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@@ -1,68 +1,13 @@
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-Additional chemical information is retrieved from the internet if available." />
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+Additional chemical information is retrieved from the internet if available."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -73,44 +18,31 @@ Additional chemical information is retrieved from the internet if available." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">chents</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
</span>
</div>
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- <span class="fas fa-home fa-lg"></span>
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+ <ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Reference</a>
</li>
- </ul>
- <ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/chents/">
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/chents/" class="external-link">
<span class="fab fa-github fa-lg"></span>
</a>
</li>
- </ul>
-
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+ </ul></div><!--/.nav-collapse -->
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+ </header><div class="row">
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<div class="page-header">
<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/master/R/chent.R'><code>R/chent.R</code></a></small>
+ <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="hidden name"><code>pai.Rd</code></div>
</div>
@@ -120,132 +52,143 @@ Additional chemical information is retrieved from the internet if available.</p>
</div>
+ <div id="format">
+ <h2>Format</h2>
+ <p>An <code>R6Class</code> generator object</p>
+ </div>
+ <div id="super-class">
+ <h2>Super class</h2>
+ <p><code><a href="chent.html">chents::chent</a></code> -&gt; <code>pai</code></p>
+ </div>
+ <div id="public-fields">
+ <h2>Public fields</h2>
+ <p></p><div class="r6-fields"><dl><dt><code>iso</code></dt>
+<dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+
+
+<dt><code>bcpc</code></dt>
+<dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
- <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="super-class"><a class="anchor" href="#super-class"></a>Super class</h2>
+</dl><p></p></div>
+ </div>
+ <div id="methods">
+ <h2>Methods</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$try_pubchem()</code></a></span></li>
+</ul></details></p><hr><a id="method-pai-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+
+<div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</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">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
- <p><code><a href='chent.html'>chents::chent</a></code> -&gt; <code>pai</code></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>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+</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">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
-<dt><code>bcpc</code></dt><dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
-</dl><p></div></p>
- <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
-
-<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
-
-<ul>
-<li><p><a href='#method-new'><code>pai$new()</code></a></p></li>
-<li><p><a href='#method-clone'><code>pai$clone()</code></a></p></li>
-</ul>
-<p><details ><summary>Inherited methods</summary>
-<ul>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-add_PUF'><code>chents::chent$add_PUF()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-add_TP'><code>chents::chent$add_TP()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-add_cwsat'><code>chents::chent$add_cwsat()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-add_p0'><code>chents::chent$add_p0()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-add_soil_degradation'><code>chents::chent$add_soil_degradation()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-add_soil_ff'><code>chents::chent$add_soil_ff()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-add_soil_sorption'><code>chents::chent$add_soil_sorption()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-add_transformation'><code>chents::chent$add_transformation()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-emf'><code>chents::chent$emf()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-get_chyaml'><code>chents::chent$get_chyaml()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-get_pubchem'><code>chents::chent$get_pubchem()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-get_rdkit'><code>chents::chent$get_rdkit()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-pdf'><code>chents::chent$pdf()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-png'><code>chents::chent$png()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></p></li>
-</ul>
-</details>
-
-<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'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
- <span class='va'>iso</span>,
- identifier <span class='op'>=</span> <span class='va'>iso</span>,
- smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
- smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
- inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
- inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
- bcpc <span class='op'>=</span> <span class='cn'>TRUE</span>,
- pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
- pubchem_from <span class='op'>=</span> <span class='st'>"auto"</span>,
- rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
- template <span class='op'>=</span> <span class='cn'>NULL</span>,
- chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
-<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></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='co'># On Travis, we get a certificate validation error,</span>
-<span class='co'># likely because the system (xenial) is so old,</span>
-<span class='co'># therefore don't run this example on Travis</span>
-<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>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 class='va'>atr</span> <span class='op'>&lt;-</span> <span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"atrazine"</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span>
-<span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
- <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span>
-<span class='op'>}</span>
-
-<span class='op'>}</span>
-</div><div class='output co'>#&gt; <span class='message'>BCPC:</span></div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='img'><img src='pai-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; &lt;pai&gt; with ISO common name $iso atrazine
-#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier atrazine
-#&gt; InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N
-#&gt; SMILES string $smiles:
-#&gt; PubChem_Canonical
-#&gt; "CCNC1=NC(=NC(=N1)Cl)NC(C)C"
-#&gt; Molecular weight $mw: 215.7
-#&gt; PubChem synonyms (up to 10):
-#&gt; [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Chromozin"
-#&gt; [6] "Aktikon" "Atrazin" "Argezin" "Atazinax" "Atranex" </div></pre>
+</dl><p></p></div>
+</div>
+
+</div>
+
+ </div>
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span>
+<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span>
+<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">atr</span> <span class="op">&lt;-</span> <span class="va">pai</span><span class="op">$</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">#&gt;</span> BCPC:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> PubChem:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./atrazine.yaml</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">#&gt;</span> &lt;pai&gt; with ISO common name $iso atrazine </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier atrazine </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem_Canonical </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 215.7 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Aktikon" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [6] "Atranex" "Chromozin" "Atazinax" "Atrasine" "Gesoprim" </span>
+</code></pre></div>
+ </div>
</div>
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