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Additional chemical information is retrieved from the +internet if available.</p> + </div> -<meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai" /> -<meta property="og:description" content="The class is initialised with an identifier which is generally an ISO common name. -Additional chemical information is retrieved from the internet if available." /> -<meta name="twitter:card" content="summary" /> + <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> +Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd> -<!-- 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]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <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"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </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">0.2.7</span> - </span> +</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$try_pubchem()</code></a></span></li> +</ul></details></p><hr><a id="method-pai-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +<p>This class is derived from <a href="chent.html">chent</a>. It makes it easy +to create a <a href="chent.html">chent</a> from the ISO common name of a pesticide active +ingredient, and additionally stores the ISO name as well as +the complete result of querying the BCPC compendium using +<a href="https://docs.ropensci.org/webchem/reference/bcpc_query.html" class="external-link">bcpc_query</a>.</p><div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</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> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<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"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<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> - - </header> -<div class="row"> - <div class="col-md-9 contents"> - <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> - <div class="hidden name"><code>pai.Rd</code></div> - </div> +<dt><code>identifier</code></dt> +<dd><p>Alternative identifier used for querying pubchem</p></dd> - <div class="ref-description"> - - <p>The class is initialised with an identifier which is generally an ISO common name. -Additional chemical information is retrieved from the internet if available.</p> - - </div> - <pre class="usage"><span class='no'>pai</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> +</dl><p></p></div> +</div> - <p>An <code>R6Class</code> generator object</p> - - <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> +</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">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> - - <dl class='dl-horizontal'> -<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</p></dd> - <dt><code>alanwood</code></dt><dd><p>List of information retreived from www.alanwood.net/pesticides</p></dd> -</dl> - +<div class="section"> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>atr</span> <span class='kw'><-</span> <span class='no'>pai</span>$<span class='fu'>new</span>(<span class='st'>"atrazine"</span>)</div><div class='output co'>#> <span class='message'>alanwood.net:</span></div><div class='output co'>#> <span class='message'>Querying atrazine.html</span></div><div class='output co'>#> <span class='message'>PubChem:</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/cids/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#> <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span> -#> <span class='message'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>atr</span>)</div><div class='output co'>#> <pai> with ISO common name $iso atrazine -#> <chent> -#> Identifier $identifier atrazine -#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N -#> SMILES string $smiles: -#> PubChem_Canonical -#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" -#> Molecular weight $mw: 215.7 -#> PubChem synonyms (up to 10): -#> [1] "2256" "atrazine" "1912-24-9" "Gesaprim" "Chromozin" -#> [6] "Oleogesaprim" "Aktikon" "Argezin" "Atazinax" "Atranex" </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - <li><a href="#fields">Fields</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> +</dl><p></p></div> +</div> - </div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span> +<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span> +<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">atr</span> <span class="op"><-</span> <span class="va">pai</span><span class="op">$</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-msg co"><span class="r-pr">#></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">#></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" "Oleogesaprim" "Aktikon" </span> +<span class="r-out co"><span class="r-pr">#></span> [6] "Atranex" "Chromozin" "Atazinax" "Atrasine" "Gesoprim" </span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - 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