt>
<dd><p>Should the BCPC compendium be queried?</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</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-pai-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-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">pai</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd>
</dl><p></p></div>
</div>
</div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span>
<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span>
<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">atr</span> <span class="op"><-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></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">atr</span><span class="op">)</span></span></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">atr</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">atr</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="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#></span> BCPC:</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> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span>
<span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></span>
<span class="r-out co"><span class="r-pr">#></span> <pai> with ISO common name $iso atrazine </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 atrazine </span>
<span class="r-out co"><span class="r-pr">#></span> InChI Key $inchikey MXWJVTOOROXGIU-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> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span>
<span class="r-out co"><span class="r-pr">#></span> Molecular weight $mw: 215.7 </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] "atrazine" "1912-24-9" "Gesaprim" "Atranex" "Oleogesaprim"</span>
<span class="r-out co"><span class="r-pr">#></span> [6] "Atazinax" "Atrasine" "Chromozin" "Gesoprim" "Hungazin" </span>
</code></pre></div>
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